Miracle-dz/UniFAR-FTUs huggingface dataset:
Level set based segmentation with intensity and curvature priors

A method is presented for segmentation of anatomical structures that incorporates prior information about the intensity and curvature profile of the structure from a training set of images and boundaries. Specifically the authors model the intensity distribution as a function of signed distance from the object boundary, instead of modeling only the intensity of the object as a whole. A curvature profile acts as a boundary regularization term specific to the shape being extracted, as opposed to simply penalizing high curvature. Using the prior model, the segmentation process estimates a maximum a posteriori higher dimensional surface whose zero level set converges on the boundary of the object to be segmented. Segmentation results are demonstrated on synthetic data and magnetic resonance imagery.
Magnetic resonance imaging study of gray matter in schizophrenia based on XGBoost

Brain structural abnormalities of schizophrenia subjects are often considered as the main neurobiological basis of this brain disease. Therefore, with the rapid development of artificial intelligence and medical imaging technologies, machine learning and structural magnetic resonance imaging have often been applied to computer-aided diagnosis of brain diseases such as schizophrenia, Alzheimer, glioma segmentation, etc. In this paper, statistical analysis of schizophrenic and normal subjects is initially made. Additionally, a slicing and weighted average method is proposed for gray matter images of the structural magnetic resonance imaging stored as three-dimensional volume data. Grey-level co-occurrence matrix texture features from the previously processed gray matter images of structural magnetic resonance imaging are then extracted and normalized. Finally, an eXtreme Gradient Boosting classifier is used for schizophrenia classification. Experiments employed 100 schizophrenic subjects and 100 normal controls. Results show the proposed method improves the respective classification accuracy of healthy controls and schizophrenic subjects by 8% and 10.6% of the area under the receiver operating characteristic. This suggests that the textural features of gray matter changes may be of diagnostic value in schizophrenia.
An LPGM method: Platform Independent Modeling and Development of Graphical User Interface

This paper introduces a new method in the area of platform independent modeling and the development of graphical user interfaces. The method bridges the gap between traditional MB-UIDEs and the modern web methodologies by enabling the modeling and development of both traditional and web user interfaces. The method is based on a proposed Presentation model and a Task Action Model which drive the development process. The modeling notation in both models is done with use of UML, and the development process is supported by a UML-compliant adaptive modeling tool. Descriptions of both the model and the method of application are included. An evaluation done using a JavaEE and a Swing widget toolkit is also mentioned.
Classification of graphs using contractible transformations. Homotopy equivalence of graphs. Basic representatives and complexity of homotopy equivalence classes

The main concept of this classification is that graphs belonging to the same equivalence class have similar topological properties. Graphs are called homotopy equivalent if one of them can be converted to the other one by contractible transformations. A basic representative and complexity of a homotopy equivalence class are defined and investigated. Finding a basic representative within a homotopy equivalence class simplifies many topological problems in digital imaging. A method is designed for the classification of graphs by complexity and basic representatives. This method relies on computer experiments which show that contractible transformations are a graph analogue of homotopy in algebraic topology. Diagrams are given of basic representatives with the complexity N less than 6.
Different Mutagenic Potential of HIV-1 Restriction Factors APOBEC3G and APOBEC3F Is Determined by Distinct Single-Stranded DNA Scanning Mechanisms

The APOBEC3 deoxycytidine deaminase family functions as host restriction factors that can block replication of Vif (virus infectivity factor) deficient HIV-1 virions to differing degrees by deaminating cytosines to uracils in single-stranded (−)HIV-1 DNA. Upon replication of the (−)DNA to (+)DNA, the HIV-1 reverse transcriptase incorporates adenines opposite the uracils, thereby inducing C/G→T/A mutations that can functionally inactivate HIV-1. Although both APOBEC3F and APOBEC3G are expressed in cell types HIV-1 infects and are suppressed by Vif, there has been no prior biochemical analysis of APOBEC3F, in contrast to APOBEC3G. Using synthetic DNA substrates, we characterized APOBEC3F and found that similar to APOBEC3G; it is a processive enzyme and can deaminate at least two cytosines in a single enzyme-substrate encounter. However, APOBEC3F scanning movement is distinct from APOBEC3G, and relies on jumping rather than both jumping and sliding. APOBEC3F jumping movements were also different from APOBEC3G. The lack of sliding movement from APOBEC3F is due to an 190NPM192 motif, since insertion of this motif into APOBEC3G decreases its sliding movements. The APOBEC3G NPM mutant induced significantly less mutations in comparison to wild-type APOBEC3G in an in vitro model HIV-1 replication assay and single-cycle infectivity assay, indicating that differences in DNA scanning were relevant to restriction of HIV-1. Conversely, mutation of the APOBEC3F 191Pro to 191Gly enables APOBEC3F sliding movements to occur. Although APOBEC3F 190NGM192 could slide, the enzyme did not induce more mutagenesis than wild-type APOBEC3F, demonstrating that the unique jumping mechanism of APOBEC3F abrogates the influence of sliding on mutagenesis. Overall, we demonstrate key differences in the impact of APOBEC3F- and APOBEC3G-induced mutagenesis on HIV-1 that supports a model in which both the processive DNA scanning mechanism and preferred deamination motif (APOBEC3F, 5′TTC; APOBEC3G 5′CCC) influences the mutagenic and gene inactivation potential of an APOBEC3 enzyme.
Profiles semantics for personalized information access

