Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular beacons for multiplex detection of four bacterial bioterrorism agents.

The advent of bioterrorism has highlighted the need for rapid, simple, and robust diagnostic assays to detect select agents. Mortality from select agents may be greatly reduced by prompt treatment (1); however, treatment may be delayed if diagnostic assays are outsourced to reference laboratories. Most bacterial species that would likely be used as bioterrorism agents infect the blood stream during the course of life-threatening disease. Furthermore, even “nonseptic” syndromes may produce hematogenous bacterial DNA that could be detected by a sensitive assay (2). This means that a rapid “molecular” version of a blood culture would fulfill many of the rapid diagnostic needs for biodefense. Bacteria can be detected in blood and other sterile body sites by the identification of species-specific DNA sequences in their 16S rRNA genes. These species-specific sequences are flanked by conserved sequences, permitting most rRNA targets to be amplified by PCR using a limited set of “universal” primers (3). Real-time PCR is well suited for sensitive and specific pathogen detection because it is performed in hermetically sealed wells, which greatly reduces the risk of cross-contamination, and it does not require post-PCR analysis (4). Real-time PCR assays have been developed for some select agents, most of which use fluorogenic 5′-nuclease (TaqMan) probes (5)(6)(7). However, TaqMan probes are difficult to use in multiplex PCR assays (8)(9). In contrast, molecular beacons are real-time PCR probes that are particularly amenable to multiplexing (10). They can be labeled with differently colored fluorophores (11), use a common nonfluorescent quenching moiety (9), and have thermodynamic properties that favor highly specific detection of nucleic acid sequences (12). Here we describe a real-time PCR assay that simultaneously detects four bacterial agents that could be used in bioterrorism. This assay is specifically designed to test sterile body fluids, where a …
MayoNLPTeam at the 2016 CLEF eHealth Information Retrieval Task 1

This paper presents the participation of MayoNLPTeam in the 2016 CLEF eHealth Information Retrieval Task (IR Task 1: ad-hoc search). We explored a Part-of-Speech (POS) based query term weighting approach which assigns different weights to the query terms according to their POS categories. The weights are learned by defining an objective function based on the mean average precision. We applied the proposed approach with the optimal weights obtained from TREC 2011 and 2012 Medical Records Track into the Query Likelihood model (Run 2) and Markov Random Field (MRF) models (Run 3). The conventional Query Likelihood model was implemented as the baseline (Run 1).
Energy Efficient Caching-on-Cache Architectures for Embedded Systems

As the number of applications for embedded and real-time systems has grown, running systems at a lower power dissipation level has become an important issue, especially for the battery-based systems. Past studies have shown that the cache is responsible for a large part of the power dissipation in a system chip. Thus, reducing the power dissipation in the cache has become an important research topic. In this paper, we present a cache architecture, the CoC, that reduces cache energy dissipation in embedded systems. The CoC can reduce the access frequency at wordlines and bitlines, which are the main power consuming components, in both tag and data arrays. In addition, we use a hierarchical address comparison (HAC) scheme to optimize energy reduction and the comparison time. Experimental results show that the CoC is practical in reducing energy dissipation in the Li cache, and that the HAC scheme can effectively minimize the comparison penalty in the CoC.
Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms

Characterizing transcriptomes in both model and non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. Each step may be accomplished in one of several different ways, using different software packages, each producing different results. This analytical complexity begs the question – Which method(s) are optimal? Using reference and non-reference based evaluative methods, I propose a set of guidelines that aim to standardize and facilitate the process of transcriptome assembly. These recommendations include the generation of between 20 million and 40 million sequencing reads from single individual where possible, error correction of reads, gentle quality trimming, assembly filtering using Transrate and/or gene expression, annotation using dammit, and appropriate reporting. These recommendations have been extensively benchmarked and applied to publicly available transcriptomes, resulting in improvements in both content and contiguity. To facilitate the implementation of the proposed standardized methods, I have released a set of version controlled open-sourced code, The Oyster River Protocol for Transcriptome Assembly, available at http://oyster-river-protocol.rtfd. org/.
Automatic Gridding of DNA Microarray Images using Optimum Subimage

