Miracle-dz/UniFAR-FTUs huggingface dataset:
The analysis of QTL and QTL x treatment experiments using spatial models for marker effects

The continued increase in the availability of markers has led to much interest in their use in genetic improvement programs of crop species, such as wheat and maize. There is a large amount of literature on this topic and much of the focus has turned from marker assisted selection and the identification of quantitative trait loci (QTL) to genomic selection. The basic idea in marker assisted selection is to exploit statistical dependencies (linkage disequilibrium, LD) existing in the joint distribution of marker and QTLs. Linkage disequilibrium between markers and QTL has two main objectives, and in some way these are not disjoint and not surprisingly the statistical models used in these two applications are similar. We refer to these objectives as (i) QTL analysis in which the aim is to infer genomic locations and effects (i.e. QTLs) which affect a (quantitative) trait and (ii) genomic selection in which the aim is to obtain predictions of genetic merit of individuals for selection as parents in a breeding program. Since the seminal paper of Meuwissen et al. (2001) there has been significant progress made in the second objective where there was a realisation that unravelling the genetic architecture of a trait via identification of (major) QTLs is not necessary for prediction of genetic merit. This concept built on the idea that a trait is the result of the influences of many, possibly small QTLs which would be very difficult if not impossible, to detect and hence routinely use within a breeding program. This working paper is available at Research Online: http://ro.uow.edu.au/niasrawp/45 This work has been submitted for publication. Copyright in this work may be transferred without further notice, and this version may no longer be accessible. National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong NSW 2522, Australia Phone +61 2 4221 5435, Fax +61 2 4221 4845. Email: karink@uow.edu.au National Institute for Applied Statistics Research Australia The University of Wollongong, Australia
Molecular Analysis of Antimicrobial Resistance Mechanisms in Neisseria gonorrhoeae Isolates from Ontario, Canada

ABSTRACT Surveillance of gonococcal antimicrobial resistance and the molecular characterization of the mechanisms underlying these resistance phenotypes are essential in order to establish correct empirical therapies, as well as to describe the emergence of new mechanisms in local bacterial populations. To address these goals, 149 isolates were collected over a 1-month period (October-November 2008) at the Ontario Public Health Laboratory, Toronto, Canada, and susceptibility profiles (8 antibiotics) were examined. Mutations in previously identified targets or the presence of some enzymes related to resistance (r), nonsusceptibility (ns) (resistant plus intermediate categories), or reduced susceptibility (rs) to the antibiotics tested were also studied. A significant proportion of nonsusceptibility to penicillin (PEN) (89.2%), tetracycline (TET) (72.3%), ciprofloxacin (CIP) (29%), and macrolides (erythromycin [ERY] and azithromycin; 22.3%) was found in these strains. Multidrug resistance was observed in 18.8% of the collection. Although all the strains were susceptible to spectinomycin and extended-spectrum cephalosporins (ESC) (ceftriaxone and cefixime), 9.4% of them displayed reduced susceptibility to extended-spectrum cephalosporins. PBP 2 mosaic structures were found in all of these ESCrs isolates. Alterations in the mtrR promoter, MtrR repressor (TETr, PENns, ESCrs, and ERYns), porin PIB (TETr and PENns), and ribosomal protein S10 (TETr) and double mutations in gyrA and parC quinolone resistance-determining regions (QRDRs) (CIPr) were associated with and presumably responsible for the resistance phenotypes observed. This is the first description of ESCrs in Canada. The detection of this phenotype indicates a change in the epidemiology of this resistance and highlights the importance of continued surveillance to preserve the last antimicrobial options available.
SPICi: a fast clustering algorithm for large biological networks

Motivation: Clustering algorithms play an important role in the analysis of biological networks, and can be used to uncover functional modules and obtain hints about cellular organization. While most available clustering algorithms work well on biological networks of moderate size, such as the yeast protein physical interaction network, they either fail or are too slow in practice for larger networks, such as functional networks for higher eukaryotes. Since an increasing number of larger biological networks are being determined, the limitations of current clustering approaches curtail the types of biological network analyses that can be performed. Results: We present a fast local network clustering algorithm SPICi. SPICi runs in time O(V log V+E) and space O(E), where V and E are the number of vertices and edges in the network, respectively. We evaluate SPICi's performance on several existing protein interaction networks of varying size, and compare SPICi to nine previous approaches for clustering biological networks. We show that SPICi is typically several orders of magnitude faster than previous approaches and is the only one that can successfully cluster all test networks within very short time. We demonstrate that SPICi has state-of-the-art performance with respect to the quality of the clusters it uncovers, as judged by its ability to recapitulate protein complexes and functional modules. Finally, we demonstrate the power of our fast network clustering algorithm by applying SPICi across hundreds of large context-specific human networks, and identifying modules specific for single conditions. Availability: Source code is available under the GNU Public License at http://compbio.cs.princeton.edu/spici Contact: mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Solving Fuzzy TSP with Ant Algorithms

