Miracle-dz/UniFAR-FTUs huggingface dataset:
Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material.
Modelling the information seeking patterns of engineers and research scientists in an industrial environment

The study explores the role of information and information seeking in the Research and Development Department of an international oil and gas company. The information seeking patterns of engineers and research scientists at Statoil’s Research Centre, in Trondheim, Norway were studied in relation to their research activities in different phases and types of project. The project phases were evaluation of alternative solutions; development and testing; and summary of experiences. The project types were incremental; radical; and fundamental. Eight major characteristics were identified in the patterns: surveying; chaining; monitoring; browsing; distinguishing; filtering; extracting and ending. The study analyses the requirements for different types of information in an environment where the need for internal and external resources are intertwined; it also compares features of the information seeking patterns of engineers and research scientists from this and previous studies. It was found that, although there were differences in the features of the information seeking patterns of the research scientists and engineers, the behavioural characteristics were similar; and the study identified identical or very similar categories of information seeking behaviour to those of previous studies of academic researchers.
Division among the ranks: the social implications of case tools for systems developers

This paper explores how the introduction of CASE tools in systems development changes the social relations among project team members. An investigation into the role of CASE tools on projects found structural changes due to modification of the systems development division of labor and shifts in patterns of dependency among project team coalitions. These changes triggered a polarization among the system developers which was evinced in acts of coercion and rebellion, the display of territorialism, resentment, and stereotyping, as well as the enactment of subcultures. These findings are interpreted within a broader social theoretic framework, and their implications for research and practice are discussed.
Master ’ s thesis Technology Acceptance Model : A Case of Electronic Health Record in Estonia

The goal of this master’s thesis is to understand key motivators and activities supporting high levels of national Electronic Health Record (EHR) usage by healthcare professionals in Estonia and relate them to findings from Technology Acceptance Model (TAM) research. This thesis aims at contributing both, to better understanding of Estonian EHR implementation case, and TAM application in national public healthcare settings. In this thesis, I found out that the key motivator for the high levels of usage of the system was legal act making it mandatory for healthcare professionals to send data to the national EHR. Despite that, I discovered that TAM variables perceived usefulness, perceived ease of use and psychological ownership played a role in Estonian EHR implementation case in positively influencing attitude towards the system. In this thesis, I argue that attitude towards the system is an important predictor of success for public systems, even if their usage is mandated by the law. I also argue that importance of psychological ownership may be especially important in the mandatory use cases. Furthermore, I discovered that in this particular case, information quality and job relevance influenced perceived usefulness, and that compatibility, self-efficacy and support influenced perceived ease of use. In Estonia, compatibility however had controversial effect on perceived ease of use and I argue that in this case, it may have influenced it negatively rather than positively.
A study of chronic obstructive pulmonary disease-specific causes of osteoporosis with emphasis on the emphysema phenotype

Background: Osteoporosis, the most common extra-pulmonary complication of chronic obstructive pulmonary disease (COPD), may be related to general causes or COPD-specific causes such as low forced expiratory volume in 1 s (FEV1) and hypoxia. A few studies reported that emphysema is an independent risk factor for osteoporosis. However, other workers considered the association to be confounded by low FEV1 and low body mass index (BMI) which cluster with emphysema. Aims: To study the association between osteoporosis and emphysema in a model that includes these potentially confounding factors. Methods: We studied prospectively 52 COPD patients with both high resolution computed tomography and carbon monoxide diffusion coefficient as diagnostic markers of emphysema. Dual-energy X-ray absorptiometry was used to measure the bone mass density (BMD) of lumbar vertebrae and neck of the femur. Vertebral fractures were evaluated using the Genant semiquantitative score. Multiple linear regression analysis was used to identify the following independent variables: age, BMI, FEV1% predicted, PaO2, emphysema score, C-reactive protein (CRP), and dyspnea score as related to BMD. P ≤ 0.05 was considered statistically significant. Results: There was no significant difference in the serum Vitamin D levels, vertebral fracture score, or BMD between the emphysematous and nonemphysematous patients. Multivariate analysis showed that (in a model including age, BMI, FEV1, PaO2, emphysema score, CRP, and dyspnea score) only reduced BMI, FEV1, and PaO2were independent risk factors for low BMD. Conclusions: The emphysematous phenotype is not a risk factor for osteoporosis independently of BMI, FEV1, and PaO2.
Crowdsourced Data Preprocessing with R and Amazon Mechanical Turk