Heterogeneity of information and users has raised the problem of defining a generic model, which would be used as a basis for various information access applications. In this article, we propose a profile generic model, which describes the general structure and semantics of any information or user profile for information access. Thanks to a graph, combining two profiles instances of the generic model, we define rules for deducing couples of profiles elements that have a compatible semantics and hence that we can match. These rules aim at improving the interoperability between different profiles and applications for infor-
Isolation and Characterization of cDNAs That Encode Homologs of a Pathogenesis-related Protein Allergen from Cryptomeria japonica

Many plant pathogenesis-related (PR) proteins are allergenic. We isolated three cDNAs, Cry j 3.1, Cry j 3.2, and Cry j 3.3, that encoded homologs of Jun a 3, a PR protein allergen in Juniperus ashei, from a cDNA library derived from the pollen of Cryptomeria japonica. The predicted amino acid sequences encoded by the three cDNAs were more than 85% identical to each other and about 57% identical to the sequence of Jun a 3. The Cry j 3 genes seemed to form a small multigene family in the genome of C. japonica. Expression of Cry j 3 was strong in roots and in female and male strobili; expression was weaker in cotyledons, leaves, stems, and pollen grains.
Bundles of Spider Silk, Braided into Sutures, Resist Basic Cyclic Tests: Potential Use for Flexor Tendon Repair

Repair success for injuries to the flexor tendon in the hand is often limited by the in vivo behaviour of the suture used for repair. Common problems associated with the choice of suture material include increased risk of infection, foreign body reactions, and inappropriate mechanical responses, particularly decreases in mechanical properties over time. Improved suture materials are therefore needed. As high-performance materials with excellent tensile strength, spider silk fibres are an extremely promising candidate for use in surgical sutures. However, the mechanical behaviour of sutures comprised of individual silk fibres braided together has not been thoroughly investigated. In the present study, we characterise the maximum tensile strength, stress, strain, elastic modulus, and fatigue response of silk sutures produced using different braiding methods to investigate the influence of braiding on the tensile properties of the sutures. The mechanical properties of conventional surgical sutures are also characterised to assess whether silk offers any advantages over conventional suture materials. The results demonstrate that braiding single spider silk fibres together produces strong sutures with excellent fatigue behaviour; the braided silk sutures exhibited tensile strengths comparable to those of conventional sutures and no loss of strength over 1000 fatigue cycles. In addition, the braiding technique had a significant influence on the tensile properties of the braided silk sutures. These results suggest that braided spider silk could be suitable for use as sutures in flexor tendon repair, providing similar tensile behaviour and improved fatigue properties compared with conventional suture materials.
Strategies and scenarios of CSRF attacks against the CAPTCHA forms

In this article, we’ve tried to examine the hypothesis of the robustness of a form by using CAPTCHA against CSRF and login CSRF attacks. Our investigations showed that unlike public opinion, common attacks to bypass CAPTCHAs such as Optical Character Recognition (OCR) and 3rd party human attacks are not applicable in the CSRF case and instead, Clickjacking is the most important scenario of CSRF and login CSRF attacks against a secure session-dependent CAPTCHA form. Remember that the Clickjacking is also applicable to bypass the well-known CSRF protections, such as the secret token and the Referer header. Therefore, although the frequent application of CAPTCHA on every page of a website negatively impacts the user experience, but the robustness of a robust session-dependent CAPTCHA against the CSRF and login CSRF attacks is almost the same as the session-dependent security token. Moreover, when a website is using a session-independent or week pattern of CAPTCHA, attackers can bypass the CAPTCHAs and launch the CSRF or login CSRF attacks by using XSS, session hijacking, replay attacks or submitting a random response.
Open Inquiry with Learning Journal Promoting Metacognitive Skills and Retention of Students with Low Academic Achievements

