Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction: Learning Gene Networks under SNP Perturbations Using eQTL Datasets

The standard approach for identifying gene networks is based on experimental perturbations of gene regulatory systems such as gene knock-out experiments, followed by a genome-wide profiling of differential gene expressions. However, this approach is significantly limited in that it is not possible to perturb more than one or two genes simultaneously to discover complex gene interactions or to distinguish between direct and indirect downstream regulations of the differentially-expressed genes. As an alternative, genetical genomics study has been proposed to treat naturally-occurring genetic variants as potential perturbants of gene regulatory system and to recover gene networks via analysis of population gene-expression and genotype data. Despite many advantages of genetical genomics data analysis, the computational challenge that the effects of multifactorial genetic perturbations should be decoded simultaneously from data has prevented a widespread application of genetical genomics analysis. In this article, we propose a statistical framework for learning gene networks that overcomes the limitations of experimental perturbation methods and addresses the challenges of genetical genomics analysis. We introduce a new statistical model, called a sparse conditional Gaussian graphical model, and describe an efficient learning algorithm that simultaneously decodes the perturbations of gene regulatory system by a large number of SNPs to identify a gene network along with expression quantitative trait loci (eQTLs) that perturb this network. While our statistical model captures direct genetic perturbations of gene network, by performing inference on the probabilistic graphical model, we obtain detailed characterizations of how the direct SNP perturbation effects propagate through the gene network to perturb other genes indirectly. We demonstrate our statistical method using HapMap-simulated and yeast eQTL datasets. In particular, the yeast gene network identified computationally by our method under SNP perturbations is well supported by the results from experimental perturbation studies related to DNA replication stress response.
Real-time semi-blind speech extraction with speaker direction tracking on Kinect

In this paper, speech recognition accuracy improvement is addressed for ICA-based multichannel noise reduction in spoken-dialogue robot. First, to achieve high recognition accuracy for the early utterance of the target speaker, we introduce a new rapid ICA initialization method combining robot image information and a prestored initial separation filter bank. From this image information, an ICA initial filter fitted to the user's direction can be used to save the user's first utterance. Next, a new permutation solving method using a probability statistics model is proposed for realistic sound mixtures consisting of point-source speech and diffuse noise. We implement these methods using user tracking on Microsoft Kinect and evaluate it by speech recognition experiment in the real environment. The experimental results show that the proposed approaches can markedly improve the word recognition accuracy.
Tagging Single Nucleotide Polymorphisms in the BRIP1 Gene and Susceptibility to Breast and Ovarian Cancer

Background BRIP1 interacts with BRCA1 and functions in regulating DNA double strand break repair pathways. Germline BRIP1 mutations are associated with breast cancer and Fanconi anemia. Thus, common variants in the BRIP1 are candidates for breast and ovarian cancer susceptibility. Methods We used a SNP tagging approach to evaluate the association between common variants (minor allele frequency≥0.05) in BRIP1 and the risks of breast cancer and invasive ovarian cancer. 12 tagging SNPs (tSNPs) in the gene were identified and genotyped in up to 2,270 breast cancer cases and 2,280 controls from the UK and up to 1,513 invasive ovarian cancer cases and 2,515 controls from the UK, Denmark and USA. Genotype frequencies in cases and controls were compared using logistic regression. Results Two tSNPs showed a marginal significant association with ovarian cancer: Carriers of the minor allele of rs2191249 were at reduced risk compared with the common homozygotes (Odds Ratio (OR) = 0.90 (95% CI, 0.82–1.0), P-trend = 0.045) and the minor allele of rs4988344 was associated with increased risk (OR = 1.15 (95%CI, 1.02–1.30), P-trend = 0.02). When the analyses were restricted to serous ovarian cancers, these effects became slightly stronger. These results were not significant at the 5% level after adjusting for multiple testing. None of the tSNPs was associated with breast cancer. Conclusions It is unlikely that common variants in BRIP1 contribute significantly to breast cancer susceptibility. The possible association of rs2191249 and rs4988344 with ovarian cancer risks warrant confirmation in independent case-control studies.
CD28 mediates transcriptional upregulation of the interleukin-2 (IL-2) promoter through a composite element containing the CD28RE and NF-IL-2B AP-1 sites