This article introduces the use of the Amazon Mechanical Turk (MTurk) crowdsourcing platform as a resource for R users to leverage crowdsourced human intelligence for preprocessing “messy” data into a form easily analyzed within R. The article first describes MTurk and the MTurkR package, then outlines how to use MTurkR to gather and manage crowdsourced data with MTurk using some of the package’s core functionality. Potential applications of MTurkR include construction of manually coded training sets, human transcription and translation, manual data scraping from scanned documents, content analysis, image classification, and the completion of online survey questionnaires, among others. As an example of massive data preprocessing, the article describes an image rating task involving 225 crowdsourced workers and more than 5500 images using just three MTurkR function calls.
Power System Security Enhancement by OPF with Phase Shifter

This paper presents an integrated optimal power flow (OPF) with phase shifter approach to enhance power system security. The general OPF calculations are hourly based and the control variables of OPF are continuous. The calculations of phase shifter are daily based, however, and the variables related to phase shifter are discrete. Therefore, the general OPF cannot be directly used to solve this problem. The paper develops the rule-based OPF with phase shifter scheme to bridge the problems. In order to effectively alleviate the line overloads, the ranking of phase shifter locations is conducted based on contingency analysis and sensitivity analysis. The best phase shifter sites are identified and selected into a rule-based system accordingly. The handshaking procedure between the adjustment of the selected phase shifters and OPF calculation is proposed using a rule-based method. The hourly based OPF problem is solved by the extended quadratic interior point method. The IEEE 30-bus system is used to test the proposed scheme.
Motion coherence based abnormal behavior detection

To improve the accuracy and speed of the global abnormal detection, a novel method based on motion coherence model is here proposed. Specifically, motion features of each tracking objects are firstly extracted; then, global abnormal behavior detection models are learned based on the energy model, dispersion model and Lagrange particle dynamics model respectively; finally, global abnormal behavior is detected and labeled based on the learned three models. The proposed method is conducted on public UMN dataset which demonstrates that the proposed method can improve the accuracy and efficiency of abnormal behavior detection.
Determining the energy efficiency of femtocell base stations with multiple antennas

Multiple antenna techniques such as MIMO are key to achieving promised high data rates in 4G LTE and LTE-A systems. In addition they can be used to reduce total transmit power by use of beamforming or diversity schemes. This paper investigates their role and use in maximizing the energy efficiency of femtocell base stations and presents a range of considerations that must be made in order to achieve their full potential. Suitable expressions for total consumed power, when using multiple antennas, are provided. Used with power consumption models, a predicted energy saving of 15% for an LTE femtocell employing 2 Tx, 1 Rx transmit diversity is shown. Extending the analysis shows there is a diminishing return on energy savings as the number of antenna elements increases.
Intergroup Helping Aid in the Aftermath of Hurricane Katrina : Inferences of Secondary Emotions and

can be found at: Group Processes & Intergroup Relations Additional services and information for http://gpi.sagepub. com/cgi/alerts Email Alerts: http://gpi.sagepub. com/subscriptions Subscriptions: http://www.sagepub. com/journalsReprints.nav Reprints: http://www.sagepub. com/journalsPermissions.nav Permissions: http://gpi.sagepub. com/cgi/content/refs/10/1/107 SAGE Journals Online and HighWire Press platforms): (this article cites 38 articles hosted on the Citations
A Study on Immunopathologic Effect of Thiram Toxicosis in Broiler Chicken

An investigation was undertaken to study the body weight gain and feed conversion efficiency in broiler chicken fed with thiram a fungicide used for treating corn and storing food grains. Forty eight birds were randomly distributed into four groups of twelve each and thiram was incorporated at 15, 30 and 60 ppm into the toxin free diet for four weeks from the day of hatch. Blood samples were collected, sera separated and HI titres were measured in the control and treated sera. Birds were sacrificed at the end of second and fourth week for detailed examination of lymphoid organs. There was a significant reduction in the antibody titre in the thiram fed birds. Lymphocyte proliferation assay conducted from the lymphocytes prepared from the spleen showed significant reduction in the stimulation index. Histopathology of the lymphoid organs including bursa, spleen thymus and caecal tonsils showed lymphoid depletion to lymphocytolysis.
Stochastic nonholonomic source seeking

We apply stochastic extremum seeking to navigate a nonholonomic unicycle towards the maximum of an unknown, spatially distributed signal field, using only the measurement of the signal at the vehicle's position but without the measurement of the vehicle's position. Keeping the forward velocity constant and controlling only the angular velocity, we design a stochastic source seeking control law which employs excitation based on filtered white noise, rather than sinusoidal perturbations used in the past work. We study stability using stochastic averaging theorems that we recently developed for general nonlinear continuous-time systems with stochastic perturbations. We prove local exponential convergence, both almost surely and in probability, to a small neighborhood near the source. We characterize the convergence speed explicitly and provide design guidelines for maximizing it, as well as for minimizing the residual set near the source.
Comparison of diagnostic capability of macular ganglion cell complex and retinal nerve fiber layer among primary open angle glaucoma, ocular hypertension, and normal population using Fourier-domain optical coherence tomography and determining their functional correlation in Indian population