A method and apparatus for conformance testing of complex entities, such as networks and their protocols. Networks that have their managed objects, attributes and notifications defined in industry standard ASN.1 notation can be methodically processed according to finite state machine models of their managed objects to provide optimum test cases for conformance testing. These test cases are optimum in that they are minimized according to a cost criterion, while designed to test each state of the finite state machine model at least once. A data base stores the optimum test cases of the managed objects to support testing of the defined and modeled network. The method further applies these optimum test cases via a test apparatus to a system-under-test, e.g. a network, to test conformance thereof to its specifications.
Throughput-optimized cross-layer routing for cognitive radio networks

Cognitive radio (CR) is a promising technology to solve the spectrum scarcity problem by enabling secondary users (SU) to utilize the spectrum holes of primary users (PU) caused by static spectrum allocation. However, SUs need to avoid the interference to PUs, imposing new challenges in routing protocol designs and throughput improvement in CR networks (CRN). In this paper we propose a cross-layer channel assignment and routing (CCAR) algorithm. Specifically, our CCAR algorithm aims at throughput maximization while addressing the interference avoidance issue in CRNs. Solving for the optimal solution towards throughput maximization is a NP problem. In contrast, we simplify this optimization problem by taking advantage of the correlation of data flow and routing information across the network nodes. Then, further making use of the adjacent hop interference (AHI) Information, we develop a heuristic approach to obtain a suboptimal solution. Theoretical analysis and simulation results show that our proposed CCAR algorithm can achieve polynomial complexity at the cost of only 20% throughput loss as compared to the optimal solution.
Global health impacts of floods: epidemiologic evidence.

Floods are the most common natural disaster in both developed and developing countries, and they are occasionally of devastating impact, as the floods in China in 1959 and Bangladesh in 1974 and the tsunami in Southeast Asia in December 2004 show (1). Their impacts on health vary between populations for reasons relating to population vulnerability and type of flood event (2–5). Under future climate change, altered patterns of precipitation and sea level rise are expected to increase the frequency and intensity of floods in many regions of the world (6). In this paper, we review the epidemiologic evidence of flood-related health impacts. The specific objectives were as follows: to summarize and critically appraise evidence of published studies, covering flood events in all regions of the world, and to identify knowledge gaps relevant to the reduction of public health impacts.
Authentication Mechanisim For Session Passwords By Imposing Color With Text

The most common method used for authentication is Textual passwords. But textual passwords are in risk to eves dropping, dictionary attacks, social engineering and shoulder surfing. Graphical passwords are introduced as alternative techniques to textual passwords. Most of the graphical schemes are helpless to shoulder surfing. To address this problem, text can be combined with images or colors to generate session passwords for authentication. Session passwords can be used only once and every time a new password is generated. In this paper, two techniques are proposed to generate session passwords using text and colors which are resistant to shoulder surfing. These methods are suitable for Personal
A 0.9-V Input Discontinuous-Conduction-Mode Boost Converter With CMOS-Control Rectifier

A 0.9-V input discontinuous-conduction-mode (DCM) boost converter delivering 2.5-V and 100-mA output is presented. A novel low-voltage pulse-width modulator is proposed. The modulator can be directly powered from the 0.9-V input instead of using the 2.5-V output as in general modulator designs. Sophisticated low-voltage analog blocks, which normally consume a large amount of power and chip area, are not required in the modulator. The impact of output-voltage ripple and transient-induced output-voltage perturbation on the operation of analog blocks inside the modulator is eliminated. Boost converter start-up sequence is also greatly simplified. A CMOS-control rectifier (CCR) is also proposed to improve converter power efficiency. The CCR is used to replace the conventional rectifying switch to provide adaptive dead-time, which helps to minimize charge-sharing loss and body-diode conduction loss. Corresponding thermal stress on the rectifying switch is hence minimized. The CCR also enables the use of small off-chip inductor and capacitor at sub-MHz switching frequency to improve light-load efficiency. This converter has been implemented in a 0.35- mum CMOS process. It is designed to operate at ~ 667 kHz with a 1 mu H inductor and 4.7 mu F output capacitor to reduce both switching loss and form factor. Experimental results prove that the converter can be directly powered from 0.9-V input with ~ 85% efficiency at 100-mA output.
Identifying Architectural Patterns Used in Open Source Software: Approaches and Challenges

