Miracle-dz/UniFAR-FTUs huggingface dataset:
An image reconstruction strategy for truncated projections of planar object in cone-beam CT

In the field of cone-beam computed tomography (CT), truncation artifacts caused by projection truncation will decrease the quality of reconstruction image. For planar object with large area to thickness ratio, projections are truncated at some views but not all views. Reconstruction of planar object is a special problem and rarely discussed ever before. In this paper, an image reconstruction strategy based on back-projection filtration (BPF) algorithm and projection onto convex set (POCS) method for truncated projections of planar object is developed. By considering the relationship between thickness of planar object and scan orbit radius, two cases are discussed in the strategy. In the first case, PI-lines parallel to the thickness direction which are non-truncated are selected and reconstructed using the BPF algorithm. In the second case, PI-lines parallel the thickness direction with no truncations are selected and reconstructed by use of BPF method firstly. And then, with the reconstructed result as a priori knowledge in the first reconstruction, PI-lines parallel to the width direction are selected and reconstructed by use of the POCS method. The proposed strategy is validated by simulations and real experiments. Results show that reconstruction image quality of our method is superior to that of the conventional FDK algorithm.
Approximate graph clustering for program characterization

An important aspect of system optimization research is the discovery of program traits or behaviors. In this paper, we present an automated method of program characterization which is able to examine and cluster program graphs, i.e., dynamic data graphs or control flow graphs. Our novel approximate graph clustering technology allows users to find groups of program fragments which contain similar code idioms or patterns in data reuse, control flow, and context. Patterns of this nature have several potential applications including development of new static or dynamic optimizations to be implemented in software or in hardware. For the SPEC CPU 2006 suite of benchmarks, our results show that approximate graph clustering is effective at grouping behaviorally similar functions. Graph based clustering also produces clusters that are more homogeneous than previously proposed non-graph based clustering methods. Further qualitative analysis of the clustered functions shows that our approach is also able to identify some frequent unexploited program behaviors. These results suggest that our approximate graph clustering methods could be very useful for program characterization.
Exogenous Spermidine Alleviates Low Temperature Injury in Mung Bean (Vigna radiata L.) Seedlings by Modulating Ascorbate-Glutathione and Glyoxalase Pathway

The role of exogenous spermidine (Spd) in alleviating low temperature (LT) stress in mung bean (Vigna radiata L. cv. BARI Mung-3) seedlings has been investigated. Low temperature stress modulated the non-enzymatic and enzymatic components of ascorbate-glutathione (AsA-GSH) cycle, increased H2O2 content and lipid peroxidation, which indicate oxidative damage of seedlings. Low temperature reduced the leaf relative water content (RWC) and destroyed leaf chlorophyll, which inhibited seedlings growth. Exogenous pretreatment of Spd in LT-affected seedlings significantly increased the contents of non-enzymatic antioxidants of AsA-GSH cycle, which include AsA and GSH. Exogenous Spd decreased dehydroascorbate (DHA), increased AsA/DHA ratio, decreased glutathione disulfide (GSSG) and increased GSH/GSSG ratio under LT stress. Activities of AsA-GSH cycle enzymes such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) increased after Spd pretreatment in LT affected seedlings. Thus, the oxidative stress was reduced. Protective effects of Spd are also reflected from reduction of methylglyoxal (MG) toxicity by improving glyoxalase cycle components, and by maintaining osmoregulation, water status and improved seedlings growth. The present study reveals the vital roles of AsA-GSH and glyoxalase cycle in alleviating LT injury.
Delivering software engineering education through LEGO robotics

The number of software engineering jobs is expected to grow faster than all other jobs over the next decade. STEM education is an important initiative to encourage young students to develop the skills they require to succeed in these positions. The First Lego League sponsors annual tournaments in which students must build and program a robot to accomplish various tasks in order to score points. Previously, the students had not used any process or documentation when developing the programs to run on the robot. This competition provides an opportunity to instruct the students in the benefits of using a formalized process that is essential in many software engineering projects commonly encountered in industry.
Evaluation of WORLDVIEW-1 Stereo Scenes