Microarray is the one of the most promising tool available for researchers in life sciences to study gene expression profile.Image processing is the first step in knowledge discovery from the microarray. The process of extracting features consist of three stages: gridding, segmentation and quantification. Gridding is to assign each spot with individual coordinates. There are different levels of sophisticated image processing algorithms, which requires certain level of user intervention for accurately gridding the microarray images. This paper presents a fully automatic grid alignment algorithm for detecting the microarray image spots. The approach is based on the detection of an optimum subimage. Using Intensity projection profile of this subimage the parameters required for gridding are calculated. Experimental result shows that this method is highly accurate when compared to a previous method of gridding that uses intensity projection profile. This algorithm was implemented using Matlab software and found very effective for gridding arrays with low intensity, poor quality spots.
Application-Defined Decentralized Access Control

DCAC is a practical OS-level access control system that supports application-defined principals. It allows normal users to perform administrative operations within their privilege, enabling isolation and privilege separation for applications. It does not require centralized policy specification or management, giving applications freedom to manage their principals while the policies are still enforced by the OS. DCAC uses hierarchically-named attributes as a generic framework for user-defined policies such as groups defined by normal users. For both local and networked file systems, its execution time overhead is between 0%-9% on file system microbenchmarks, and under 1% on applications. This paper shows the design and implementation of DCAC, as well as several real-world use cases, including sandboxing applications, enforcing server applications' security policies, supporting NFS, and authenticating user-defined sub-principals in SSH, all with minimal code changes.
Database Refactoring: Lessons from the Trenches

Although database refactoring has been advocated as an important area of database development, little research has studied its implications. A small software development firm refactored a database related to an application that lets clients optimize their logistics processes. This project was based on the design of clear database development conventions and the need to package documentation in the database itself. The experience led to five key lessons learned: refactoring should be automated whenever possible, the database catalog is crucial, refactoring is easier when it's done progressively, refactoring can help optimize an application and streamline its code base, and refactoring related to application development requires a complex skill set and must be applied sensibly. This article is part of a special issue on Refactoring.
An Asm Implementation of a Self-applicable Partial Evaluator

Partial evaluation is a technique for specializing programs with respect to parts of their input. We describe an o ine partial evaluator mixASM for Abstract State Machines, written in the ASM language itself. The partial evaluator is self-applicable, so some problems related to self-application are discussed. This work concentrates on the implementation of mixASM , presenting all algorithms in detail.
A 100 µW Decimator for a 16 bit 24 kHz bandwidth Audio ΔΣ Modulator

A decimation filter for a low power Delta Sigma (ΔΣ) modulator with 24 kHz bandwidth and an in band resolution of 16 bits is designed with standard cells in a 1.8 V, 0. 18µm CMOS process. Retiming, Canonical Signed Digits (CSD) encoding along with optimal selection of data width are coded with a hardware description language (HDL) to obtain optimality for power and an automated design. The filter occupies an area of 0.46 mm2 and consumes 100µW from a supply of 1.8 V and is operational down to a supply voltage of 0.9 V. This makes it suitable for use with very low power ΔΣ data converters for digital audio.
Variation in Incidence and Severity of Injuries among Crown-of-Thorns Starfish (Acanthaster cf. solaris) on Australia’s Great Barrier Reef

Despite the presence of numerous sharp poisonous spines, adult crown-of-thorns starfish (CoTS) are vulnerable to predation, though the importance and rates of predation are generally unknown. This study explores variation in the incidence and severity of injuries for Acanthaster cf. solaris from Australia’s Great Barrier Reef. The major cause of such injuries is presumed to be sub-lethal predation such that the incidence of injuries may provide a proxy for overall predation and mortality rates. A total of 3846 Acanthaster cf. solaris were sampled across 19 reefs, of which 1955 (50.83%) were injured. Both the incidence and severity of injuries decreased with increasing body size. For small CoTS ( 60% of individuals had injuries, and a mean 20.7% of arms (±2.9 SE) were affected. By comparison, 450 mm total diameter) CoTS had injuries, and, among those, only 8.3% of arms (±1.7 SE) were injured. The incidence of injuries varied greatly among reefs but was unaffected by the regulations of local fisheries.
WAVELET SHRINKAGE FOR CORRELATED DATA AND INVERSE PROBLEMS: ADAPTIVITY RESULTS

Johnstone and Silverman (1997) described a level-dependent thresholding method for extracting signals from correlated noise. The thresholds were chosen to minimize a data based unbiased risk criterion. Here we show that in certain asymptotic models encompassing short and long range dependence, these methods are simultaneously asymptotically minimax up to constants over a broad range of Besov classes. We indicate the extension of the methods and results to a class of linear inverse problems possessing a wavelet vaguelette decomposition.
LINGO1 Variants in the French-Canadian Population

