Miracle-dz/UniFAR-FTUs huggingface dataset:
Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana

Maintenance of cytosine methylation in plants is controlled by three DNA methyltransferases. MET1 maintains CG methylation, and DRM1/2 and CMT3 act redundantly to enforce non-CG methylation. RPS, a repetitive hypermethylated DNA fragment from Petunia hybrida, attracts DNA methylation when transferred into Petunia or other species. In Arabidopsis thaliana, which does not contain any RPS homologues, RPS transgenes are efficiently methylated in all sequence contexts. To test which DNA methylation pathways regulate RPS methylation, we examined maintenance of RPS methylation in various mutant backgrounds. Surprisingly, CG methylation was lost in a drm1/2/cmt3 mutant, and non-CG methylation was almost completely eliminated in a met1 mutant. An unusual cooperative activity of all three DNA methyltransferases is therefore required for maintenance of both CG and non-CG methylation in RPS. Other unusual features of RPS methylation are the independence of its non-CG methylation from the RNA-directed DNA methylation (RdDM) pathway and the exceptional maintenance of methylation at a CCmTGG site in some epigenetic mutants. This is indicative of activity of a methylation system in plants that may have evolved from the DCM methylation system that controls CCmWGG methylation in bacteria. Our data suggest that strict separation of CG and non-CG methylation pathways does not apply to all target regions, and that caution is required in generalizing methylation data obtained for individual genomic regions.
A Genome-Wide Analysis Reveals No Nuclear Dobzhansky-Muller Pairs of Determinants of Speciation between S. cerevisiae and S. paradoxus, but Suggests More Complex Incompatibilities

The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts, which have small genomes and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair, comprising a mitochondrially targeted product of a nuclear gene and a mitochondrially encoded locus, has been found. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. We report here the first detailed genome-wide analysis of rare meiotic products from an otherwise sterile hybrid and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions, likely involving multiple loci having weak effects, may be responsible for their post-zygotic separation. The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that the accumulation of polymorphisms leads to gamete inviability due to the activities of anti-recombination mechanisms and/or incompatibilities between the species' transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation.
Agents on Robots : Mixed Reality Robots with Changeable Appearances depending on the Situation

This paper presents a communication system between humans and character agents, Agents on Robots (AoR), which combines the ability of expressions of character agents with the presence of robots. This system attaches an AR marker on mobile robots and allows users to communicate with CG agents through a Head Mounted Display (HMD). In our experiments, we compared the difference of impressions between AoR and communication robots which have the same surface appearance. As a result, we found the item “Activity” for AoR in the questionnaires to be statistically higher than that for a robot. This result support usefulness of our proposed system.
A Comparative Exploration of Accounting Institutions

Institutions shape the nature and form of the accounting practice; yet, little if anything is known about whether some institutional designs will be more effective in providing highquality standards. Here, we examine three stylized institutions: (a) office-driven politicians, (b) private-sector self-regulation or (c) mission-driven regulators. Among other things, we show that office-driven politicians typically pass excessive disclosure, self-regulation leads to conservative-like disclosure with few disclosures of good news and a mission-driven regulator implements lower disclosure levels (than the other two regimes) when it is not properly insulated from external pressures. What we argue is this: a strong politically-independent body is required to produce high-quality socially-desirable standards.
Defective i6A37 Modification of Mitochondrial and Cytosolic tRNAs Results from Pathogenic Mutations in TRIT1 and Its Substrate tRNA

Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i6A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i6A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i6A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNASer(UCN) mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i6A37 modification. These data demonstrate that deficiencies of i6A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.
Real-time visual-inertial mapping, re-localization and planning onboard MAVs in unknown environments

In this work, we present an MAV system that is able to relocalize itself, create consistent maps and plan paths in full 3D in previously unknown environments. This is solely based on vision and IMU measurements with all components running onboard and in real-time. We use visual-inertial odometry to keep the MAV airborne safely locally, as well as for exploration of the environment based on high-level input by an operator. A globally consistent map is constructed in the background, which is then used to correct for drift of the visual odometry algorithm. This map serves as an input to our proposed global planner, which finds dynamic 3D paths to any previously visited place in the map, without the use of teach and repeat algorithms. In contrast to previous work, all components are executed onboard and in real-time without any prior knowledge of the environment.
Assessing in-kind Middle School teachers' concern about & use of SOARS: School Online Assessment Reporting System