Context: Analysis of diagnostic ability of macular ganglionic cell complex and retinal nerve fiber layer (RNFL) in glaucoma. Aim: To correlate functional and structural parameters and comparing predictive value of each of the structural parameters using Fourier-domain (FD) optical coherence tomography (OCT) among primary open angle glaucoma (POAG) and ocular hypertension (OHT) versus normal population. Setting and Design: Single centric, cross-sectional study done in 234 eyes. Materials and Methods: Patients were enrolled in three groups: POAG, ocular hypertensive and normal (40 patients in each group). After comprehensive ophthalmological examination, patients underwent standard automated perimetry and FD-OCT scan in optic nerve head and ganglion cell mode. The relationship was assessed by correlating ganglion cell complex (GCC) parameters with mean deviation. Results were compared with RNFL parameters. Statistical Analysis: Data were analyzed with SPSS, analysis of variance, t-test, Pearson′s coefficient, and receiver operating curve. Results: All parameters showed strong correlation with visual field (P < 0.001). Inferior GCC had highest area under curve (AUC) for detecting glaucoma (0.827) in POAG from normal population. However, the difference was not statistically significant (P > 0.5) when compared with other parameters. None of the parameters showed significant diagnostic capability to detect OHT from normal population. In diagnosing early glaucoma from OHT and normal population, only inferior GCC had statistically significant AUC value (0.715). Conclusion: In this study, GCC and RNFL parameters showed equal predictive capability in perimetric versus normal group. In early stage, inferior GCC was the best parameter. In OHT population, single day cross-sectional imaging was not valuable.
Escherichia coli Common Pilus (ECP) Targets Arabinosyl Residues in Plant Cell Walls to Mediate Adhesion to Fresh Produce Plants*

Background: Bacterial fimbriae mediate binding to host tissue through specific interactions. Results: ECP interacts with arabinosyl residues in pectin and other plant cell wall components. Conclusion: ECP-arabinan interactions facilitate binding of E. coli to plant hosts. Significance: The prevalence of arabinan targets in produce plants together with ECP expression may explain the association of pathogenic bacteria in edible plants. Outbreaks of verotoxigenic Escherichia coli are often associated with fresh produce. However, the molecular basis to adherence is unknown beyond ionic lipid-flagellum interactions in plant cell membranes. We demonstrate that arabinans present in different constituents of plant cell walls are targeted for adherence by E. coli common pilus (ECP; or meningitis-associated and temperature-regulated (Mat) fimbriae) for E. coli serotypes O157:H7 and O18:K1:H7. l-Arabinose is a common constituent of plant cell wall that is rarely found in other organisms, whereas ECP is widespread in E. coli and other environmental enteric species. ECP bound to oligosaccharides of at least arabinotriose or longer in a glycan array, plant cell wall pectic polysaccharides, and plant glycoproteins. Recognition overlapped with the antibody LM13, which binds arabinanase-sensitive pectic epitopes, and showed a preferential affinity for (1→5)-α-linked l-arabinosyl residues and longer chains of arabinan as demonstrated with the use of arabinan-degrading enzymes. Functional adherence in planta was mediated by the adhesin EcpD in combination with the structural subunit, EcpA, and expression was demonstrated with an ecpR–GFP fusion and ECP antibodies. Spinach was found to be enriched for ECP/LM13 targets compared with lettuce. Specific recognition of arabinosyl residues may help explain the persistence of E. coli in the wider environment and association of verotoxigenic E. coli with some fresh produce plants by exploitation of a glycan found only in plant, not animal, cells.
3D sound field reproduction using diverse loudspeaker patterns

Sound field reproduction (SFR) in a cubic region is addressed using a finite planar array of loudspeakers with diverse radiation patterns. An acoustic transfer function (ATF) matrix that best approximates the desired field under a power constraint is found from singular value decomposition (SVD). The loudspeaker patterns are then derived to match the ATF. Free-space-based simulations indicate that in 3D SFR, higher order loudspeakers offer better reproduction fidelity than low-order patterns, as can be expected from the extra degrees of freedom, and as previously reported for 2D SFR. The optimized patterns turn out to be highly diverse, even if they are all of the same order. These would have to be implemented from sub-arrays or reconfigurable loudspeaker designs.
Cultivable Anaerobic Microbiota of Severe Early Childhood Caries