Essential tremor (ET) is a complex genetic disorder for which no causative gene has been found. Recently, a genome-wide association study reported that two variants in the LINGO1 locus were associated to this disease. The aim of the present study was to test if this specific association could be replicated using a French-Canadian cohort of 259 ET patients and 479 ethnically matched controls. Our genotyping results lead us to conclude that no association exists between the key variant rs9652490 and ET (Pcorr = 1.00).
PDF neuron firing phase-shifts key circadian activity neurons in Drosophila

Our experiments address two long-standing models for the function of the Drosophila brain circadian network: a dual oscillator model, which emphasizes the primacy of PDF-containing neurons, and a cell-autonomous model for circadian phase adjustment. We identify five different circadian (E) neurons that are a major source of rhythmicity and locomotor activity. Brief firing of PDF cells at different times of day generates a phase response curve (PRC), which mimics a light-mediated PRC and requires PDF receptor expression in the five E neurons. Firing also resembles light by causing TIM degradation in downstream neurons. Unlike light however, firing-mediated phase-shifting is CRY-independent and exploits the E3 ligase component CUL-3 in the early night to degrade TIM. Our results suggest that PDF neurons integrate light information and then modulate the phase of E cell oscillations and behavioral rhythms. The results also explain how fly brain rhythms persist in constant darkness and without CRY. DOI: http://dx.doi. org/10.7554/eLife.02780. 001
Visual access to an agent-based simulation model to support political decision making

Decision making in the field of policy making is a complex task. On the one hand conflicting objectives influence the availability of alternative solutions for a given problem. On the other hand economic, social, and environmental impacts of the chosen solution have to be considered. In the political context, these solutions are called policy options. To tackle societal problems a thorough analysis of policy options needs to be executed before a policy can be put into practice. Computational simulation is a method considered for measuring the impacts of policy options. However, due to their complexity, the underlying models and their output may be difficult to access by decision makers. In this work, we present a visual-interactive interface for an agent-based simulation model that enables decision makers to evaluate the impacts of alternative policy options in the field of regional energy planning. The decision maker can specify different subsidy strategies for supporting public photovoltaic installations as input and evaluate their impact on the actual adoption via the simulation output. We show the usability and usefulness of the visual interface in a real-world example evolved from the European research project ePolicy.
Le stress, l'hyperactivation et l'insomnie

This thesis aimed to improve the understanding of the role of stress and hyperarousal in insomnia. First, an observational study was conducted. Participants included 22 individuals with insomnia, 23 good sleepers with high vulnerability to insomnia, and 24 good sleepers with low vulnerability to insomnia, who were matched for age and sex. Over one week, they wore wrist actigraph, collected saliva samples for cortisol, and completed daily self-monitoring questionnaires assessing stress, bedtime arousal, and sleep. Results suggested that individuals with insomnia perceived daily events as more stressful, reported higher pre-sleep cognitive and somatic arousal, and had greater bedtime cortisol secretion than good sleepers with low vulnerability to insomnia. Analyses also revealed that pre-sleep cognitive arousal but not physiological arousal (cortisol) plays an important mediating role in the relation between stress and sleep disturbances, particularly among individuals with heightened sleep reactivity, including good sleepers with high vulnerability to insomnia and those with insomnia disorder. In the second study, a subsample composed of 10 individuals with insomnia, 10 good sleepers with high vulnerability to insomnia, and 10 good sleepers with low vulnerability to insomnia underwent two consecutive nights of polysomnography in the sleep laboratory. A standardized experimental stressor was administered, and various psychological and physiological arousal indices were assessed. Individuals with insomnia showed greater acute cortisol response, higher cortisol secretion at bedtime, as well as higher pre-sleep cognitive arousal than good sleepers with low vulnerability to insomnia. Good sleepers with high vulnerability to insomnia did not differ from those with low vulnerability to insomnia or those who already had insomnia on any arousal variable. Further, stress-induced hyperarousal was associated with more disturbed sleep. Overall results of the thesis support the hyperarousal conceptualization of insomnia and highlight the potential existence of a continuum of insomnia disorder. Heightened stress-related sleep reactivity and bedtime hyperarousal might represent a trait-like vulnerability in certain good
Dual port microstrip patch antennas and circuits with high interport isolation for in-band full duplex (IBFD) wireless applications