The expected skill to face the 21st century is the level of thinking that involves high order thinking concept known as metacognition, which is also believed as a notable predictor on retention. The purpose of this study is to investigate the effect of open inquiry model combined with a learning journal on metacognitive skills and retention of students with low and high learning achievement levels. This study was quasi-experimental research, using the equivalent post-test only with control group design. The subjects of the experiment comprised 60 eleventh grade students. The samples were randomly assigned in a 2 x 2 factorial design. Two learning models were compared: open inquiry and conventional models, and two learning achievement: high and low. The metacognitive skills and retention of students were measured by an essay test integrated with achievement test. The result of a 2-way ANOVA test confirmed that open inquiry with learning journal has a significant effect on metacognitive skills and retention of students with different learning achievement levels. Open inquiry with learning journal appears to be an effective strategy among students with high and low learning achievement levels. Keywords—metacognitive skills, retention, open inquiry, learning journal, and learning achievement
Deacetylation of FoxO by Sirt1 Plays an Essential Role in Mediating Starvation-Induced Autophagy in Cardiac Myocytes

Rationale: Autophagy, a bulk degradation process of cytosolic proteins and organelles, is protective during nutrient starvation in cardiomyocytes (CMs). However, the underlying signaling mechanism mediating autophagy is not well understood. Objective: We investigated the role of FoxOs and its posttranslational modification in mediating starvation-induced autophagy. Methods and Results: Glucose deprivation (GD) increased autophagic flux in cultured CMs, as evidenced by increased mRFP-GFP-LC3 puncta and decreases in p62, which was accompanied by upregulation of Sirt1 and FoxO1. Overexpression of either Sirt1 or FoxO1 was sufficient for inducing autophagic flux, whereas both Sirt1 and FoxO1 were required for GD-induced autophagy. GD increased deacetylation of FoxO1, and Sirt1 was required for GD-induced deacetylation of FoxO1. Overexpression of FoxO1(3A/LXXAA), which cannot interact with Sirt1, or p300, a histone acetylase, increased acetylation of FoxO1 and inhibited GD-induced autophagy. FoxO1 increased expression of Rab7, a small GTP-binding protein that mediates late autophagosome–lysosome fusion, which was both necessary and sufficient for mediating FoxO1-induced increases in autophagic flux. Although cardiac function was maintained in control mice after 48 hours of food starvation, it was significantly deteriorated in mice with cardiac-specific overexpression of FoxO1(3A/LXXAA), those with cardiac-specific homozygous deletion of FoxO1 (c-FoxO1−/−), and beclin1+/− mice, in which autophagy is significantly inhibited. Conclusions: These results suggest that Sirt1-mediated deacetylation of FoxO1 and upregulation of Rab7 play an important role in mediating starvation-induced increases in autophagic flux, which in turn plays an essential role in maintaining left ventricular function during starvation.
Either greedy or well informed: The reward maximization – unbiased evaluation trade-off

People often believe that they exert control on uncontrollable outcomes, a phenomenon that has been called illusion of control. Psychologists tend to attribute this illusion to personality variables. However, we present simulations showing that the illusion of control can be explained at a simpler level of analysis. In brief, if a person desires an outcome and tends to act as often as possible in order to get it, this person will never be able to know that the outcome could have occurred with the same probability if he/she had done nothing. Our simulations show that a very high probability of action is usually the best possible strategy if one wants to maximize the likelihood of occurrence of a desired event, but the choice of this strategy gives rise to illusion of control.
The theory and practiceof change champions inlocal government in Northern Ireland

There is little empirical research on how change champions operate in practice; even less on how they operate in elected authorities, and no research to date on their role in the management of change in local government in Northern Ireland. The initial aim of this research was therefore to examine; the roles, skills, resistance encountered, and the development needs of the change champions, in order to develop an improvement agenda and best practice recommendations. During the research process additional issues emerged about the culture of local government, its readiness for change and the particular problems faced by change champions operating in a political environment.
Federal Disaster Assistance after Hurricanes Katrina, Rita, Wilma, Gustav, and Ike

Report that provides information on federal financial assistance provided to the Gulf States after major disasters were declared in Alabama, Florida, Louisiana, Mississippi, and Texas in response to the widespread destruction that resulted from Hurricanes Katrina, Rita, and Wilma in 2005 and Hurricanes Gustav and Ike in 2008. This includes a brief summary of each hurricane and a discussion concerning federal to state cost-shares.
iotools: High-Performance I/O Tools for R

The iotools package provides a set of tools for Input/Output (I/O) intensive datasets processing in R (R Core Team, 2014). Efficent parsing methods are included which minimize copying and avoid the use of intermediate string representations whenever possible. Functions for applying chunk-wise operations allow for computing on streaming input as well as arbitrarily large files. We present a set of example use cases for iotools, as well as extensive benchmarks comparing comparable functions provided in both core-R as well as other contributed packages.
Interpreting Outliers: Localized Logistic Regression for Density Ratio Estimation

