Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrospective Correction of Physiological Noise in DTI Using an Extended Tensor Model and Peripheral Measurements

Diffusion tensor imaging is widely used in research and clinical applications, but this modality is highly sensitive to artefacts. We developed an easy‐to‐implement extension of the original diffusion tensor model to account for physiological noise in diffusion tensor imaging using measures of peripheral physiology (pulse and respiration), the so‐called extended tensor model. Within the framework of the extended tensor model two types of regressors, which respectively modeled small (linear) and strong (nonlinear) variations in the diffusion signal, were derived from peripheral measures. We tested the performance of four extended tensor models with different physiological noise regressors on nongated and gated diffusion tensor imaging data, and compared it to an established data‐driven robust fitting method. In the brainstem and cerebellum the extended tensor models reduced the noise in the tensor‐fit by up to 23% in accordance with previous studies on physiological noise. The extended tensor model addresses both large‐amplitude outliers and small‐amplitude signal‐changes. The framework of the extended tensor model also facilitates further investigation into physiological noise in diffusion tensor imaging. The proposed extended tensor model can be readily combined with other artefact correction methods such as robust fitting and eddy current correction. Magn Reson Med 70:358–369, 2013. © 2012 Wiley Periodicals, Inc.
A novel multimodal image fusion method using Shift invariant Discrete Wavelet Transform and Support Vector Machines

In this paper, a multimodal image fusion technique using Shift invariant Discrete Wavelet Transform (SIDWT) and Support Vector Machines (SVM) suitable for surveillance applications is proposed. This technique uses SIDWT for multiresolution decomposition as it is translation invariant. A Support Vector Machine is trained to select the coefficient blocks with significant features, extracted from the SIDWT coefficients. The corresponding selected coefficients are used in forming the composite fused coefficient representation. The proposed method is tested for a number of multimodal images and found to outperform other traditional image fusion algorithms in terms of the various fusion metrics. Experimental results show that the quality of the fused image is significantly improved for multimodal images.
Maternal B vitamin status in pregnancy week 18 according to reported use of folic acid supplements.

SCOPE Epidemiological studies on the association between pregnancy outcomes and use of periconceptional folic acid are often based on maternal reported intake. Use of folic acid during pregnancy is associated with a higher socioeconomic status known to have an impact on diet quality. We have studied plasma B vitamin status according to reported use of folic acid supplements during the periconceptional period in Norwegian women. METHODS AND RESULTS Plasma levels of folate, cobalamin, pyridoxal 5'-phosphate (vitamin B6), riboflavin, and the metabolic markers total homocysteine, methylmalonic acid and 3-hydro-xykynurenine were measured in pregnancy week 18 and related to reported intake of folic acid from 4 weeks prior to conception throughout week 18 in 2911 women from the Norwegian Mother and Child Cohort Study (MoBa) conducted by the Norwegian Institute of Public Health. Being a folic acid user during the periconceptional period was associated with a better socioeconomic status, and a higher intake of several micronutrients, including vitamins, trace-metals, and omega 3 fatty acids. Folic acid users had a significantly better plasma B vitamin status. CONCLUSION Epidemiological data based on maternal reported intake of folic acid supplements during pregnancy, should take into account the numerous nutritional implications, in addition to higher blood folate levels, of being a folic acid user.
A maternal cafeteria diet during gestation and lactation promotes adiposity and impairs skeletal muscle development and metabolism in rat offspring at weaning

We examined the effects of a maternal cafeteria diet on skeletal muscle and adipose tissue development in the offspring at weaning. Rats born to mothers fed the cafeteria diet either during gestation alone or during both gestation and lactation exhibited a 25% reduction in muscle cross‐sectional area with approximately 20% fewer fibres compared with pups fed a balanced chow diet. Maintaining the cafeteria diet during lactation increased intramuscular lipid content and fat pad weights characterized by adipocyte hypertrophy but not hyperplasia. These pups also had elevated muscle IGF‐1, IGF‐1 receptor, and PPARγ mRNA levels, which may indicate an attempt to maintain normal insulin sensitivity. The increased adiposity and elevated IGF‐1, IGF‐1 receptor and PPARγ mRNAs were not seen in the pups rehabilitated to the balanced diet during lactation. However, these pups exhibited reduced muscle cell proliferation (PCNA) with reduced insulin receptor and a trend towards reduced glucose transporter (GLUT)‐4 mRNAs when compared with pups fed a balanced chow diet, indicating possible alterations in glucose uptake by muscle tissue. Therefore, rats born to mothers fed a cafeteria diet during gestation alone or during both gestation and lactation exhibited impaired skeletal muscle development and metabolic disorders normally associated with insulin resistance as early as the weaning stage.
A Case of Native Cytomegalovirus Pancreatitis Following Deceased-Donor Renal Transplantation