This paper describes the investigations carried out at ETH Zurich on the very-high resolution optical satellite sensor WorldView-1. The dataset includes a stereopair acquired in November 2007 over Morrison, Colorado, USA, consisting of a quasi-nadir scene with mean GSD close to 51cm and an off-nadir scene, with GSD up to 73cm. The radiometry of the images was evaluated through the estimation of the noise level (standard deviation of the digital number) in non-homogeneous areas. For the orientation of the scenes, we used ground control points to estimate the parameters of an affine transformation and improve the orientation related to the Rational Polynomial Coefficients (RPC) provided in the metadata files. The next step included the automatic DSM generation with quality assessment. In all our tests the matching and the final DSM generation was realized with our in-house software package SATPP (Satellite Image Precision Processing) which has already been successfully used for other satellite sensors like IKONOS, ALOS/PRISM, Cartosat-1 and airborne linear and frame cameras. For the evaluation of the potential of a WorldView-1 stereo image pair for DSM generation, reference data are fundamental. As no DSM with a suitable resolution was available in this dataset, we generated the reference DSM from 1:15’000 scale infrared aerial images purchased from USGS. The aerial images were acquired in April 2002 with an analogue camera and scanned with a resolution of 14μm. No GCPs were available for the area covered by the aerial images. Therefore we defined a sufficient number of well-defined texture points in the oriented stereo pair of WorldView-1 as GCPs and determined their 3D coordinates using the orientation parameter of the satellite stereo pair. These points were used for the image orientation of the aerial images, which leads to a good relative orientation between the two different image sets. By this we investigated the quality of the matching process with WorldView-1 stereo image data mostly independent of the exterior orientation parameters. We will present here our accuracy assessment by visual and quantitative analysis (3D residuals distribution and statistics). The difference between the acquisition times of the two data sets (about 2.5 years) caused changes in the land cover, e.g. in correspondence of vegetation and buildings. In order to avoid the influence of temporal differences in our analysis, we compared the surface models in areas where no significant time depending changes could be expected. In addition, we evaluated the potential of the scenes for 3D building model extraction. The results are presented and discussed.
Analytical noise treatment for low-dose CT projection data by penalized weighted least-square smoothing in the K-L domain

By analyzing the noise properties of calibrated low-dose Computed Tomography (CT) projection data, it is clearly seen that the data can be regarded as approximately Gaussian distributed with a nonlinear signal-dependent variance. Based on this observation, the penalized weighted least-square (PWLS) smoothing framework is a choice for an optimal solution. It utilizes the prior variance-mean relationship to construct the weight matrix and the two-dimensional (2D) spatial information as the penalty or regularization operator. Furthermore, a K-L transform is applied along the z (slice) axis to further consider the correlation among different sinograms, resulting in a PWLS smoothing in the K-L domain. As a tool for feature extraction and de-correlation, the K-L transform maximizes the data variance represented by each component and simplifies the task of 3D filtering into 2D spatial process slice by slice. Therefore, by selecting an appropriate number of neighboring slices, the K-L domain PWLS smoothing fully utilizes the prior statistical knowledge and 3D spatial information for an accurate restoration of the noisy low-dose CT projections in an analytical manner. Experimental results demonstrate that the proposed method with appropriate control parameters improves the noise reduction without the loss of resolution.
A comparison of clustering quality indices using outliers and noise

Quality indices in clustering are used not only to assess the quality of the partitions but also to determine the number of clusters in the final result. When these indices are evaluated in a case study, real data conditions or different clustering algorithms are seldom taken into account. Here, some of the standard indices used in the literature are compared using more realistic databases that include outliers or noisy dimensions, which is more like a real problem-solving approach. Besides, three different clustering methods are used in an attempt to identify different behaviours. Also, the performance of the quality index-clustering algorithm tandem is compared to random grouping, with the aim of running an additional check. The indices are ranked, and index-based conclusions are drawn for all the scenarios.
Mesoscopic Organization Reveals the Constraints Governing Caenorhabditis elegans Nervous System

One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental stimuli. Investigating the intermediate or mesoscopic level of organization in the nervous system is a vital step towards understanding how the integration of micro-level dynamics results in macro-level functioning. The coordination of many different co-occurring processes at this level underlies the command and control of overall network activity. In this paper, we have considered the somatic nervous system of the nematode Caenorhabditis elegans, for which the entire neuronal connectivity diagram is known. We focus on the organization of the system into modules, i.e., neuronal groups having relatively higher connection density compared to that of the overall network. We show that this mesoscopic feature cannot be explained exclusively in terms of considerations such as, optimizing for resource constraints (viz., total wiring cost) and communication efficiency (i.e., network path length). Even including information about the genetic relatedness of the cells cannot account for the observed modular structure. Comparison with other complex networks designed for efficient transport (of signals or resources) implies that neuronal networks form a distinct class. This suggests that the principal function of the network, viz., processing of sensory information resulting in appropriate motor response, may be playing a vital role in determining the connection topology. Using modular spectral analysis we make explicit the intimate relation between function and structure in the nervous system. This is further brought out by identifying functionally critical neurons purely on the basis of patterns of intra- and inter-modular connections. Our study reveals how the design of the nervous system reflects several constraints, including its key functional role as a processor of information.
Mapping human intentions to robot motions via physical interaction through a jointly-held object