We propose an inlier-based outlier detection method capable of both identifying the outliers and explaining why they are outliers, by identifying the outlier-specific features. Specifically, we employ an inlier-based outlier detection criterion, which uses the ratio of inlier and test probability densities as a measure of plausibility of being an outlier. For estimating the density ratio function, we propose a localized logistic regression algorithm. Thanks to the locality of the model, variable selection can be outlier-specific, and will help interpret why points are outliers in a high-dimensional space. Through synthetic experiments, we show that the proposed algorithm can successfully detect the important features for outliers. Moreover, we show that the proposed algorithm tends to outperform existing algorithms in benchmark datasets.
Distributed compression in a dense microsensor network - IEEE Signal Processing Magazine

The distributed nature of the sensor network architecture introduces unique challenges and opportunities for collaborative networked signal processing techniques that can potentially lead to significant performance gains. Many evolving low-power sensor network scenarios need to have high spatial density to enable reliable operation in the face of component node failures as well as to facilitate high spatial localization of events of interest. This induces a high level of network data redundancy, where spatially proximal sensor readings are highly correlated. In this article, we propose a new way of removing this redundancy in a completely distributed manner, i.e., without the sensors needing to talk to one another. Our constructive framework for this problem is dubbed DISCUS (distributed source coding using syndromes) and is inspired by fundamental concepts from information theory. In this article, we review the main ideas, provide illustrations, and give the intuition behind the theory that enables this framework.
Intake and chewing behavior of steers consuming switchgrass preserved as hay or silage.

Effect of preservation method on intake and chewing behavior was examined using a first, late vegetative harvest (mid-June) of Kanlow switchgrass (Panicum virgatum L.). For silage (S), forage was harvested with a commercial field chopper (1.5 to 4 cm average chop length) and ensiled directly in silos 1.2 m in diameter and 3.6 m in height. For hay (H), forage was harvested with a flail-chopper (7 to 15 cm average chop length) and cured as hay in a drier at 77 degrees C. Diets of H and S were fed to six Hereford steers (338+/-5 kg) in a single crossover experiment. Chewing behavior was monitored for 4 d with a computerized system. At feeding, H was higher in DM and contained greater concentrations (DM basis) of NDF, CP, and hemicellulose, but lower concentrations of ADF and cellulose, and had lower in vitro DM disappearance values. Steers fed S had higher intakes of DM (P < .02) and NDF (P < .04) and consumed less water from the water supply (P < .01) than animals fed H. However, total amount of water (from water supply and feed) consumed per kilogram of DMI did not differ between diets. Crude protein intake was similar between diets. Preservation method had no effect on eating time, number of boli ruminated, bolus duration, and number of rumination chews per bolus. Steers fed S made fewer eating chews (P < .10) and ruminated for a longer time (P < .05) while making a greater number of rumination chews (P < .04) than steers fed H. Rumination intercycle time was slightly shorter in steers fed H (P < .05) than in steers fed S. When expressed per kilogram of NDF intake, steers fed S spent less time eating (P < .03) and made fewer eating chews (P < .02) than steers fed H; however, rumination time, number of rumination chews, and number of boli ruminated were not affected by preservation method. Steers fed S ingested feed at a greater rate (P < .03), excreted smaller fecal particles (P < .03), had meals of shorter duration (P < .06), spent less time eating during main meals (meals following feed distribution: P < .05), had more rumination periods (P < .01), and a shorter morning (P < .06) latency time (interval between end of main meal and onset of rumination) than steers fed H. These results indicate that preservation method with its concomitant differences in chop length affected forage chemical composition and voluntary intake, and that differences in chewing behavior occurred mostly during eating.
A fast convergence algorithm for echo cancellers in full duplex transmission using back projection from slicer

The problem of accelerating echo canceller tracking, during full duplex transmission, in single carrier (data) receivers with adaptive equalization is addressed. The scheme presented accelerates the convergence rate by orders of magnitude, with a minor increase in complexity, which can be traded for speed. The complexity may be reduced to a fraction of that of previously published acceleration schemes, while providing substantial speedup factors with respect to conventional echo cancellers. The new scheme is based on measuring the residual echo signal at the slicer (symbol-by-symbol detector) but applying the correction to the conventional echo canceller. Measuring changes in a low-noise (post-slicer) environment enables speedup of the adaptation. Updating the pre-equalizer echo canceller both reduces complexity and distills the echo from the noisy equalizer input.