Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting spatial memory to design efficient command interfaces

A common goal for user interface designers is to design efficient UIs that facilitate high levels of performance. In point-and-click interfaces, spatial memory has been shown to play an important role in reaching this level of performance, since it allows users to make quick decisions about item locations rather than resorting to slow visual search. However, spatial memory is rarely exploited by modern applications. Hierarchical menus force users through laborious action sequences to access commands, while window content is frequently elided and reshuffled in response to changing window geometries. In order to inform the design of UIs that better support spatial memory, we are studying the human and interface factors that affect the growth and resilience of spatial knowledge, and producing a series of exemplar interfaces that exploit users' spatial memory to rapidly achieve high levels of performance. A new command selection technique called CommandMaps demonstrates that when users have spatial memory of an interface, target acquisition can be vastly improved by removing control hierarchies. StencilMaps builds on the CommandMap technique, highlighting salient commands to accelerate novice visual search. Our ongoing research investigates the robustness of spatial memory and the role of 'effortful' learning in the development of spatial automaticity.
CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data

Abstract CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis. Scope of CEBS: CEBS currently holds 22 studies of rats, four studies of mice and one study of Caenorhabditis elegans. CEBS can also accommodate data from studies of human subjects. Toxicogenomics studies currently in CEBS comprise over 4000 microarray hybridizations, and 75 2D gel images annotated with protein identification performed by MALDI and MS/MS. CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Additionally, clinical chemistry and histopathology findings from over 1500 animals are included in CEBS. CEBS/BID: The BID (Biomedical Investigation Database) is another component of the CEBS system. BID is a relational database used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee (in preparation). BID has been shared with Health Canada and the US Environmental Protection Agency. CEBS is available at http://cebs.niehs. nih.gov. BID can be accessed via the user interface from https://dir-apps.niehs. nih.gov/arc/. Requests for a copy of BID and for depositing data into CEBS or BID are available at http://www.niehs. nih.gov/cebs-df/.
Randomized Gradient-Free Method for Multiagent Optimization Over Time-Varying Networks

In this brief, we consider the multiagent optimization over a network where multiple agents try to minimize a sum of nonsmooth but Lipschitz continuous functions, subject to a convex state constraint set. The underlying network topology is modeled as time varying. We propose a randomized derivative-free method, where in each update, the random gradient-free oracles are utilized instead of the subgradients (SGs). In contrast to the existing work, we do not require that agents are able to compute the SGs of their objective functions. We establish the convergence of the method to an approximate solution of the multiagent optimization problem within the error level depending on the smoothing parameter and the Lipschitz constant of each agent's objective function. Finally, a numerical example is provided to demonstrate the effectiveness of the method.
Abnormal gray matter volume and impulsivity in young adults with Internet gaming disorder

Reduced executive control is one of the central components of model on the development and maintenance of Internet gaming disorder (IGD). Among the various executive control problems, high impulsivity has consistently been associated with IGD. We performed voxel‐based morphometric analysis with diffeomorphic anatomical registration by using an exponentiated Lie algebra algorithm (DARTEL) to investigate the relationship of gray matter abnormalities to impulsivity in IGD. Thirty‐one young male adults whose excessive Internet gaming began in early adolescence, and 30 age‐matched male healthy controls were examined. IGD subjects showed smaller gray matter volume (GMV) in brain regions implicated in executive control, such as the anterior cingulate cortex and the supplementary motor area. The GMVs in the anterior cingulate cortex and the supplementary motor area were negatively correlated with self‐reporting scales of impulsiveness. IGD subjects also exhibited smaller GMV in lateral prefrontal and parietal cortices comprising the left ventrolateral prefrontal cortex and the left inferior parietal lobule when compared with healthy controls. The GMVs in the left ventrolateral prefrontal cortex were negatively correlated with lifetime usage of Internet gaming. These findings suggest that gray matter abnormalities in areas related to executive control may contribute to high impulsivity of young adults with IGD. Furthermore, alterations in the prefrontal cortex were related with long‐term excessive Internet gaming during adolescence.
Mas-Based Pursuit-Evasion Algorithm Under Unknown Environment