Cytomegalovirus (CMV) is a known cause of pancreatitis in immunocompromised patients, usually in associa- tion with the human immunodeficiency virus (1). A handful of cases have been reported of CMV pancreatitis occurring in a transplanted pancreas secondary to immunosuppression associated with organ transplantation. Herein, we report a rare case of CMV pancreatitis following deceased-donor renal transplantation in which a patient's native pancreas was in- fected by CMV transmitted by donor renal tissue. After seroconversion from a CMV-positive donor, a 41 year old female with a history of autosomal dominant polycystic kidney disease presented with pancreatitis in her native pancreas follow- ing deceased donor renal transplantation, thus illustrating how a patient's native pancreas can be infected by CMV from donor renal tissue.
Adaptive locomotion controller and reflex system for humanoid robots

This paper deals with reflexes against sudden obstacles for humanoid robots, which are combined with a proposed piecewise-linear pattern generator. The reflex action consists of modulating the motorspsila commands by the outputs of the force sensors located under the robot legs, and through a given primitive neural network previously proposed. Eventually, the primitive reflex is modified by the afferent signals to be more adaptable and robust against sudden obstacles. The final reflex structure enables the response of the sensory signals to be coordinated and modulated with locomotion controllerpsilas outputs to achieve an intended stabilizing behavior of the robot. The effectiveness of the proposed reflex is demonstrated by experiment using Fujitsupsilas humanoid robot HOAP-3. It is shown that the primitive reflex movement previously proposed becomes robust against sudden obstacle that hits the robot sole plate at different locations. The proposed reflex system, therefore, contributes towards the safer interaction of the humanoid robot with the environment.
Acquiring visual servoing reaching and grasping skills using neural reinforcement learning

In this work we present a reinforcement learning system for autonomous reaching and grasping using visual servoing with a robotic arm. Control is realized in a visual feedback control loop, making it both reactive and robust to noise. The controller is learned from scratch by success or failure without adding information about the task's solution. All of the system's major components are implemented as neural networks. The system is applied to solving a combined reaching and grasping task involving uncertainty directly on a real robotic platform. Its main parts and the conditions for their successful interoperation are described. It will be shown that even with minimal prior knowledge, the system can learn in a short amount of time to reliably perform its task. Furthermore, we describe the control system's ability to react to changes and errors.
An Invariant of Integral Homology 3-Spheres Which Is Universal For All Finite Type Invariants

In [LMO] a 3-manifold invariant $\Omega(M)$ is constructed using a modification of the Kontsevich integral and the Kirby calculus. The invariant $\Omega$ takes values in a graded Hopf algebra of Feynman 3-valent graphs. Here we show that for homology 3-spheres the invariant $\Omega$ is {\em universal} for all finite type invariants, i.e. $\Omega_n$ is an invariant of order $3n$ which dominates all other invariants of the same order. This shows that the set of finite type invariants of homology 3-spheres is equivalent to the Hopf algebra of Feynman 3-valent graphs. Some corollaries are discussed. A theory of groups of homology 3-spheres, similar to Gusarov's theory for knots, is presented.
Discovery of Stable and Variable Differences in the Mycobacterium avium subsp. paratuberculosis Type I, II, and III Genomes by Pan-Genome Microarray Analysis

ABSTRACT Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.
Graph mapping: Multi-scale community visualization of massive graph data

Graph visualizations increase the perception of entity relationships in a network. However, as graph size and density increases, readability rapidly diminishes. In this article, we present an end-to-end, tile-based visual analytic approach called graph mapping that utilizes cluster computing to turn large-scale graph (node–link) data into interactive visualizations in modern web browsers. Our approach is designed for end-user analysis of community structure and relationships at macro- and micro scales. We also present the results of several experiments using alternate methods for qualitatively improving comprehensibility of hierarchical community detection visualizations by proposing constraints to state-of-the-art modularity maximization algorithms.
Optimal Collusion with Private Information