In recent years technology has been integrated into every sector of education. Using Student Online Assessment Reporting System (SOARS) to assess score results and design instructional strategies for improved learning is a challenge and will cause concern to teachers. This is a descriptive comparative study designed to measure select Middle School teachers’ Stages of Concern and Levels of Use regarding the SOARS assessment tool. SOARS was adopted by Jeffco Public Schools (CO) to chart student progress by presenting Colorado Student Assessment Program (CSAP) score data. This study determined if there was a significant difference between the Stages of Concern and Levels of Use of High Profile and Low Profile Middle School teachers. High Profile Middle Schools have demographic data that show the highest percentile levels of free/reduced lunches, ethnicity rates, and mobility rates and Low Profile Middle Schools have the lowest percentile levels. This study targeted a select group (N=72) of coresubject teachers (Language Arts, Math, and Science) from High and Low Profile Middle Schools. There were three High Profile Middle Schools and three Low Profile Middle Schools that participated in this study.
WiFi electronic nose for indoor air monitoring

Several indoor chemical contaminants such as CO and NO2 are highly toxic. Inhalation of CO or NO2 as low as ppm level may cause respiratory distress or failure. Therefore, detection of indoor air is very important in the industrial, medical, and environmental applications. In this paper, a new electronic nose (E-nose) architecture has been proposed for the real-time quantification and qualification of indoor air contaminations. The metal oxide TGS gas sensors were used as the sensing part. The principal component analysis (PCA) method and a set of mathematical model were employed in data analysis. By combining with the proposed mathematical model, this E-nose can estimate the amount of CO gas contaminations in air at ppm levels. Moreover, the PCA results can clearly show a classification between two different rooms.
Quest for Equality

As the United States championed principles of freedom and equality during World War II, it denied fundamental rights to many non-white citizens. In the wake of President Franklin Roosevelt's 'Good Neighbor' policy with Latin America, African American and Mexican American civil rights leaders sought ways to make that policy of respect and mutual obligations apply at home as well as abroad. They argued that a whites-only democracy not only denied constitutional protection to every citizen but also threatened the war effort and FDR's aims. Neil Foley examines the complex interplay among regional, national, and international politics that plagued the efforts of Mexican Americans and African Americans to find common ground in ending employment discrimination in the defense industries and school segregation in the war years and beyond. Underlying differences in organizational strength, political affiliation, class position, and level of assimilation complicated efforts by Mexican and black Americans to forge strategic alliances in their fight for economic and educational equality. The prospect of interracial cooperation foundered as Mexican American civil rights leaders saw little to gain and much to lose in joining hands with African Americans. Over a half century later, African American and Latino civil rights organizations continue to seek solutions to relevant issues, including the persistence of de facto segregation in our public schools and the widening gap in wealth and income in America. Yet they continue to grapple with the difficulty of forging solidarity across lines of cultural, class, and racial-ethnic difference, a struggle that remains central to contemporary American life.
Revocable Identity-Based Cryptosystem Revisited: Security Models and Constructions

Boneh and Franklin gave a naive revocation method in identity-based encryption (IBE) which imposes a huge overhead into the key generation center. Later, Boldyreva, Goyal, and Kumar proposed an elegant way of achieving an IBE with efficient revocation, called revocable IBE (RIBE). In this paper, we revisit RIBE from the viewpoint of both security models and constructions. First, we introduce a realistic threat, which we call decryption key exposure, and show that all prior RIBE constructions, except the Boneh-Franklin one, are vulnerable to decryption key exposure. Next, we propose the first scalable RIBE scheme with decryption key exposure resistance by combining the (adaptively secure) Waters IBE scheme and the (selectively secure) Boneh-Boyen IBE scheme, and show that our RIBE scheme is more efficient than all previous adaptively secure scalable RIBE schemes. In addition, we extend our interest into identity-based signatures; we introduce a new security definition of revocable identity-based signature (RIBS) with signing key exposure resistance, and propose the first scalable RIBS scheme based on the Paterson-Schuldt IBS. Finally, we provide implementation results of our schemes to adduce the feasibility of our schemes.
A Spectral-Spatial Classification of Hyperspectral Images Based on the Algebraic Multigrid Method and Hierarchical Segmentation Algorithm