Mutagenesis studies have demonstrated the requirement for the CD28-responsive element (CD28RE) within the interleukin-2 (IL-2) promoter for transcriptional upregulation by CD28. Here, we demonstrate that CD28 responsiveness is conferred by a composite element containing both the CD28RE and the NF-IL-2B AP-1 sites (RE/AP). Mutations at either site within the RE/AP composite element abolish activity. The RE/AP composite element is a site for signal integration within the IL-2 promoter, since its activation is dependent on at least two separate signalling pathways being activated, through the T-cell receptor, CD28, and/or phorbol myristate acetate. Activation is maximal when all three signals occur simultaneously. By using a panel of CD28 cytoplasmic domain mutants, it was found that the transcriptional activation of the RE/AP composite element correlates exactly with the pattern of IL-2 secretion induced by these mutants upon stimulation. Similar to the upregulation of IL-2 secretion, the transcriptional upregulation of the RE/AP composite element by CD28 is FK506 insensitive. The pattern of activation of the RE/AP composite element is different from that observed for either an NFAT or consensus AP-1 site, implying that RE/AP represents a unique element. Using gel shift analysis, we demonstrate that stimulation by CD28 induces the association of the NF-kappaB family member c-Rel to the CD28RE within the RE/AP composite element. The transcriptional upregulation of IL-2 by CD28 appears, therefore, to be mediated through the RE/AP composite element, involving the association of c-Rel with the CD28RE.
Carbon sequestration in topsoil for forage-based cropping systems

C sequestration in soils is a potential way to mitigate climate change and increase the fertility of arable soils. Ley has long been known to deliver more C to its root systems compared to annual crops. Therefore, it has been suggested as a potential C sequestration strategy. My objective was to evaluate the SOC sequestration potential of ley in Nordic countries by studying three Swedish long-term experimental sites. From each site a ley rotation and bar-ley monoculture rotation were selected, and mineral- was compared to combined fertilization. Two of the sites (in N. Sweden) were measured for SOC stocks, while corresponding data was available for the third site (in S. Sweden). Higher topsoil SOC stocks was found for ley rotation than barley rota-tion for all sites. The effect from SOC stocks on soil aggregate stability was determined on the soil samples by analysing readily dispersible clay (RDC) and water stable aggregates (WSA). Ley might have influenced RDC positively, while mineral fertilization and WSA was found to correlate positively. As a second part of the study, I modelled SOC stock changes with ICBM, a SOC model used in National SOC Inventory reporting system and in the consultant tool OP. OP uses a simplified version of ICBM with default values. Samples from the soil archive from each of the northern experiments were included in the modelling. I used yield data records to estimate belowground C inputs from plant residues using shoot to root ratios. The predictions with OP matched in many cases better to measured SOC stocks than ICBM, sug-gesting that the default values in OP worked relatively well. The models matched the measured SOC stocks in the southern site. However, the models did not always apply to the northern sites. One explanation lies in the high uncertainty when estimating initial SOC stocks and imprecision in estimations of belowground C. Although the SOC stocks decreased in the northern sites (all treatments), the SOC stocks remained higher in ley rotation than in barley rotation. Combined fertilization had a positive effect upon the SOC sequestering potential of ley at the northern sites. This could however not be evaluated for the southern site. Finally, the SOC stocks increased for ley rotation in the southern site and the SOC stocks in ley rotation in one of the northern sites did not start to decrease until after 30 years, suggesting a SOC preserving potential in addition to the observed SOC sequestering potential of ley.
A mass assignment algorithm for Dempster-Shafer approach

In this work, a new methodology is proposed for probability mass assignment to be used in Dempster-Shafer approach. The approach is developed for the cases where the prior and the current information are represented by probability density functions. Masses are assigned by comparing the prior and the current probability density functions which are assumed to be Gaussian. The proposed method is tested by artificial data and compared with the method given in [13] which is most similar to the proposed one in the literature.
V&V of flight and mission-critical software

The use of software verification and validation to assure the safety of flight control systems is described. The process considered is performed by the system's developers, not by a separate group as is typical, and it examines the software as part of the system, with emphasis on techniques for review, simulation, and integration and system testing. The use of hardware-in-the-loop simulations for dynamic system verification and flight qualification is discussed. <<ETX>>
Oscillatory fluid flow influences primary cilia and microtubule mechanics

Many tissues are sensitive to mechanical stimuli; however, the mechanotransduction mechanism used by cells remains unknown in many cases. The primary cilium is a solitary, immotile microtubule‐based extension present on nearly every mammalian cell which extends from the basal body. The cilium is a mechanosensitive organelle and has been shown to transduce fluid flow‐induced shear stress in tissues, such as the kidney and bone. The majority of microtubules assemble from the mother centriole (basal body), contributing significantly to the anchoring of the primary cilium. Several studies have attempted to quantify the number of microtubules emanating from the basal body and the results vary depending on the cell type. It has also been shown that cellular response to shear stress depends on microtubular integrity. This study hypothesizes that changing the microtubule attachment of primary cilia in response to a mechanical stimulus could change primary cilia mechanics and, possibly, mechanosensitivity. Oscillatory fluid flow was applied to two different cell types and the microtubule attachment to the ciliary base was quantified. For the first time, an increase in microtubules around primary cilia both with time and shear rate in response to oscillatory fluid flow stimulation was demonstrated. Moreover, it is presented that the primary cilium is required for this loading‐induced cellular response. This study has demonstrated a new role for the cilium in regulating alterations in the cytoplasmic microtubule network in response to mechanical stimulation, and therefore provides a new insight into how cilia may regulate its mechanics and thus the cells mechanosensitivity. © 2014 Wiley Periodicals, Inc.
Spatial Information Fusion: Coping with Uncertainty in Conceptual Structures

