Miracle-dz/UniFAR-FTUs huggingface dataset:
Ozone, Fine Particulate Matter, and Chronic Lower Respiratory Disease Mortality in the United States.

RATIONALE Short-term effects of air pollution exposure on respiratory disease mortality are well established. However, few studies have examined the effects of long-term exposure, and among those that have, results are inconsistent. OBJECTIVES To evaluate long-term association between ambient ozone, fine particulate matter (PM2.5, particles with an aerodynamic diameter of 2.5 μm or less), and chronic lower respiratory disease (CLRD) mortality in the contiguous United States. METHODS We fit Bayesian hierarchical spatial Poisson models, adjusting for five county-level covariates (percentage of adults aged ≥65 years, poverty, lifetime smoking, obesity, and temperature), with random effects at state and county levels to account for spatial heterogeneity and spatial dependence. MEASUREMENTS AND MAIN RESULTS We derived county-level average daily concentration levels for ambient ozone and PM2.5 for 2001-2008 from the U.S. Environmental Protection Agency's down-scaled estimates and obtained 2007-2008 CLRD deaths from the National Center for Health Statistics. Exposure to ambient ozone was associated with an increased rate of CLRD deaths, with a rate ratio of 1.05 (95% credible interval, 1.01-1.09) per 5-ppb increase in ozone; the association between ambient PM2.5 and CLRD mortality was positive but statistically insignificant (rate ratio, 1.07; 95% credible interval, 0.99-1.14). CONCLUSIONS This study links air pollution exposure data with CLRD mortality for all 3,109 contiguous U.S. counties. Ambient ozone may be associated with an increased rate of death from CLRD in the contiguous United States. Although we adjusted for selected county-level covariates and unobserved influences through Bayesian hierarchical spatial modeling, the possibility of ecologic bias remains.
Cascade-based control of a benchmark system

A cascade-based control method is proposed for the translational oscillator with a rotational actuator (TORA) system. Specifically, the original dynamic equations are transformed into a cascade form through some coordinate transformations. Then, a virtual control input is designed for the first subsystem and a deviation-based subsystem is introduced. Based on the deviation-based subsystem, a linear filter is presented and a nonlinear controller is proposed straightforwardly. Simulation results are provided to evaluate the performance of the proposed method in the presence of different initial conditions, uncertain parameters, and external disturbances.
Harnessing manpower for creating semantics

The effective information processing (e.g. search, organization) of the heterogeneous information spaces requires metadata layer above the resources. However, the acquisition of resource metadata and domain models are challenging tasks. Here, the crowdsourcing has emerged as an alternative to expert-based and automated semantics acquisition approaches. One of its branches are the games with a purpose (GWAPs) which encapsulate the semantics acquisition tasks into the game processes. We analyze existing GWAPs and propose their classification. Furthermore we devised our own GWAP-based approaches. For acquisition of lightweight term relationship network, we devised a search query formulation game, usable also for specific domain models. For acquisition of (personal) image tags, we devised a card game, where players memorize positions of concealed cards and identify identical pairs. For validation of music metadata, we devised a multi-choice question-based game, where players identify tag sets that are characteristic to music tracks they hear. We also looked at the GWAPs from their design perspectives. We present a design oriented classification system for GWAPs, adress several design issues recurring in GWAPs and present new design patterns to solve them.
Mobile Robot Diagnosis with Bayesian Filters

In the following paper we consider a problem of fault detection for a mobile robot. The robot which our work is related to, is based on a new type of the steering principle [1]. The crucial part of the steering system are axle position sensors. A failure of one of them might result in an interruption of operation and/or serious damages to hardware and environment elements. To avoid the risk of such events, a reliable fault detection system has to be implemented. Fault detection is facilitated by incorporating measurements from various sensors located on board of the robot (incremental encoders, absolute encoders, sonar, cameras, compass, GPS). In our work we consider the Bayesian approach (Kalman filter [2,3] and particle filters [4,5,6]) to create a diagnostic system of the robot. Due to the limited resources of the computing unit it is necessary to strongly optimize the efficiency of applied algorithms. In our work we plan to perform simulations to find the best suited algorithm for our vehicle. Accordingly, we build a numerical tool in MATLAB to simulate mobile robot navigation and fault diagnosis tasks. We also present the construction of our robot and explain how a reliable fault detection system is important for the proper functioning and safety of the mobile robot. We introduce the fault detection algorithms which we plan to apply in the described hardware solution. At the end, we summarize our work and provide an outlook on our future research plans.
Effects of commercial diazinon and imidacloprid on microbial urease activity in soil and sod.

