Miracle-dz/UniFAR-FTUs huggingface dataset:
A multi-layer graph analytics to identify bioinformatics tool usage practices from tool directories and PubMed indexed cross-citations

The essence of bioinformatics is to research, develop, or apply computational tools to biology related data. We confirmed in this paper that bioinformatics tools have been emerging exponentially from 1988–2016. To aide in tool discovery, many directories were established. Though the number of citations to the tools were provided in some directories, none describe how the tools were used. Currently reviewing the literature in a continuous manner remains the key method to keep up with the rapidly changing best practices. To reduce this burden, we proposed a method to systematically gather the documented usage from literature and analyzed them such that the active tool combinations can be derived. Implementation of our method found a total of 4,832 bioinformatics tools, published during 1988–2016, with known PubMed unique identifiers. From January to July 2016, the tools were cited in 13,619 publications. From those publications, 57 function sets (i.e. analysis patterns) were deduced by clustering the usage instances according to the tool functionalities used. A total of 666 tool combinations were observed from those function sets. The top five function sets consisted of 30–98 combinations each; the additional 43 function sets contained 2–9 combinations. The nonhomogeneous tool preferences elicits the search for their influential factors to guide the improvement of tool discovery methods.
The reporting of sensitive behavior by adolescents: A methodological experiment in Kenya

Does audio computer-assisted self-interviewing (ACASI) produce more valid reporting of sexual activity and related behaviors than face-to-face interviews or self-administered interviews? This analysis, based on data collected from over 6,000 unmarried adolescents in two districts of Kenya—Nyeri and Kisumu—indicates substantial and significant differences in reported rates of premarital sex across interview modes, although not always in the expected direction. Our assumption that girls underreport sexual activity in face-to-face interviews by comparison with ACASI is not confirmed by the Nyeri data, but our results from Kisumu are considerably more promising. As for boys, who we believe exaggerate their level of sexual activity in face-to-face interviews, a more nuanced set of expectations regarding the reporting of sensitive behaviors was offered; our results from Kisumu, although not always significant, by and large conform to expectations.
A Survey of Green, Energy-Aware Security and Some of Its Recent Developments in Networking and Mobile Computing

Since its inception, the field of Green, Energy-Aware Security (GEAS) has gathered momentum and has seen many interesting developments in some of its different declinations. In this paper we will analyze some of the most recent evolutions and we will summarize the current state of the art describing some of the most interesting and promising advancements. More in details, we will focus on i) energy management in network nodes, ii) exploitation of security mechanisms to save energy and iii) use of energy consumption as a marker for malicious activities in energy constrained computational platforms.
Beeclust: A Swarm Algorithm Derived from Honeybees Derivation of the Algorithm, Analysis by Mathematical Models and Implementation on a Robot Swarm

We demonstrate the derivation of a powerful and simple, as well as robust and flexible algorithm for a swarm robotic system derived from observations of honeybees’ collective behavior. We show how such observations made in a natural system can be translated into an abstract representation of behavior (algorithm) working in the sensor-actor world of small autonomous robots. By developing several mathematical models of varying complexity, the global features of the swarm system are investigated. These models support us in interpreting the ultimate reasons of the observed collective swarm behavior and they allow us to predict the swarm’s behavior in novel environmental conditions. In turn these predictions serve as inspiration for new experimental setups with both, the natural system (honeybees and other social insects) as well as the robotic swarm. This way, a deeper understanding of the complex properties of the collective algorithm, taking place in the bees and in the robots, is achieved.
Investigating the size and dynamics of voltage-gated sodium channel fenestrations

Eukaryotic voltage-gated sodium channels (VGSCs) are essential for the initiation and propagation of action potentials in electrically excitable cells, and are important pharmaceutical targets for the treatment of neurological disorders such as epilepsy, cardiac arrhythmias, and chronic pain. Evidence suggests that small, hydrophobic, VGSC-blocking drugs can gain access to binding residues within the central cavity of these channels by passing through lateral, lipid-filled “fenestrations” which run between the exterior of the protein and its central pore. Here, we use molecular dynamics simulations to investigate how the size and shape of fenestrations change over time in several bacterial VGSC models and a homology model of Nav1.4. We show that over the course of the simulations, the size of the fenestrations is primarily influenced by rapid protein motions, such as amino acid side-chain rotation, and highlight that differences between fenestration bottleneck-contributing residues are the primary cause of variations in fenestration size between the 6 bacterial models. In the eukaryotic channel model, 2 fenestrations are wide, but 2 are narrow due to differences in the amino acid sequence in the 4 domains. Lipid molecules are found to influence the size of the fenestrations by protruding acyl chains into the fenestrations and displacing amino acid side-chains. Together, the results suggest that fenestrations provide viable pathways for small, flexible, hydrophobic drugs.
Meeting Great Expectations: Integrating Early Education Program Standards in Child Care.