A logical formalism associating properties to space parcels in so-called attribute formulas, is proposed. Properties are related through the axioms of a taxonomy graph, and parcels through a partonomy graph. Attributive formulas establish relations between parcels and properties, and we use them to align different taxonomies, over a compatible partonomy, using Formal Concept Analysis. We discuss uncertainty in attributive formulas, which we extend in a possibilistic logic manner, including two modalities: true everywhere in the parcel, or at least true somewhere. Then, we discuss how our formalism can perform a possibilistic fusion on attributive formulas originating from independent sources, based on the aligned taxonomy. The issues may come from (a) the uncertainty of sources, (b) the possible inconsistency of fusion results, (c) the use of different partonomies that may not explicit the somewhere or everywhere reading associated to the information.
Influence of weather conditions on the flight of migrating black storks

This study tested the potential influence of meteorological parameters (temperature, humidity, wind direction, thermal convection) on different migration characteristics (namely flight speed, altitude and direction and daily distance) in 16 black storks (Ciconia nigra). The birds were tracked by satellite during their entire autumnal and spring migration, from 1998 to 2006. Our data reveal that during their 27-day-long migration between Europe and Africa (mean distance of 4100 km), the periods of maximum flight activity corresponded to periods of maximum thermal energy, underlining the importance of atmospheric thermal convection in the migratory flight of the black stork. In some cases, tailwind was recorded at the same altitude and position as the birds, and was associated with a significant rise in flight speed, but wind often produced a side azimuth along the birds' migratory route. Whatever the season, the distance travelled daily was on average shorter in Europe than in Africa, with values of 200 and 270 km d−1, respectively. The fastest instantaneous flight speeds of up to 112 km h−1 were also observed above Africa. This observation confirms the hypothesis of thermal-dependant flight behaviour, and also reveals differences in flight costs between Europe and Africa. Furthermore, differences in food availability, a crucial factor for black storks during their flight between Europe and Africa, may also contribute to the above-mentioned shift in daily flight speeds.
An empirical investigation into a location sensing system based on RF signal strength of TinyOS motes

With the increasing usage of handheld, mobile wireless devices and the unprecedented popularity of celluar phones, the ability to know where a mobile device is physically located at any given time is fast becoming an intrinsic feature of any wireless application and service. This paper will primarily deal with an investigation into the feasibility of using TinyOS motes to build a system in incremental stages that would be able to locate tagged objects within an acceptable boundary of error. The paper will be divided as follows. Section 1 will give a brief outline and history of the problem. This will be followed by Section 2 which will give an overview of the experiments performed and results obtained. Each proceeding experiment will attempt to build on the preceeding one. Limitations, advantages and disadvantages will be detailed carefully. Section 3 will finally dwell on a possible implementation of a location and tracking system.
The epidemiology of melioidosis in the Balimo region of Papua New Guinea

SUMMARY The distribution of Burkholderia pseudomallei was determined in soil collected from a rural district in Papua New Guinea (PNG) where melioidosis had recently been described, predominately affecting children. In 274 samples, 2·6% tested culture-positive for B. pseudomallei. Pulsed-field gel electrophoresis using SpeI digests and rapid polymorphic DNA PCR with five primers demonstrated a single clone amongst clinical isolates and isolates cultured from the environment that was commonly used by children from whom the clinical isolates were derived. We concluded that individuals in this region most probably acquired the organism through close contact with the environment at these sites. Burkholderia thailandensis, a closely related Burkholderia sp. was isolated from 5·5% of samples tested, an observation similar to that of melioidosis-endemic areas in Thailand. This is the first report of an environmental reservoir for melioidosis in PNG and confirms the Balimo district in PNG as melioidosis endemic.
Sensor fusion based on multi-self-organizing maps for SLAM