The algebraic multigrid (AMG) method is used to solve linear systems of equations on a series of progressively coarser grids and has recently attracted significant attention for image segmentation due to its high efficiency and robustness. In this paper, a novel spectral-spatial classification method for hyperspectral images based on the AMG method and hierarchical segmentation (HSEG) algorithm is proposed. Our method consists of the following steps. First, the AMG method is applied to hyperspectral imagery to construct a multigrid structure of fine-to-coarse grids based on the anisotropic diffusion partial differential equation (PDE). The vertices in the multigrid structure are then considered as the initial seeds (markers) for growing regions and are clustered to obtain a sequence of segmentation results. In the next step, a maximum vote decision rule is employed to combine the pixel-wise classification map and the segmentation maps. Finally, a final classification map is produced by choosing the optimal grid level to extract representative spectra. Experiments based on three different types of real hyperspectral datasets with different resolutions and contexts demonstrate that our method can obtain 3.84%–13.81% higher overall accuracies than the SVM classifier. The performance of our method was further compared to several marker-based spectral-spatial classification methods using objective quantitative measures and a visual qualitative evaluation.
CHECK THE DATE : Reader Revocation in PKI-Based RFID Systems

One prominent open problem with RFID tags that support public key cryptography is revocation of reader certificates. This is an important issue considering that highend RFID tags are geared for public key applications such as e-documents and contactless payment instruments. Furthermore, the problem is unique to public key-based RFID systems, since tags have no clock and thus cannot use traditional (time-based) off-line revocation checking methods. Whereas, on-line methods require unrealistic connectivity assumptions. We address the problem of reader revocation in PKI-Based RFID systems. We begin by observing an important distinguishing feature of personal RFID tags used in authentication, access control or payment applications the involvement of a human user. We then take advantage of the user’s awareness and presence to construct a simple, efficient, secure and (most importantly) feasible solution for reader revocation checking. And finally, we evaluate our solution via a user study and a discussion of its application feasibility. In our approach, the main extra feature is the requirement for a small passive on-tag display. However, modern low-power display technology is low-cost and appealing for other security purposes such as user-to-tag authentication and transaction verification.
AUTOMATED 3D MAPPING & SHAPE ANALYSIS OF THE LATERAL VENTRICLES VIA FLUID REGISTRATION OF MULTIPLE SURFACE-BASED ATLASES

We developed and validated a new method to create automated 3D parametric surface models of the lateral ventricles, designed for monitoring degenerative disease effects in clinical neuroscience studies and drug trials. First we used a set of parameterized surfaces to represent the ventricles in a manually labeled set of 9 subjects' MRIs (atlases). We fluidly registered each of these atlases and mesh models to a set of MRIs from 12 Alzheimer's disease (AD) patients and 14 matched healthy elderly subjects, and we averaged the resulting meshes for each of these images. Validation experiments on expert segmentations showed that (1) the Hausdorff labeling error rapidly decreased, and (2) the power to detect disease-related alterations monotonically improved as the number of atlases, N, was increased from 1 to 9. We then combined the segmentations with a radial mapping approach to localize ventricular shape differences in patients. In surface-based statistical maps, we detected more widespread and intense anatomical deficits as we increased the number of atlases, and we formulated a statistical stopping criterion to determine the optimal value of N. Anterior horn anomalies in Alzheimer's patients were only detected with the multi-atlas segmentation, which clearly outperformed the standard single-atlas approach.
The Effect of Factor VIII Deficiencies and Replacement and Bypass Therapies on Thrombus Formation under Venous Flow Conditions in Microfluidic and Computational Models