Based on the interaction protocols of Contract Net and Subscribe-publish, a distributive pursuit-evasion algorithm is proposed for multi-agents with limited detection ranges to pursue multi-evaders in an unknown grid map with obstacles. The pursuit agents first explore the map according to the method of Artificial Potential Field. When any obstacle is detected within the neighborhood of a pursuer, it updates the map. If an evader is detected, the pursuer (initiator) sends call-for-proposals messages to other pursuers. The other pursuers use D* algorithm to calculate their steps to reach the evader and submit their proposals. The initiator picks up the proposals and evaluates, chooses the nearest ones to join the pursuit team, sends accept-proposals to the selected agents and manages the team during the process of pursuit. If the evader is within the kill radius of all pursuit team members, the task is done; otherwise, D* algorithm is applied by each pursuit member to plan a new path once the evader moves to a new position. Distributive in nature, it allows a large-scale robot fleet to perform complicated tasks in a coordinated way. The algorithm can be easily extended to 3D cases. Simulation results show that the pursuit agents can dynamically form a pursuit team to catch evaders efficiently.
Perfomance Models for Blocked Sparse Matrix-Vector Multiplication Kernels

Sparse Matrix-Vector multiplication (SpMV) is a very challenging computational kernel, since its performance depends greatly on both the input matrix and the underlying architecture. The main problem of SpMV is its high demands on memory bandwidth, which cannot yet be abudantly offered from modern commodity architectures. One of the most promising optimization techniques for SpMV is blocking, which can reduce the indexing structures for storing a sparse matrix, and therefore alleviate the pressure to the memory subsystem. However, blocking methods can severely degrade performance if not used properly. In this paper, we study and evaluate a number of representative blocking storage formats and present a performance model that can accurately select the most suitable blocking storage format and the corresponding block shape and size for a specific sparse matrix. Our model considers both the memory and computational part of the kernel, which can be non-negligible when applying blocking, and also assumes an overlapping of memory accesses and computations that modern commodity architectures can offer through hardware prefetching mechanisms.
Mimotopes of the Vi Antigen of Salmonella enterica Serovar Typhi Identified from Phage Display Peptide Library

ABSTRACT The capsular polysaccharide Vi antigen (ViCPS) is an essential virulence factor and also a protective antigen of Salmonella enterica serovar Typhi. A random 12-mer phage-displayed peptide library was used to identify mimotopes (epitope analogues) of this antigen by panning against a ViCPS-specific monoclonal antibody (MAb) ATVi. Approximately 75% of the phage clones selected in the fourth round carried the peptide sequence TSHHDSHGLHRV, and the rest of the clones harbored ENHSPVNIAHKL and other related sequences. These two sequences were also obtained in a similar panning process by using pooled sera from patients with a confirmed diagnosis of typhoid fever, suggesting they mimic immunodominant epitopes of ViCPS antigens. Binding of MAb ATVi to the mimotopes was specifically blocked by ViCPS, indicating that they interact with the same binding site (paratope) of the MAb. Data and reagents generated in this study have important implications for the development of peptide-base diagnostic tests and peptide vaccines and may also provide a better understanding of the pathogenesis of typhoid fever.
Salmonella enterica Serovar Typhimurium Lacking hfq Gene Confers Protective Immunity against Murine Typhoid

Salmonella enterica is an important enteric pathogen and its various serovars are involved in causing both systemic and intestinal diseases in humans and domestic animals. The emergence of multidrug-resistant strains of Salmonella leading to increased morbidity and mortality has further complicated its management. Live attenuated vaccines have been proven superior over killed or subunit vaccines due to their ability to induce protective immunity. Of the various strategies used for the generation of live attenuated vaccine strains, focus has gradually shifted towards manipulation of virulence regulator genes. Hfq is a RNA chaperon which mediates the binding of small RNAs to the mRNA and assists in post-transcriptional gene regulation in bacteria. In this study, we evaluated the efficacy of the Salmonella Typhimurium Δhfq strain as a candidate for live oral vaccine in murine model of typhoid fever. Salmonella hfq deletion mutant is highly attenuated in cell culture and animal model implying a significant role of Hfq in bacterial virulence. Oral immunization with the Salmonella hfq deletion mutant efficiently protects mice against subsequent oral challenge with virulent strain of Salmonella Typhimurium. Moreover, protection was induced upon both multiple as well as single dose of immunizations. The vaccine strain appears to be safe for use in pregnant mice and the protection is mediated by the increase in the number of CD4+ T lymphocytes upon vaccination. The levels of serum IgG and secretory-IgA in intestinal washes specific to lipopolysaccharide and outer membrane protein were significantly increased upon vaccination. Furthermore, hfq deletion mutant showed enhanced antigen presentation by dendritic cells compared to the wild type strain. Taken together, the studies in murine immunization model suggest that the Salmonella hfq deletion mutant can be a novel live oral vaccine candidate.
Robust Parametric Fault Estimation in a Hopper System