Diazinon [O,O-diethyl O-2-isopropyl-6-methyl(pyrimidine-4-yl) phosphorothioate] and imidacloprid [1-(1-[6-chloro-3-pyridinyl]methyl)-N-nitro-2-imidazolidinimine] are applied to lawns for insect control simultaneously with nitrogenous fertilizers such as urea, but their potential effect on urease activity and nitrogen availability in turfgrass management has not been evaluated. Urease activity in enzyme assays, washed cell assays, and soil slurries was examined as a function of insecticide concentration. Intact cores from field sites were used to assess the effect of insecticide application on urease activity in creeping bentgrass (Agrostis palustris Huds.) and bluegrass (Poa pratensis L.) sod. Bacterial urease from Bacillus pasteurii and plant urease from jack bean [Canavalia ensiformis (L.) DC. ] were unaffected by the insecticides. Both insecticides inhibited the growth of Proteus vulgaris, a urease-producing bacterium, but only diazinon significantly reduced urease activity in washed cells; neither insecticide inhibited urease activity in sonicated cells. Neither diazinon nor imidacloprid inhibited urease activity in Woolper soil (fine, mixed, mesic Typic Argiudoll) slurries, but diazinon slightly inhibited urease activity in Maury soil (fine, mixed, semiactive, mesic Typic Paleudalf) slurries. Imidacloprid had no effect on urease activity in creeping bentgrass or bluegrass sod at up to 10 times the commercial application rate. Diazinon briefly, but significantly, reduced urease activity in bluegrass sod. Co-application of imidacloprid and urea appears to be benign with respect to urease activity in soil and sod. Diazinon, in contrast, appears to have a significant, short-term, inhibitory effect on the microbial urease-producing community, but that effect depends on soil type.
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model

MOTIVATION Pathway analysis to reveal biological mechanisms for results from genetic association studies have great potential to better understand complex traits with major human disease impact. However, current approaches have not been optimized to maximize statistical power to identify enriched functions/pathways, especially when the genetic data derives from studies using platforms (e.g. Immunochip and Metabochip) customized to have pre-selected markers from previously identified top-rank loci. We present here a novel approach, called Minimum distance-based Enrichment Analysis for Genetic Association (MEAGA), with the potential to address both of these important concerns. RESULTS MEAGA performs enrichment analysis using graphical algorithms to identify sub-graphs among genes and measure their closeness in interaction database. It also incorporates a statistic summarizing the numbers and total distances of the sub-graphs, depicting the overlap between observed genetic signals and defined function/pathway gene-sets. MEAGA uses sampling technique to approximate empirical and multiple testing-corrected P-values. We show in simulation studies that MEAGA is more powerful compared to count-based strategies in identifying disease-associated functions/pathways, and the increase in power is influenced by the shortest distances among associated genes in the interactome. We applied MEAGA to the results of a meta-analysis of psoriasis using Immunochip datasets, and showed that associated genes are significantly enriched in immune-related functions and closer with each other in the protein-protein interaction network. AVAILABILITY AND IMPLEMENTATION http://genome.sph. umich.edu/wiki/MEAGA CONTACT: : tsoi.teen@gmail.com or goncalo@umich.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Significance The arbuscular mycorrhizal symbiosis between fungi of the Glomeromycota phylum and plants involves more than two-thirds of all known plant species, including important crop species. This mutualistic symbiosis, involving one of the oldest fungal lineages, is arguably the most ecologically and agriculturally important symbiosis in terrestrial ecosystems. The Glomeromycota are unique in that their spores and coenocytic hyphae contain hundreds of nuclei in a common cytoplasm, which raises important questions about the natural selection, population genetics, and gene expression of these highly unusual organisms. Study of the genome of Rhizophagus irregularis provides insight into genes involved in obligate biotrophy and mycorrhizal symbioses and the evolution of an ancient asexual organism, and thus is of fundamental importance to the field of genome evolution. The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants*

Complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. Here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in Chagas Disease, an exemplar of a human infectious disease caused by the protozoan Trypanosoma cruzi. We designed a high-density peptide microarray containing more than 175,000 overlapping 15mer peptides derived from T. cruzi proteins. Peptides were synthesized in situ on microarray slides, spanning the complete length of 457 parasite proteins with fully overlapped 15mers (1 residue shift). Screening of these slides with antibodies purified from infected patients and healthy donors demonstrated both a high technical reproducibility as well as epitope mapping consistency when compared with earlier low-throughput technologies. Using a conservative signal threshold to classify positive (reactive) peptides we identified 2,031 disease-specific peptides and 97 novel parasite antigens, effectively doubling the number of known antigens and providing a 10-fold increase in the number of fine mapped antigenic determinants for this disease. Finally, further analysis of the chip data showed that optimizing the amount of sequence overlap of displayed peptides can increase the protein space covered in a single chip by at least ∼threefold without sacrificing sensitivity. In conclusion, we show the power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples, thus setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens.
Peer-assisted view-dependent progressive mesh streaming

Progressive mesh streaming is increasingly used in 3D networked applications, such as online games, virtual worlds, and digital museums. To scale such applications to a large number of users without high infrastructure cost, we apply peer-to-peer techniques to mesh streaming. We consider two issues: how to partition a progressive mesh into chunks and how to lookup the provider of a chunk. For the latter issue, we investigated into two solutions, which trade off server overhead and response time. The first uses a simple centralized lookup service, while the second organizes peers into groups according to the hierarchical structure of the progressive meshes to take advantage of access pattern. Simulation results show that our proposed systems are robust under high churn rate, reduce the server overhead by more than 90%, keep control overhead below 10%, and achieve low average response time.
Gesture marking of disfluencies in spontaneous speech

Speakers effectively use both visual and acoustic cues to convey information in speech. While earlier research has concentrated on the association of visual cues (provided by gestures) with fluent prosodic structure, this study looks at the relationship between visual cues, prosodic markers and spoken disfluencies. Preliminary results suggested that speakers preferentially perform gestures in the eye region in spoken disfluencies, but a more careful frame-by-frame analysis capturing all gestures revealed that movements of the eye region (blinks, frowns, eyebrow raises and changes in direction of eyegaze) occur with high frequency in both fluent and non-fluent speech. The paper describes a method for frame-by-frame labelling of speechaccompanying gestures for a speech sample, whose output can then be combined with independently derived labels of the prosody. Initial analysis of 3 minute samples from two speakers reveals that one speaker produces eye movements in association with disfluencies and the other does not, and that this tendency does not result from alignment of brow gestures with pitch accents.
Respiratory Chain Supercomplexes

Respiratory chain supercomplexes have been isolated from mammalian and yeast mitochondria, and bacterial membranes. Functional roles of respiratory chain supercomplexes are catalytic enhancement, substrate channelling, and stabilization of complex I by complex III in mammalian cells. Bacterial supercomplexes are characterized by their relatively high detergent‐stability compared to yeast or mammalian supercomplexes that are stable to sonication. The mobility of substrate cytochrome c increases in the order bacterial, yeast, and mammalian respiratory chain. In bacterial supercomplexes, the electron transfer between complexes III and IV involves movement of the mobile head of a tightly bound cytochrome c, whereas the yeast S. cerevisiae seems to use substrate channelling of a mobile cytochrome c, and mammalian respiratory chains have been described to use a cytochrome c pool. Dimeric ATP synthase seems to be specific for mitochondrial OXPHOS systems. Monomeric complex V was found in Acetobacterium woodii and Paracoccus denitrificans .
The Relationship between Muscle Temperature , MUAP Conduction Velocity and the Amplitude and Frequency Components of the Surface EMG During Isometric Contractions

The relationship between the tension developed during brief isometric contractions and the frequency and amplitude components of the surface EMG were recorded in 5 male subjects after immersion of their arms and legs in water at 24, 27, 34 and 37 deg. C. for 20 min. The muscles examined were the handgrip, biceps, quadriceps, and gastrocnemius muscles. For the three warmest water temperatures, the muscle strength was unaffected by the water bath temperature. Muscle strength was lower for all muscles examined at the coldest muscle temperature. For all temperatures, the relationship between EMG amplitude and tension for brief isometric contractions was nearly linear. The frequency components of the EMG as assessed by Fourier Analysis of the raw EMG and MUAP conduction velocity, were largely unaffected by muscle tension but was dramatically affected by muscle temperature. During fatiguing contractions at a tension of 40% MVC, the shift in frequency was similar for the warmest three muscle temperatures while for the coldest temperature, the shift in center frequency was much less. The results show the feasibility of use of EMG amplitude to assess muscle use in most physiological conditions but draws doubt on using the frequency components of the EMG as a measure of fatigue under circumstances where muscle temperature may vary.
Improved Maximum-Likelihood Time Delay Estimation for GPS Positioning in Multipath, Interference and Low SNR Environments