Background: Open Source Software (OSS) is increasingly used in product development. Besides some much-reported benefits of this approach, using OSS products also presents new challenges. One such challenge is identifying relevant, high-quality OSS products among the hundreds of thousands that are available. One approach for doing that is to identify architectural patterns, since these patterns have a direct effect on a product's quality attributes, such as performance and reliability. However, there are no well-defined methods or tools available to identify architectural patterns. Research aim: Our goal is to identify approaches taken by novice software engineers that have no or little experience in identifying architectural patterns. We aim to get insight into how these novices tackle this problem, what challenges they encounter and what suggestions they have for improving this process. Method: We collected data from seven M. Sc. student teams that performed a pattern identification assignment. We conducted semi-structured interviews with eight students from two teams. We studied reflection reports from four teams that reported their experiences as part of their final report. Furthermore, during his M. Sc. course, one of the authors performed the assignment as a member of a team. We also included his experiences. Results and conclusions: We identified a number of approaches that students have taken in order to identify architectural patterns, as well as a number of challenges that they encountered in this task. Furthermore, based on suggestions from the students, we present a proposal to improve this process.
Quality-Based Fusion of Multiple Video Sensors for Video Surveillance

In this correspondence, we address the problem of fusing data for object tracking for video surveillance. The fusion process is dynamically regulated to take into account the performance of the sensors in detecting and tracking the targets. This is performed through a function that adjusts the measurement error covariance associated with the position information of each target according to the quality of its segmentation. In this manner, localization errors due to incorrect segmentation of the blobs are reduced thus improving tracking accuracy. Experimental results on video sequences of outdoor environments show the effectiveness of the proposed approach.
Kobe University Repository : Kernel タイトル Tit le Neuroprotect ive Effect of D-Fructose-1 , 6-Bisphosphate against beta-Amyloid Induced Neurotoxicity in Rat Hippocampal Organotypic Slice Culture : Involvement of PLC and MEK / ERK Signaling Pathways

タイトル Tit le Neuroprotect ive Effect of D-Fructose-1,6-Bisphosphate against betaAmyloid Induced Neurotoxicity in Rat Hippocampal Organotypic Slice Culture : Involvement of PLC and MEK/ERK Signaling Pathways 著者 Author(s) Song, Xiuzhen / Wu, Bin / Takata, Toshihiro / Wang, Xiaonan / Oizumi, Ximena Sayuri / Akisaki, Taichi / Yokono, Koichi / Sakurai, Takashi 掲載誌・巻号・ページ Citat ion The Kobe journal of the medical sciences,51(5/6):73-83
Early sucking and swallowing problems as predictors of neurodevelopmental outcome in children with neonatal brain injury: a systematic review

Aim Early sucking and swallowing problems may be potential markers of neonatal brain injury and assist in identifying those infants at increased risk of adverse outcomes, but the relation between early sucking and swallowing problems and neonatal brain injury has not been established. The aim of the review was, therefore, to investigate the relation between early measures of sucking and swallowing and neurodevelopmental outcomes in infants diagnosed with neonatal brain injury and in infants born very preterm (<32wks) with very low birthweight (<1500g), at risk of neonatal brain injury.
Supervoxel Segmentation with Voxel-Related Gaussian Mixture Model

Extended from superpixel segmentation by adding an additional constraint on temporal consistency, supervoxel segmentation is to partition video frames into atomic segments. In this work, we propose a novel scheme for supervoxel segmentation to address the problem of new and moving objects, where the segmentation is performed on every two consecutive frames and thus each internal frame has two valid superpixel segmentations. This scheme provides coarse-grained parallel ability, and subsequent algorithms can validate their result using two segmentations that will further improve robustness. To implement this scheme, a voxel-related Gaussian mixture model (GMM) is proposed, in which each supervoxel is assumed to be distributed in a local region and represented by two Gaussian distributions that share the same color parameters to capture temporal consistency. Our algorithm has a lower complexity with respect to frame size than the traditional GMM. According to our experiments, it also outperforms the state-of-the-art in accuracy.
A nationwide study of discrimination and chronic health conditions among Asian Americans.