In order to achieve the expectations for children's learning stipulated by the No Child Left Behind Act of 2001, greater attention needs to be given to child care policy and funding. This report details a study examining strategies in seven states that have integrated early education program standards in child care, by directly tying standards to funding. The strategies examined are: the delivery of state prekindergarten (Georgia, New Jersey, and New York) and Head Start (Ohio, Oklahoma, and Oregon) in child care settings, and the use of contracts that require standards for child care providers (California) . The report is organized into four sections. Section 1 discusses why program standards are critical to meeting raised goals for education and why child care must be part of this strategy. Section 2 presents findings from a group of states in which program standards and oversight of child care centers that participate in these early education initiatives (both prekindergarten and Head Start) clearly exceeded those of the basic state licensing rules. This section also showcases California's experience with child care contracts as an example of the potential of this strategy. Section 3 describes how Georgia funded the integration of a state prekindergarten program into child care. Section 4 recommends goals for policy and future research. The report notes that perhaps the greatest barrier to integrating high program standards in child care is financial-with budget crises forcing many states to make policy changes that reduce access to child care subsidies--and cautions that reductions in early care and education investments will lead to greater costs in the long run. Appended are program standards by state. (Contains 86 endnotes.) (KB) Reproductions supplied by EDRS are the best that can be made from the original document. ng One riKpaECOLEZ0 Integrating Early Education Program Standards in Child Care By Rachel Schumacher, Kate Irish, and Joan Lombardi
Development of magnetic materials and processing techniques applicable to integrated micromagnetic devices

In this research, electroplated magnetically isotropic and anisotropic soft alloys and screen-printed soft ferrites applicable to micromachined micromagnetic devices are fabricated and characterized using in situ measurement techniques. Appropriate magnetic materials and deposition methods, such as electroplating and screen-printing techniques, are examined and material test structures are fabricated. Following material characterization, micromachined inductors with three-dimensional structure are fabricated to determine the usefulness of the magnetic materials and deposition methods. The micromachined inductor is a key component and geometry for realizing micromagnetic devices such as amplifiers, filters, sensors and actuators. Three different material types are studied in this work. Electroplated magnetically isotropic soft alloys, permalloy (Ni80Fe20), orthonol (Ni50Fe50) and amorphous cobalt-iron-copper (CoFeCu) alloys, are studied, followed by electroplated magnetically anisotropic soft alloys of permalloy (Ni80Fe20) and supermalloy (NiFeMo), which have magnetically easy and hard axes. Finally, screen-printed polymers filled with soft ferrite (NiZn and MnZn) powders are fabricated and characterized.
Full-Processor Timing Channel Protection with Applications to Secure Hardware Compartments

This paper presents timing compartments, an architecture abstraction that explicitly removes microarchitecture-level timing channels between groups of software running concurrently on a shared multi-core processor. The capability to eliminate timing channels coupled with conventional software isolation enables strong isolation comparable to running software on separate physical machines. This paper shows that such a strong timing isolation can be achieved by systematically removing timing interference in shared resources in a multi-core, and formally checked using information flow analysis on an RTL implementation. Through this systematic process, we identify and remove new sources of timing channels, including cache coherence mechanisms and module interfaces, and introduce new performance optimizations. We also demonstrate how timing compartments may be extended to support a hardwareonly TCB which ensures security even when the system is managed by an untrusted OS or hypervisor. Experimental studies show that the performance overheads of strict timing isolation can be surprisingly low for a small number of timing compartments; executing two timing compartments reduces system throughput by less than 7% on average and by less than 2% for compute-bound workloads.
Study of HRV Dynamics and Comparison Using Wavelet Analysis and Pan Tompkins Algorithm

Heart rate variability (HRV) provides a non-invasive means of quantifying cardiac autonomic activity. It has been shown to be a powerful predictor of arrhythmia related complications in patients surviving the acute phase of myocardial infarction. It has also increasingly been used to measure autonomic nervous system activities. This work aims to study heart rate variability during normal or abnormal functioning of the heart and whether it can be used to predict the occurrence of any abnormality. Additionally, it aims to compare results based on wavelet analysis and Pan Tompkins algorithm. Both time domain analysis and frequency domain analysis of HRV are presented. The HRV dynamics is evaluated using non-parametric (Fast Fourier Transform) method. Results of stimulations in MATLAB are presented.
Economic structure and social order type in post-communist Europe

The paper is organized in the following way. The first section outlines the basic conceptual framework, emphasizing the symbiotic relationship between economics and politics. Social orders are defined and are shown to differ in the degree to which competition is prevalent, and the extent to which this competition is resolved according to impersonal, universally enforced rules. The second section proposes an explanation for the variation in how competition is channeled across the postcommunist region. It is suggested that different patterns of integration with the international economy, as manifested in the structure of a country’s export profile, can help increase our understanding of the sources of social order across the region. The third section provides some preliminary evidence to support this explanation.
Why Things Go Wrong: A Formal Theory of Causal Reasoning