In-Band Full Duplex (IBFD) is one effective way to increase the spectral efficiency and the throughput of wireless communication systems by transmitting and receiving simultaneously on the same frequency band but the coupling (called Self Interference or SI) of transmit signal to its receiver is one major problem. IBFD operation can be realized successfully by suppressing this coupling or Self Interference (SI). The required amount of SI cancellation depends on the power and bandwidth of transmitted signal. Generally, the SI should be suppressed to RF transceiver noise floor. To achieve this amount of SI suppression, SI suppression mechanism is normally implemented at three stages across the IBFD transceiver and they are known as antenna cancellation, RF/analog cancellation and digital base-band cancellation. Most of the SI suppression is achieved at antenna stage to relax the required amount of SI cancellation at the rest of two stages . Thus, a dual port microstrip patch antenna with very high port to port RF isolation is required in addition to digital self interference cancellation techniques to enable simultaneous transmit and receive wireless operation at same carrier frequency using single antenna for full duplex radio transceivers. The objective of my research work presented in this dissertation is to design, implement and measure dual port microstrip patch antennas which deploy different feeding techniques along with Self Interference Cancellation (SIC) circuits to get high interport isolation to enable such antennas for realization of IBFD wireless operation using single/shared antenna architecture. The goal is to achieve high interport isolation for dual port antenna with minimum effect on radiation performance of antennas.
Human Neuroscience

STN, right IFG, and preSMA (Aron et al., 2007), which further supports the existence of this network. Lastly, both age and behavior have been found to correlate with brain activity in these regions, indicating that individual differences in the engagement of this network may relate to variability in behavior. For example, adults have greater activity than children during inhibition in the right IFG (Bunge et al., 2002; Durston et al., 2002; Rubia et al., 2007). It has also been found that activity in the right IFG and STN rises with increasingly successful response inhibition in adults (Aron and Poldrack, 2006). The stop-signal paradigm (Logan, 1994) is commonly used to measure the rapid engagement of response inhibition. In this task, participants are presented with a simple choice response task (e.g., pressing a left or right button in response to an arrow pointing left or right), but a small proportion of trials are presented with a " stop-signal " (often an auditory tone), which signals to participants to withhold their response. A unique feature of this task is the ability to estimate a continuous measure of response inhibition, known as the " stop-signal reaction time " (SSRT), using a model known as the independent race model (Logan and Cowan, 1984;
IPM-G: Enabling Collaborative Filtering Using Multi-Application Interest Models

He Interest Profile Manager (IPM) plays the central role in inferring user interest during document triage. The IPM collects information about interest-related activity from the potentially many triage applications. In this paper, we extend the IPM framework to enable community-based navigation using inferred user interests from information gathering tasks involving the use of multiple applications. We call IPM running on server, Global IPM (IPM-G), and IPM-G can generate similarity assessments, and thus recommendations, based on three different levels: tasks, documents, and annotations. As a result, CF methods can be applied to each level to get results at these three levels of granularity. By representing inferred interests based on the features of their tasks, documents, and annotations, we make possible six potential collaborative filtering (CF) modes in the IPM-G. This paper describes why collaborative filtering based on multi-application interest models is important, abstractly describes the representation of the interest models, and presents details of one of these filtering modes.
Numerical simulations and analytical analyses of the orbital capture manoeuvre as a part of the manipulator-equipped servicing satellite design

The lifetime of a considerable number of satellites is significantly shortened by malfunctions occurring during operational period; therefore, unmanned satellite servicing missions are considered. This paper presents an approach for analyses of various configurations and parameters of manipulator intended for on-orbit servicing. It is based on analytical method used to analyse workspace and singularities of the manipulator mounted on a free-floating satellite, and on numerical simulations of mission-specific manoeuvers (e.g., capture of malfunctioned satellite). The application of this approach to obtain parameters of the manipulator most suitable for defined servicing tasks is presented.
A novel night vision image color fusion method based on scene recognition

Infrared and low light level image color fusion can make target detection and recognition more precise. Different from the existing color transfer fusion method using fixed reference image, this paper presents a color fusion method based on a combination of scene classification, fusion quality measure and color transfer. We introduce the scene classification method into the color fusion algorithm, which is based on the Gist descriptor and SVM classifier. Afterwards we use the proposed color fusion quality measure structure to find out the best matched reference image for each classified input image. Meanwhile, we get the high quality color fusion image using color transfer method. This method is verified in both linear and non-linear color space. Results show that this method can effectively improve the color fusion effect. More importantly, it can be used in the condition with few prior information.