OBJECTIVES We examined whether self-reported everyday discrimination was associated with chronic health conditions among a nationally representative sample of Asian Americans. METHODS Data were from the Asian American subsample (n = 2095) of the National Latino and Asian American Study conducted in 2002 and 2003. Regression techniques (negative binomial and logistic) were used to examine the association between discrimination and chronic health conditions. Analyses were conducted for the entire sample and 3 Asian subgroups (Chinese, Vietnamese, and Filipino). RESULTS Reports of everyday discrimination were associated with many chronic conditions, after we controlled for age, gender, region, per capita income, education, employment, and social desirability bias. Discrimination was also associated with indicators of heart disease, pain, and respiratory illnesses. There were some differences by Asian subgroup. CONCLUSIONS Everyday discrimination may contribute to stress experienced by racial/ethnic minorities and could lead to chronic illness.
An Aerosol-Dipole Event Over the Tropical Indian Ocean During 2006

Using aerosol optical depth (AOD at 550 nm) from the moderate-resolution imaging spectroradiometer, surface winds, outgoing long-wave radiation from National Centers for Environmental Prediction/National Center for Atmospheric Research reanalysis, and rainfall from Tropical Rainfall Measuring Mission data sets, we report a dipolelike variability in the aerosol concentration over the region (40°E-130° E; 10° S-10°;N) during September, October, and November 2006. Positive AOD anomalies (+ 0.4 to + 0.6) (relative to the 2000-2008 climatological average) along the equatorial East Indian Ocean and Indonesia and negative AOD anomalies (-0.2 to -0.4) over the western, northwestern, and central Indian Ocean characterize an aerosol-dipolelike variability. This east-west variability of the aerosol loading along the Indian Ocean is linked to the anomalously weak easterlies associated with the 2006 Indian Ocean Dipole event. The weaker easterlies lead to the hovering of the aerosol plume over Indonesia/Sumatra coast (98° E), enhancing the positive anomalies of AODs, while excessive rainfall over the central Arabian Sea caused the negative AOD anomalies.
Avoiding File System Micromanagement with Range Writes

We introduce range writes, a simple but powerful change to the disk interface that removes the need for file system micromanagement of block placement. By allowing a file system to specify a set of possible address targets, range writes enable the disk to choose the final on-disk location of the request; the disk improves performance by writing to the closest location and subsequently reporting its choice to the file system above. The result is a clean separation of responsibility; the file system (as high-level manager) provides coarse-grained control over placement, while the disk (as low-level worker) makes the final fine-grained placement decision to improve write performance. We show the benefits of range writes through numerous simulations and a prototype implementation, in some cases improving performance by a factor of three across both synthetic and real workloads.
Impairment in Holistic Face Processing Following Early Visual Deprivation

Unlike most objects, faces are processed holistically: They are processed as a whole rather than as a collection of independent features. We examined the role of early visual experience in the development of this type of processing of faces by using the composite-face task, a measure of holistic processing, to test patients deprived of visual experience during infancy. Visually normal control subjects showed the expected composite-face effect: They had difficulty perceiving that the top halves of two faces were the same when the top halves were aligned with different bottom halves. Performance improved when holistic processing was disrupted by misaligning the top and bottom halves. Deprived patients, in contrast, showed no evidence of holistic processing, and in fact performed significantly better than control subjects when top and bottom halves were aligned. These findings suggest that early visual experience is necessary to set up or maintain the neural substrate that leads to holistic processing of faces.
Novel Substrate Integrated Waveguide Filters With Mixed Cross Coupling (MCC)

A new type of substrate integrated waveguide filter with mixed cross coupling (MCC) is proposed, with its mechanism of generating extra transmission zeros using MCC investigated. Less mixed coupling is needed to obtain the same number of transmission zeros in comparison with inline filters, with good agreements obtained between the measured and the simulated S-parameters of the developed filters.
Combating digital document forgery using new secure information hiding algorithm

The recent digital revolution has facilitated communication, data portability and on-the-fly manipulation. Unfortunately, this has brought along some critical security vulnerabilities that put digital documents at risk. The problem is in the security mechanism adopted to secure these documents by means of encrypted passwords; however, this security shield does not actually protect the documents which are stored intact. We propose a solution to this real world problem through a 1D hash algorithm coupled with 2D irFFT (irreversible fast Fourier transform) to encrypt digital documents in the 2D spatial domain. This method is described elsewhere in [1]. Further by applying an imperceptible information hiding technique we can add another security layer which is resistant to noise and to a certain extent JPEG compression. We support this assertion by showing a practical example which is drawn from our set of experiments. Our proposal not only points out forgery but also lets a jury or a forensics expert have access to the original document despite being manipulated. This would undoubtedly be very useful in cases of disputes or claims.
View infinity: a zoomable interface for feature-oriented software development

Software product line engineering provides efficient means to develop variable software. To support program comprehension of software product lines (SPLs), we developed View Infinity, a tool that provides seamless and semantic zooming of different abstraction layers of an SPL. First results of a qualitative study with experienced SPL developers are promising and indicate that View Infinity is useful and intuitive to use.