We analyze collusion in an infinitely repeated Bertrand game, where prices are publicly observed and each firm receives a privately observed, i.i. d. cost shock in each period. Productive efficiency is possible only if high-cost firms relinquish market share. In the most profitable collusive schemes, firms implement productive efficiency, and high-cost firms are favored with higher expected market share in future periods. If types are discrete, there exists a discount factor strictly less than one above which first-best profits can be attained using history-dependent reallocation of market share between equally efficient firms. We also analyze the role of communication and side-payments.
High Motility Reduces Grazing Mortality of Planktonic Bacteria

ABSTRACT We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 μm s−1 as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 μm s−1) and a highly motile strain (>45 μm s−1) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 μm3. Grazing mortality was lowest for cells of >0.5 μm3 and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (≤0.1 μm3, >50 μm s−1) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.
Dentigerous cyst with parietal and intracystic calcifications: A case report and literature review

Background Dentigerous cyst appears surrounding the crown of an included tooth. On the radiographic exam, a radiolucent rounded well-defined lesion can be observed. Material and Methods This study reports a clinical case of a 34-years old man with a pericoronal radiolucent lesion associated to an impacted lower third molar with the presence of radiopaque material inside. The radiological differential diagnosis was calcifying odontogenic tumor, adenomatoid odontogenic tumor and dentigerous cyst. The impacted third molar was removed and the lesion was sent for the histopathological exam. Results The histopathological diagnosis was dentigerous cyst with capsular calcifications. Specifically, parietal calcifications on its connective wall and a piece of cemento-osseous tissue inside. Conclusions Non-neoplastic lesions such as dentigerous cysts could develop radiopacities inside the radiolucent pericoronal area. Key words:Dentigerous cyst, calcifications, third molar, differential diagnosis.
oriC Region and Replication Termination Site, dif, of the Xanthomonas campestris pv. campestris 17 Chromosome

ABSTRACT A 13-kb DNA fragment containing oriC and the flanking genes thdF, orf900, yidC, rnpA, rpmH, oriC, dnaA, dnaN, recF, and gyrB was cloned from the gram-negative plant pathogen Xanthomonas campestris pv. campestris 17. These genes are conserved in order with other eubacterial oriC genes and code for proteins that share high degrees of identity with their homologues, except for orf900, which has a homologue only in Xylella fastidiosa. The dnaA/dnaN intergenic region (273 bp) identified to be the minimal oriC region responsible for autonomous replication has 10 pure AT clusters of four to seven bases and only three consensus DnaA boxes. These findings are in disagreement with the notion that typical oriCs contain four or more DnaA boxes located upstream of the dnaA gene. The X. campestris pv. campestris 17 attB site required for site-specific integration of cloned fragments from filamentous phage φLf replicative form DNA was identified to be a dif site on the basis of similarities in nucleotide sequence and function with the Escherichia coli dif site required for chromosome dimer resolution and whose deletion causes filamentation of the cells. The oriC and dif sites were located at 12:00 and 6:00, respectively, on the circular X. campestris pv. campestris 17 chromosome map, similar to the locations found for E. coli sites. Computer searches revealed the presence of both the dif site and XerC/XerD recombinase homologues in 16 of the 42 fully sequenced eubacterial genomes, but eight of the dif sites are located far away from the 6:00 point instead of being placed opposite the cognate oriC. The differences in the relative position suggest that mechanisms different from that of E. coli may participate in the control of chromosome replication.
Effect of Formative and Ability Test Results on Early Learning of Students