ABSTRACT Severe early childhood caries (ECC), while strongly associated with Streptococcus mutans using selective detection (culture, PCR), has also been associated with a widely diverse microbiota using molecular cloning approaches. The aim of this study was to evaluate the microbiota of severe ECC using anaerobic culture. The microbial composition of dental plaque from 42 severe ECC children was compared with that of 40 caries-free children. Bacterial samples were cultured anaerobically on blood and acid (pH 5) agars. Isolates were purified, and partial sequences for the 16S rRNA gene were obtained from 5,608 isolates. Sequence-based analysis of the 16S rRNA isolate libraries from blood and acid agars of severe ECC and caries-free children had >90% population coverage, with greater diversity occurring in the blood isolate library. Isolate sequences were compared with taxon sequences in the Human Oral Microbiome Database (HOMD), and 198 HOMD taxa were identified, including 45 previously uncultivated taxa, 29 extended HOMD taxa, and 45 potential novel groups. The major species associated with severe ECC included Streptococcus mutans, Scardovia wiggsiae, Veillonella parvula, Streptococcus cristatus, and Actinomyces gerensceriae. S. wiggsiae was significantly associated with severe ECC children in the presence and absence of S. mutans detection. We conclude that anaerobic culture detected as wide a diversity of species in ECC as that observed using cloning approaches. Culture coupled with 16S rRNA identification identified over 74 isolates for human oral taxa without previously cultivated representatives. The major caries-associated species were S. mutans and S. wiggsiae, the latter of which is a candidate as a newly recognized caries pathogen.
A method of remote sensing image auto classification based on interval type-2 fuzzy c-means

The pattern set of a remote sensing image contains many kinds of uncertainties. Uncertain information can create imperfect expressions for pattern sets in various pattern recognition algorithms, such as clustering algorithms. Methods based the fuzzy c-means algorithm can manage some uncertainties. As soft clustering methods, They are known to perform better on auto classification of remote sensing images than hard clustering methods. However, if the clusters in a pattern set are of different density and high order uncertainty, performance of FCM may significantly vary depending on the choice of fuzzifiers. Thus, we cannot obtain satisfactory results by using type-1 fuzzy set. Type-2 fuzzy sets permit us to model various uncertainties which cannot be appropriately managed by type-1 fuzzy sets. This paper introduces the theory of interval type-2 fuzzy set into the unsupervised classification of remote sensing images and proposes the automatic remote sensing image classification method based on the interval type-2 fuzzy c-means. Experimental results indicate that our method can obtain more coherent clusters and more accurate boundaries from the data with density difference. Our type-2 fuzzy model can manage the uncertainties of remote sensing images more appropriately and get a more desirable result.
Hierarchical control of cooperative nonlinear dynamical systems

Cooperative control methods that are scalable with low computational cost are crucial for networked dynamical systems to respond quickly in unknown or cluttered environments. In an attempt to make the problem tractable, many existing cooperative controls are designed with oversimplified assumptions and/or without the capabilities of rapidly handling different environmental and dynamical constraints. In this article, proposed is a two-level hierarchical, cooperative control framework using a divide-and-conquer strategy so that challenges can be separately handled at different levels. It is scalable and has low computational cost. Based on a simplified homogeneous double-integrator dynamic model, the top-level planner first computes cooperative trajectories satisfying obstacle avoidance requirements. Then at the lower level, state and control constraints, nonlinear dynamics and self-collision/obstacle avoidance as related to the real system are addressed through a bio-inspired fast trajectory planning algorithm. The stability of the overall hierarchical structure is proven. Two examples, a differential-drive ground vehicle formation control and an unmanned aerial vehicle formation flight, are used to illustrate the advantages of the proposed hierarchical framework.
Real-Time Synthesis of Natural Head Motion on A 3D AVATAR from Reconstructed 3D Frontal Face Data

In this paper, we describe an algorithm for the synthesis of natural head motion on a 3D avatar from reconstructed 3D frontal face data with the goal of making 3D video games immersive, engaging and fun when played on 3D displays. The idea is that frame by frame natural head motion of a user is calculated without utilizing any markers from stereo image pair and transmitted to the avatar to generate realistic motion. Thus, the head motion is regenerated with the avatar in the video sequence in real-time. Obviously, the tools developed for these scenarios are applicable to other applications such as virtual space 3D teleconferencing with avatars or human-computer interface applications.