This paper presents a theory of generalized temporal reasoning. We focus on the related problems of 1. Temporal Projection—determining all the facts true in a chronicle, given a partial description of that chronicle, and 2. Explanation—figuring out what went wrong if an unexpected outcome occurs. We present a non-monotonic temporal logic based on the notion that actions only happen if they are motivated. We demonstrate that this theory handles generalized temporal projection correctly, and in particular, solves the Yale Shooting Problem and a related class of problems. We then show how our model lends itself to a very natural characterization of the concept of an adequate explanation for an unexpected outcome.
A Perspective-Oriented Approach for Information Mining & Its Contribution to Design, Control & Automation Issues

In this paper, some perspectives are suggested for information mining from extraction viewpoint, based upon which the essential methodology for mining can be systematically determined in response with the user's objectives. The ideas developed in this paper can help the organizational knowledge managers and the knowledge engineers in design, control and automation environments, develop potential intelligent tools for improving/enhancing the performance of the related issues on the basis of the information existing in the related engineering reports.
Detecting heap-spray attacks in drive-by downloads: Giving attackers a hand

In the anatomy of drive-by download attacks, one of the key steps is to place malicious code (shellcode) in the memory of the browser process in order to carry out a drive-by download attack. There are two common techniques to carry out this task: stack-based and heap-based injections. However, introduction of stack protection makes the stack-based injection harder to carry out successfully. The heap-based injections become common methods to deliver shellcode to the heap memory of the web browsers. This paper presents the role of heap-spray in drive-by download attacks. We propose a new detection mechanism which makes shellcode in heap-spray executed in order to detect drive-by download attack. The solution not only benefits detection of drive-by download attacks but also analysis of malware behavior.
The Present-Value Model of the Current Account: Results from Norway

In this thesis I present and test an intertemporal model for the current account. The model predicts a nation that prefers a smooth consumption pro le where the current account balance is used as a tool to smooth consumption based on expectations about future changes in net output. The model implies a present-value relationship between the current account and future changes in net output. The present-value model (PVM) is a nested version of a general vector autoregression (VAR). I estimate this general VAR for quarterly Norwegian data for the period 1981 to 2011. The cross-equation restrictions on this VAR that are implied by the PVM is rejected for Norwegian data, but I present some favorable, less formal results from the intertemporal model.
A comparison between human walking and passive dynamic walking

Root mean square error is presented as a quantitative measure for the similarity between human walking and passive dynamic walking. Normalized root mean square error of the hip angle and angular velocity between both walkers in a walking cycle is 6.9% and 12.2% on average, respectively. It shows a strong similarity between human walking and passive dynamic walking. A comparison is made between human walking and passive dynamic walking in four phases divided from a gait cycle. The reasons for resulting in the differences are studied.
A Markov-Blanket-Based Model for Gene Regulatory Network Inference

An efficient two-step Markov blanket method for modeling and inferring complex regulatory networks from large-scale microarray data sets is presented. The inferred gene regulatory network (GRN) is based on the time series gene expression data capturing the underlying gene interactions. For constructing a highly accurate GRN, the proposed method performs: 1) discovery of a gene's Markov Blanket (MB), 2) formulation of a flexible measure to determine the network's quality, 3) efficient searching with the aid of a guided genetic algorithm, and 4) pruning to obtain a minimal set of correct interactions. Investigations are carried out using both synthetic as well as yeast cell cycle gene expression data sets. The realistic synthetic data sets validate the robustness of the method by varying topology, sample size, time delay, noise, vertex in-degree, and the presence of hidden nodes. It is shown that the proposed approach has excellent inferential capabilities and high accuracy even in the presence of noise. The gene network inferred from yeast cell cycle data is investigated for its biological relevance using well-known interactions, sequence analysis, motif patterns, and GO data. Further, novel interactions are predicted for the unknown genes of the network and their influence on other genes is also discussed.
Tragic Orphans: Indians in Malaysia

In 1938, noting that the bulk of the Indian population formed a ""landless proletariat"" and despairing of the ability of the factionalized Indian community to unite in pursuit of common objectives, activist K.A. Neelakanda Ayer forecast that the fate of Indians in Malaya would be to become Tragic orphans of whom India has forgotten and Malaya looks down upon with contempt. "" Ayer's words continue to resonate; as a minority group in a nation dominated politically by colonially derived narratives of ""race"" and ethnicity and riven by the imperatives of religion, the general trajectory of the economically and politically impotent Indian community has been one of increasing irrelevance. This book explores the history of the modern Indian presence in Malaysia, and traces the vital role played by the Indian community in the construction of contemporary Malaysia. In this comprehensive new study, Carl Vadivella Belle offers fresh insights on the Indian experience spanning the period from the colonial recruitment of Indian labour to the post-Merdeka political, economic and social marginalization of Indians. While recent Indian challenges to the political status quo -- a regime described as that of ""benign neglect"" -- promoted Indian hopes of reform, change and uplift, the author concludes that the dictates of political discourse permeated by the ideologies of communalism offer limited prospects for meaningful change.
MARSYAS SUBMISSIONS TO MIREX 2007