This paper proposes the use of topological maps in order to provide a method of SLAM feature, based on sensor fusion, that treats better the problem of inaccuracy of the current systems. The contribution of the work is in the algorithm that uses multiple sensory sources, multiple topological maps, to improve the estimation of localization, in order to be as generic as possible, so the same is valid for both internal and external environments (structured or not). When this is made with sensors of clashing characteristics we can obtain better results, because something not perceived by a sensor might be perceived by others, so we can also reduce the effects of error measurement and obtaining a method that works with the uncertainties of the sensors. A simulator was developed to validate the proposed system, through a series of tests with a set of real data. The results show the robustness of the system in relation to the sensorial imprecision and to the gain in predicting the robot's location, resulting in a more appropriate treatment to the errors associated with each sensor
Flexible Hybrid Screening Solutions for Flexography

This study investigates the use of AM/FM hybrid screening in conjunction with computer to plate (CTP) technology in order to obtain an optimum hybrid screening combination for the flexography printing process. The study employs the true experimental method to design 11 different hybrid (FM-AM-FM) screening combinations in accordance with one of the few flexible hybrid screening technology. Hybrid screening and CTP technologies were used in flexography to print a specially-designed test form on PVC substrate. Differences in print attributes between PVC substrates printed via the 11 hybrid screening combinations were measured, and statistical analyses were used to identify a combination with an optimal FM-AM-FM tone percentage. It is hoped that the results of this study can help flexography printers to better understand the characteristics of various screening techniques, allowing them to improve printing quality and achieve the highest customer satisfaction. The best hybrid screening combination of FM-AM-FM (highlight-midtone-shadow) found in this study is provided to printers as a reference enabling them to improve production effectiveness and quality, while reducing printing costs and waste, enabling the quality of flexography in Taiwan to progress.
Two Parallel Deep Convolutional Neural Networks for pedestrian detection

Pedestrian detection attracts lots of attentions in the field of computer vision in recent years. It is difficult to handle data imbalance between positive and negative examples and easy-to-confused negative samples for pedestrian detection when training a single deep convolutional neural network (CNN) model. In this paper, we present a deep learning approach that combines two parallel deep CNN models for pedestrian detection. We propose using two deep CNNs, and each of which is capable of solving a particular mission-oriented task to form parallel classification models. Then, the models are integrated to build a more robust pedestrian detector. Experimental results on the Caltech dataset demonstrate the effectiveness of our approach for pedestrian detection compared to other state-of-the-art deep CNN methods.
Parallel selection algorithms with analysis on clusters

We present three deterministic parallel selection algorithms with analysis on clusters. The first and second algorithms are proposed on the CGM (Coarse Grained Multicomputer) model. The first algorithm achieves optimality with respect to its computation time and runs in O(n/p) computation time and O(min(log p, log log n)) communication rounds if n/p/spl ges/p/sup /spl epsiv// for any /spl epsiv/>0, where n is the number of input elements and p is the number of processors. The second algorithm achieves optimality with respect to the number of communication rounds and runs in O(n/p log p) computation time and the constant number of communication rounds if n/p>p/sup /spl epsiv// for any /spl epsiv/>0. The third selection algorithm is a hybrid algorithm of the above two algorithms and suitable for practical cluster computing. The algorithms are implemented using PVM, and its experimental results are also presented.
A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.

BACKGROUND The likelihood of distant recurrence in patients with breast cancer who have no involved lymph nodes and estrogen-receptor-positive tumors is poorly defined by clinical and histopathological measures. METHODS We tested whether the results of a reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay of 21 prospectively selected genes in paraffin-embedded tumor tissue would correlate with the likelihood of distant recurrence in patients with node-negative, tamoxifen-treated breast cancer who were enrolled in the National Surgical Adjuvant Breast and Bowel Project clinical trial B-14. The levels of expression of 16 cancer-related genes and 5 reference genes were used in a prospectively defined algorithm to calculate a recurrence score and to determine a risk group (low, intermediate, or high) for each patient. RESULTS Adequate RT-PCR profiles were obtained in 668 of 675 tumor blocks. The proportions of patients categorized as having a low, intermediate, or high risk by the RT-PCR assay were 51, 22, and 27 percent, respectively. The Kaplan-Meier estimates of the rates of distant recurrence at 10 years in the low-risk, intermediate-risk, and high-risk groups were 6.8 percent (95 percent confidence interval, 4.0 to 9.6), 14.3 percent (95 percent confidence interval, 8.3 to 20.3), and 30.5 percent (95 percent confidence interval, 23.6 to 37.4). The rate in the low-risk group was significantly lower than that in the high-risk group (P<0.001). In a multivariate Cox model, the recurrence score provided significant predictive power that was independent of age and tumor size (P<0.001). The recurrence score was also predictive of overall survival (P<0.001) and could be used as a continuous function to predict distant recurrence in individual patients. CONCLUSIONS The recurrence score has been validated as quantifying the likelihood of distant recurrence in tamoxifen-treated patients with node-negative, estrogen-receptor-positive breast cancer.