Clinical evidence suggests that individuals with factor VIII (FVIII) deficiency (hemophilia A) are protected against venous thrombosis, but treatment with recombinant proteins can increase their risk for thrombosis. In this study we examined the dynamics of thrombus formation in individuals with hemophilia A and their response to replacement and bypass therapies under venous flow conditions. Fibrin and platelet accumulation were measured in microfluidic flow assays on a TF-rich surface at a shear rate of 100 s−1. Thrombin generation was calculated with a computational spatial-temporal model of thrombus formation. Mild FVIII deficiencies (5–30% normal levels) could support fibrin fiber formation, while severe (<1%) and moderate (1–5%) deficiencies could not. Based on these experimental observations, computational calculations estimate an average thrombin concentration of ∼10 nM is necessary to support fibrin formation under flow. There was no difference in fibrin formation between severe and moderate deficiencies, but platelet aggregate size was significantly larger for moderate deficiencies. Computational calculations estimate that the local thrombin concentration in moderate deficiencies is high enough to induce platelet activation (>1 nM), but too low to support fibrin formation (<10 nM). In the absence of platelets, fibrin formation was not supported even at normal FVIII levels, suggesting platelet adhesion is necessary for fibrin formation. Individuals treated by replacement therapy, recombinant FVIII, showed normalized fibrin formation. Individuals treated with bypass therapy, recombinant FVIIa, had a reduced lag time in fibrin formation, as well as elevated fibrin accumulation compared to healthy controls. Treatment of rFVIIa, but not rFVIII, resulted in significant changes in fibrin dynamics that could lead to a prothrombotic state.
Robust stabilization of nonlinear networked control systems with quasi-one-sided Lipschitz condition

This paper investigates the robust stabilization problem for a class of nonlinear networked control systems (NCSs) with a more general family of nonlinear functions, namely quasi-one-sided Lipschitz functions. Based on a time-varying delay system transformed from the NCSs, an augmented Lyapunov functional containing more useful information is constructed. A less conservative sufficient condition is established such that the closed-loop system stability and a prescribed H∞ performance are satisfied while both time-varying network-induced delay and packet losses are taken into account. The controller design scheme is given in terms of linear matrix inequalities (LMIs). Numerical simulation is provided to illustrate the effectiveness and merits of the proposed method.
Full covariance state duration modeling for HMM-based speech synthesis

This paper proposes a state duration modeling method using full covariance matrix for HMM-based speech synthesis. In this method, a full covariance matrix instead of the conventional diagonal covariance matrix is adopted in the multi-dimensional Gaussian distribution to model the state duration of each context-dependent phoneme. At synthesis stage, the state durations are predicted using the clustered context-dependent distributions with full covariance matrices. Experimental results show that the synthesized speech using full-covariance state duration models is more natural than the conventional method when we change the speaking rate of synthesized speech.
Mechanical defect detection of SF6 high voltage circuit breaker using wavelet based vibration signal analysis

High voltage circuit breaker is a device that requires frequent maintenance. This leads to high cost and time consuming. If the internal component of circuit breaker can be inspected without any disassembly. The period of the maintenance can be extended. This paper proposes the method of indirect internal component inspection. The experiment was applied with 110 kV SF6 puffer-type circuit breaker with hydraulic operating mechanism. The defect circuit breakers were tested. Then the vibration signals were recorded. The analyzing of vibration signal in time domain is difficult for the detection of small defect. Using wavelet transform, the detection of small defect can be performed. This detection reduces the risk of the failure in operation of circuit breaker.
Improving Memory-Based Collaborative Filtering using a Factor-Based Approach

Collaborative Filtering (CF) systems generate recommendations for a user by aggregating item ratings of other like-minded users. The memory-based approach is a common technique used in CF. This approach first uses statistical methods such as Pearson’s Correlation Coefficient to measure user similarities based on their previous ratings on different items. Users will then be grouped into different neighborhood depending on the calculated similarities. Finally, the system will generate predictions on how a user would rate a specific item by aggregating ratings on the item cast by the identified neighbors of his/her. However, current memory-based CF method only measures user similarities by simply looking at their rating trends while ignoring other aspects of overall rating patterns. To address this limitation, we propose a novel factor-based approach by incorporating user rating average, user rating variance, and number of overlapping ratings into the measurement of user similarity. The proposed method was empirically evaluated against the traditional memory-based CF method and other existing approaches including case amplification, significance weighting, and z-score using the MovieLens dataset. The results showed that the prediction accuracy of the proposed factor-based approach was significantly higher than existing approaches.