The objective of this study was to examine the relationship of formative tests to early learning ability of students in the science learning style. This research used an experimental method with a 2 x 2 factorial design. The participants comprised all the students in class VII of the Islamic Junior High School State of Kolaka, a total of 343 students from 9 classes. Sampling was based on the use of a two-stage cluster sampling technique to randomly select four classes of students. The four classes were re-randomized, with two being given formative tests and two being given multiple choice tests. The t-test was used to measure the student learning outcomes. The results showed: (1) the use of formative tests in narrative form in the learning process can provide a measure of higher learning output compared with the use of formative multiple choice tests. (2) For those students who have a high initial ability, the use of formative tests can provide higher learning outcomes compared with the use of multiple choice tests. (3) For those students who have a lower initial ability, the use of formative tests in narrative form does not provide a different outcome to tests in multiple choice formats.
Two Novel AP2/EREBP Transcription Factor Genes TaPARG Have Pleiotropic Functions on Plant Architecture and Yield-Related Traits in Common Wheat

AP2/EREBPs play significant roles in plant growth and development. A novel, pleiotropic TaPARG (PLANT ARCHITECTURE-RELATED GENE), a member of the AP2/EREBP transcription factor gene family, and its flanking sequences were isolated in wheat (Triticum aestivum L.). Two TaPARG genes were identified and named as TaPARG-2A and TaPARG-2D. Their amino acid sequences were highly similar especially in the functional domains. TaPARG-2A on chromosome 2A was flanked by markers Xwmc63 and Xgwm372. TaPARG-2D was mapped to chromosome 2D. Subcellular localization revealed that TaPARG-2D was localized in the nucleus. The results of tissue expression pattern, overexpression in rice, association analysis and distinct population verification jointly revealed that TaPARG functions during the entire growth cycle of wheat. Its functions include regulation of plant architecture-related and yield-related traits. Association analysis, geographic distribution and allelic frequencies suggested that favored haplotypes Hap-2A-2 and Hap-2A-3 were selected in Chinese wheat breeding programs. Both favored haplotypes might be caused by a single amino acid substitution (His/Tyr). These results suggest that TaPARG is a regulatory factor in plant growth and development, and that the favored alleles might be useful for improving plant architecture and grain yield of wheat.
Automatic Acquisition of Chinese Novel Noun Compounds

Automatic acquisition of novel compounds is notoriously difficult because most novel compounds have relatively low frequency in a corpus. The current study proposes a new method to deal with the novel compound acquisition challenge. We model this task as a two-class classification problem in which a candidate compound is either classified as a compound or a non-compound. A machine learning method using SVM, incorporating two types of linguistically motivated features: semantic features and character features, is applied to identify rare but valid noun compounds. We explore two kinds of training data: one is virtual training data which is obtained by three statistical scores, i.e. co-occurrence frequency, mutual information and dependent ratio, from the frequent compounds; the other is real training data which is randomly selected from the infrequent compounds. We conduct comparative experiments, and the experimental results show that even with limited direct evidence in the corpus for the novel compounds, we can make full use of the typical frequent compounds to help in the discovery of the novel compounds.
Provisioning virtual IPTV delivery networks using hybrid genetic algorithm

Nowadays, IPTV services are delivered over physical delivery networks, which suffer from the lack of flexibility in control and management. Virtual delivery networks, as a cost-effective alternative, tend to be the dominant delivery option in the near future due to its advantages for service providers. However, virtual networks provisioning is more complicated as it integrates resources allocation, resources diminishing, and content replication interdependently. In this paper, we investigate the problem of virtual IPTV delivery network provisioning over the recent architecture, peer-service area architecture. The Genetic Algorithm as an optimization tool has been used to find the optimal provisioning parameters including storage, bandwidth, and CPU consumption. The experiments have been conducted on two data sets with different popularity distributions. The experimental results showed the impact of content popularity on the provisioning process.
Pastoral Bearings: Lived Religion and Pastoral Theology

Pastoral Bearings signifies a culmination of major shifts in the field of pastoral theology in a number of ways. First, religious practice is no longer viewed as the prerogative of the religious community or its officially sanctioned leaders alone, whose interest may be the maintenance of a set of ideological tenets. Religious practice is now viewed as a complex set of lived experience by which the participating persons in it exercise their agency and navigate in the religious geography that is informed by the experience of the past, present, and other contexts (Bevans, 2002). The changing religious topography in the United States coupled with the decline of mainline Protestant communities is likely to have contributed partially to this change. Pastoral Bearings is an excellent example of a collection of pastoral contextual theology in action that addresses the empowerment of individuals and their postmodern context-dependent meaningmaking processes (cf. Patton, 1993; Ramsay, 1998; Lartey, 2006).