In this paper, we propose a robust maximum like- lihood (RML) approach for delay and amplitude estimation of weak GPS signals in multipath and interference environments such as that encountered in indoor applications. First, to formu- late the problem we exploit the fact that during the acquisition period the propagation delay causes only a circular shift to the spreading C/A code vector. This allows the decomposition of the received data vector into a constant component plus an undesired signals component. Then, a sample mean model is developed using a moving average over long time durations to reduce the effect of undesired zero-mean signals to one of a colored Gaussian noise. The developed model has an anti- jam structure which relies on the exploitation of a temporal structure property of the GPS signal, namely the replication of the C/A-code. An efficient temporal whitening technique is derived from the sample covariance matrix and applied to suppress the colored noise effect. The ML time-delay estimation of the superimposed multipath parameters becomes tractable and results in an efficient algorithm by adopting a sequential procedure.
RESILIENT MODULUS FOR NEW HAMPSHIRE SUBGRADE SOILS FOR USE IN MECHANISTIC AASHTO DESIGN

Abstract : Resilient modulus tests were conducted on five subgrade soils commonly found in the state of New Hampshire. Tests were conducted on samples prepared at optimum density and moisture content. To determine the effective resilient modulus of the various soils for design purposes, tests were conducted at room temperature and at freezing temperatures. The AASHTO TP 46 test protocol was used for testing room temperature and thawing soils. At freezing temperatures, the CRREL test protocol was used. The results from this test program are presented in this report. In addition, suggested effective resilient modulus for the five soils are presented.
Organisational Barriers to Including Web Data in Traditional BI Practice

The importance of Business Intelligence (BI) within organisations is increasing with insights being used across organisations for tasks ranging from daily management decision support to executive strategic planning. With the increasingly important role the internet plays in consumers' lives, an abundance of valuable data is to be found online. This data can be used to enhance the ability of BI to deliver important information to all levels within the organisation. Yet including web data in traditional BI practice has not yet delivered value seamlessly. Hence the primary question asked in this paper is: What are the organisational barriers which prevent the inclusion of unstructured web data in BI practice? By means of a single case study within an Insurance company in the Western Cape, and by using a hybrid inductive and deductive research approach, this research identifies the key barriers in this organisation to the adoption of this advanced BI innovation. The major factors were found to be the lack of management support, poor understanding of the potential benefits of using web data, the reliability and privacy concerns related to this data, and no innovation champion driving the adoption. The resultant causal model of barriers can be used by organisations wanting to adopt this BI innovation to suggest possible actions which can be undertaken to eliminate some of the barriers.
Towards Multimodal Error Management: Experimental Evaluation of User Strategies in Event of Faulty Application Behavior in Automotive Environments

In this work, we present the results of a study analyzing the reactions of subjects on simulated errors of a dedicated in-car interface for controlling infotainment and communication services. The test persons could operate the system, using different input modalities, such as natural or command speech as well as head and hand gestures, or classical tactile paradigms. In various situational contexts, we scrutinized the interaction patterns the test participants applied to overcome different operation tasks. Moreover, we evaluated individual user behavior concerning modality transitions and individual fallback strategies in case of system errors. Two different error types (Hidden System Errors and Apparent System Errors) were provoked. As a result, we found out that initially, i.e. with the system working properly, most users prefer tactile or speech interaction. In case of Hidden System Errors, mostly changes from speech to tactile interaction and vice versa occurred. Concerning Apparent System Errors, 87% of the subjects automatically interrupted or cancelled their input procedure. 73% of all test persons who continued interaction, when the reason for the faulty system behavior was gone, strictly kept the selected modality. Regarding the given input vocabulary, none of the subjects selected head or hand gesture input as the leading fallback modality.