Marsyas is an open source software framework for audio analysis, synthesis and retrieval with specific emphasis on Music Information Retrieval. It is developed by an international team of programmers and researchers led by George Tzanetakis. In MIREX 2007 we participated in the following tasks: Audio Artist Identification, Audio Classical Composer Identification, Audio Genre Classification, Audio Music Mood Classification, and Audio Music Similarity and Retrieval Results. In this abstract we describe the specific algorithmic details of our submission and provide information about how researchers can use our system using the MIREX input/output conventions on their own datasets. Also some comments on the results are provided especially highlighting the excellent running time performance of our system (an order of magnitude faster than any other submission while remaining competitive in task performance).
Interlaboratory Comparison of HER-2 Oncogene Amplification as Detected by Chromogenic and Fluorescence in situ Hybridization

Purpose: Chromogenic in situ hybridization (CISH) is a new modification of the fluorescence in situ hybridization (FISH) technique for detection of oncogene amplification in archival tumor samples. In CISH, the oncogene probe is detected using a peroxidase reaction, allowing use of transmitted light microscopy. We compared detection of HER-2/neu amplification by CISH with a Food and Drug Administration-approved two-color FISH test in an interlaboratory setting. Experimental Design: Formalin-fixed paraffin-embedded tumor samples from 197 breast cancers were analyzed for HER-2 amplification by CISH. Two-color FISH (PathVysion) CISH of 17 centromere was done if the observer considered it necessary to ascertain amplification status in tumors with borderline HER-2 CISH copy numbers. Results: Paired CISH/FISH results were available from 192 (97%) of 197 cases, no clear difference in success rates of either method was observed. Centromere 17 CISH was considered necessary in seven tumors. CISH and two-color FISH results were concordant in 180 cases (93.8%). There were 92 and 88 tumors found HER-2 amplified and nonamplified, respectively, by both methods. Eight tumors were amplified by CISH but not by FISH, and four tumors exhibited the opposite condition (kappa coefficient 0.875). In 7 of 12 cases differences between the two methods could have related to a lack of CISH chromosome 17 information. The remaining cases were explained by difficult histology (ductal carcinoma in situ, poor representativity, dense lymphocytic infiltration, or intratumoral heterogeneity). Conclusions: These results indicate that CISH could provide an accurate and practical alternative to FISH for clinical diagnosis of HER-2/neu oncogene amplification in archival formalin-fixed breast cancer samples.
A self-oscillating ionic polymer-metal composite bending actuator

This paper presents an electromechanical model of an ionic polymer-metal composite (IPMC) material. The modeling technique is a finite element method (FEM). An applied electric field causes the drift of counterions (e.g., Na+), which, in turn, drags water molecules. The mass and charge imbalance inside the polymer is the main cause of the bending motion of the IPMC. The studied physical effects have been considered as time dependent and modeled with FEM. The model takes into account the mechanical properties of the Nafion polymer as well as the thin coating of the platinum electrodes and the platinum diffusion layer. The modeling of the electrochemical reactions, in connection with the self-oscillating behavior of an IPMC, is also considered. Reactions occurring on the surface of the platinum electrode, which is immersed into formaldehyde (HCHO) solution during the testing, are described using partial differential equations and also modeled using FEM. By coupling the equations with the rest of the model, .
A System for Improving Application Performance Through System Call Composition

Long-running server applications can easily execute millions of common data-intensive system calls each day, incurring large data copy overheads. We introduce a new framework, Compound System Calls (Cosy), to enhance the performance of such applications. Cosy provides a mechanism to safely execute data-intensive code segments in the kernel. Cosy encodes a C code segment containing system calls in a compound structure. The kernel executes this aggregate compound directly, thus avoiding data copies between user-space and kernel-space. With the help of a Cosy-GCC compiler, regular C code can use Cosy facilities with minimal changes. Cosy-GCC automatically identifies and encodes zero-copy opportunities across system calls. To ensure safety in the kernel, we use a combination of static and dynamic checks, and we also exploit kernel preemption and hardware features such as x86 segmentation. We implemented the system on Linux and instrumented a few data-intensive applications such as those with database access patterns. Our benchmarks show performance improvements of 20–80% for non-I/O bound applications.