In this paper we consider the problem of human-robot collaborative manipulation of an object, where the human is active in controlling the motion, and the robot is passively following the human's lead. Assuming that the human grasp of the object only allows for transfer of forces and not torques, there is a disambiguity as to whether the human desires translation or rotation. In this paper, we analyze different approaches to this problem both theoretically and in experiment. This leads to the proposal of a control methodology that uses switching between two different admittance control modes based on the magnitude of measured force to achieve disambiguation of the rotation/translation problem.
A prototype of a VHDL-based fault injection tool

This paper presents the prototype of an automatic and model-independent fault injection tool, to use on an IBM-PC (or compatible) platform. The tool has been built around a commercial VHDL simulator. With this tool, both transient and permanent faults, of a wide range of types, can be injected into medium-complexity models. Another remarkable aspect of the tool is the fact that it is able to analyse the results obtained from the injection campaigns, in order to study the error syndrome of the system model and/or validate its fault-tolerance mechanisms. Some results of a fault injection campaign carried out to validate the dependability of a fault tolerant microcomputer system are shown. We have analysed the pathology of the propagated errors, measured their latencies, and calculated both error detection and recovery latencies and coverages.
Overexpression of Akt1 Enhances Adipogenesis and Leads to Lipoma Formation in Zebrafish

Background Obesity is a complex, multifactorial disorder influenced by the interaction of genetic, epigenetic, and environmental factors. Obesity increases the risk of contracting many chronic diseases or metabolic syndrome. Researchers have established several mammalian models of obesity to study its underlying mechanism. However, a lower vertebrate model for conveniently performing drug screening against obesity remains elusive. The specific aim of this study was to create a zebrafish obesity model by over expressing the insulin signaling hub of the Akt1 gene. Methodology/Principal Findings Skin oncogenic transformation screening shows that a stable zebrafish transgenic of Tg(krt4Hsa.myrAkt1)cy18 displays severely obese phenotypes at the adult stage. In Tg(krt4:Hsa.myrAkt1)cy18, the expression of exogenous human constitutively active Akt1 (myrAkt1) can activate endogenous downstream targets of mTOR, GSK-3α/β, and 70S6K. During the embryonic to larval transitory phase, the specific over expression of myrAkt1 in skin can promote hypertrophic and hyperplastic growth. From 21 hour post-fertilization (hpf) onwards, myrAkt1 transgene was ectopically expressed in several mesenchymal derived tissues. This may be the result of the integration position effect. Tg(krt4:Hsa.myrAkt1)cy18 caused a rapid increase of body weight, hyperplastic growth of adipocytes, abnormal accumulation of fat tissues, and blood glucose intolerance at the adult stage. Real-time RT-PCR analysis showed the majority of key genes on regulating adipogenesis, adipocytokine, and inflammation are highly upregulated in Tg(krt4:Hsa.myrAkt1)cy18. In contrast, the myogenesis- and skeletogenesis-related gene transcripts are significantly downregulated in Tg(krt4:Hsa.myrAkt1)cy18, suggesting that excess adipocyte differentiation occurs at the expense of other mesenchymal derived tissues. Conclusion/Significance Collectively, the findings of this study provide direct evidence that Akt1 signaling plays an important role in balancing normal levels of fat tissue in vivo. The obese zebrafish examined in this study could be a new powerful model to screen novel drugs for the treatment of human obesity.
Validation of trace-driven simulation models: regression analysis revisited

For the validation of trace-driven simulation models this paper recommends a simple statistical test that uses elementary regression analysis in a novel way. This test concerns a (joint) null-hypothesis: the outputs of the simulated and the real systems have the same means and the same variances. Technically, the differences between simulated and real outputs are regressed on their sums, and the resulting slope and intercept are tested to be zero. This paper further proves that it is wrong to use a naive test that regresses the simulation outputs on the real outcomes, and hypothesizes that the resulting regression line gives a 45 /spl deg/ line through the origin. The new and the old tests are investigated in Monte Carlo experiments with inventory systems. The conclusion is that the new test has the correct type I error probability, whereas the old test (falsely) rejects a valid simulation model substantially more often than the nominal alpha level. The power of the new test increases, as the simulation model deviates more from the real system.
Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells

Guanine-rich DNA of a particular sequence adopts four-stranded structural forms known as G-quadruplex or G4 DNA. Though in vitro formation of G4 DNA is known for several years, in vivo presence of G4 DNA was only recently noted in eukaryote telomeres. Recent bioinformatics analyses showing prevalence of G4 DNA within promoters of human and related species seems to implicate G4 DNA in a genome-wide cis-regulatory role. Herein we demonstrate that G4 DNA may present regulatory sites on a genome-wide scale by showing widespread effect on gene expression in response to the established intracellular G4 DNA-binding ligands. This is particularly relevant to genes that harbor conserved potential G4 DNA (PG4 DNA) forming sequence across human, mouse and rat promoters of orthologous genes. Genes with conserved PG4 DNA in promoters show co-regulated expression in 79 human and 61 mouse normal tissues (z-score > 3.5; P < 0.0001). Conservation of G4 DNA across related species also emphasizes the biological importance of G4 DNA and its role in transcriptional regulation of genes; shedding light on a relatively novel mechanism of regulation of gene expression in eukaryotes.
PROPOSAL Image-space wave-equation tomography for anisotropic parameters

Anisotropic models are widely needed by many anisotropic migration and interpretation schemes to obtain clearer image and thereby better understanding of the complex subsurface. However, anisotropic model building is a notoriously challenging problem because of its non-linearity and the existence of trade-off among the anisotropic parameters. I propose an approach to build the anisotropic model using Wave-Equation Tomography (WETom) with two major features: first, WE-Tom will be performed in the image-space, and provide a direct link between the model perturbation and the image perturbation; and second, WETom will include various regularization schemes to incorporate as much prior information as possible. Previous implementation of WETom operator builds the cornerstone of the proposed process, and the preliminary results on simple 2-D examples demonstrate its feasibility. Ultimately, I aim to utilize all the information available – surface seismic data and the borehole data; measure of image in terms of both focusness and moveout – to build a consistent, reliable anisotropic model, and produce a well-focused image at the same time. Since first reported in exploration seismology in the 1930s (McCollum and Snell, 1932), the importance of anisotropy has been continuously increased in seismic imaging and exploration. This is partially due to acquisition with increasingly longer offsets and exploration in areas with strong geological deformation. In these circumstances , accurate understanding of the anisotropic behavior of wave propagation is crucial to the overall success of an imaging project. Seismic data processing that ignores anisotropy leads to kinematic errors, which become worse when imaging steep reflectors such as salt flanks or steep faults. This could cause severe consequences for potential drilling or production. Therefore, numerous anisotropic migration and processing schemes have been developed during the past decade but their application requires knowledge of the anisotropic velocity model. Obviously, it is far more complicated to recover several independent elastic coefficients needed to construct the anisotropic velocity function than to perform conventional velocity analysis for isotropic media. There are two main difficulties that cause the estimation of anisotropic model unreliable: first, current anisotropic model-building schemes are mostly ray-based approach, measuring the non-hyperbolic moveout along the traveltime curve, which are prone to errors and unrealistic results when multi-pathing exists in areas of complex overburden; and second, the trade-off among the anisotropic parameters cannot be resolved by surface reflection data only due to the lack of vertical information. Recently , researches on anisotropic tomography near wells have been presented …
VLSI/PCB placement with obstacles based on sequence-pair

In a typical very large scale integration/printed circuit board (VLSI/PCB) design, some modules are preplaced in advance, and the other modules are requested to be placed without overlap with each other and with these preplaced mod- ules. The presence of such obstacles introduces inconsistency to a coding scheme, called sequence pair, which has been proposed for an obstacle free placement problem. We solve this difficulty by proposing a procedure called "adaptation" which transforms an inconsistent sequence pair to a consistent one with the utmost consideration for minimizing the modification. It is shown that a simulated annealing is well organized so that it tests only feasible placements by the adaptation procedure. As a design example, a Microelectronics Center of North Carolina (MCNC) benchmark data "ami49" is packed with treating ten modules among 49 modules as preplaced ones. Further, a PCB example which includes 32 free modules and four preplaced modules (connectors) is laid out successfully by our method with a conventional wiring estimation followed by a commercial router.
Bnymble (a Short Paper) More Anonymous Blacklisting at Almost No Cost

Anonymous blacklisting schemes allow online service providers to prevent future anonymous access by abusive users while preserving the privacy of all anonymous users (both abusive and non-abusive). The first scheme proposed for this purpose was Nymble, an extremely efficient scheme based only on symmetric primitives; however, Nymble relies on trusted third parties who can collude to de-anonymize users of the scheme. Two recently proposed schemes, Nymbler and Jack, reduce the trust placed in these third parties at the expense of using less-efficient asymmetric crypto primitives. We present BNymble, a scheme which matches the anonymity guarantees of Nymbler and Jack while (nearly) maintaining the efficiency of the original Nymble. The key insight of BNymble is that we can achieve the anonymity goals of these more recent schemes by replacing only the infrequent “User Registration” protocol from Nymble with asymmetric primitives. We prove the security of BNymble, and report on its efficiency.