Abstract The ability of diagnosis of the possible faults is a necessity for satellite launch vehicles during their mission. In this paper, a structural analysis method is employed to divide the complex propulsion system into simpler subsystems for fault diagnosis filter design. A robust fault diagnosis method, which is an optimization based approach, is applied to the subsystems of the propulsion system. The optimization problem has been solved within two different tools and the results are compared with two other optimization based approaches. The turbo-pump system is used to illustrate the employed methods and obtained results.
Delayed coupling theory of vertebrate segmentation

Rhythmic and sequential subdivision of the elongating vertebrate embryonic body axis into morphological somites is controlled by an oscillating multicellular genetic network termed the segmentation clock. This clock operates in the presomitic mesoderm (PSM), generating dynamic stripe patterns of oscillatory gene‐expression across the field of PSM cells. How these spatial patterns, the clock's collective period, and the underlying cellular‐level interactions are related is not understood. A theory encompassing temporal and spatial domains of local and collective aspects of the system is essential to tackle these questions. Our delayed coupling theory achieves this by representing the PSM as an array of phase oscillators, combining four key elements: a frequency profile of oscillators slowing across the PSM; coupling between neighboring oscillators; delay in coupling; and a moving boundary describing embryonic axis elongation. This theory predicts that the segmentation clock's collective period depends on delayed coupling. We derive an expression for pattern wavelength across the PSM and show how this can be used to fit dynamic wildtype gene‐expression patterns, revealing the quantitative values of parameters controlling spatial and temporal organization of the oscillators in the system. Our theory can be used to analyze experimental perturbations, thereby identifying roles of genes involved in segmentation.
Plasmid Construction Using Recombination Activity in the Fission Yeast Schizosaccharomyces pombe

Background Construction of plasmids is crucial in modern genetic manipulation. As of now, the common method for constructing plasmids is to digest specific DNA sequences with restriction enzymes and to ligate the resulting DNA fragments with DNA ligase. Another potent method to construct plasmids, known as gap-repair cloning (GRC), is commonly used in the budding yeast Saccharomyces cerevisiae. GRC makes use of the homologous recombination activity that occurs within the yeast cells. Due to its flexible design and efficiency, GRC has been frequently used for constructing plasmids with complex structures as well as genome-wide plasmid collections. Although there have been reports indicating GRC feasibility in the fission yeast Schizosaccharomyces pombe, this species is not commonly used for GRC as systematic studies of reporting GRC efficiency in S. pombe have not been performed till date. Methodology/Principal Findings We investigated GRC efficiency in S. pombe in this study. We first showed that GRC was feasible in S. pombe by constructing a plasmid that contained the LEU2 auxotrophic marker gene in vivo and showed sufficient efficiency with short homology sequences (>25 bp). No preference was shown for the sequence length from the cut site in the vector plasmid. We next showed that plasmids could be constructed in a proper way using 3 DNA fragments with 70% efficiency without any specific selections being made. The GRC efficiency with 3 DNA fragments was dramatically increased >95% in lig4Δ mutant cell, where non-homologous end joining is deficient. Following this approach, we successfully constructed plasmid vectors with leu1+, ade6+, his5+, and lys1+ markers with the low-copy stable plasmid pDblet as a backbone by applying GRC in S. pombe. Conclusions/Significance We concluded that GRC was sufficiently feasible in S. pombe for genome-wide gene functional analysis as well as for regular plasmid construction. Plasmids with different markers constructed in this research are available from NBRP-yeast (http://yeast.lab.nig.ac.jp/).
Plasmonic Photothermal Heating of Intraperitoneal Tumors through the Use of an Implanted Near-Infrared Source

Plasmonic nanomaterials including gold nanorods are effective agents for inducing heating in tumors. Because near-infrared (NIR) light has traditionally been delivered using extracorporeal sources, most applications of plasmonic photothermal therapy have focused on isolated subcutaneous tumors. For more complex models of disease such as advanced ovarian cancer, one of the primary barriers to gold nanorod-based strategies is the adequate delivery of NIR light to tumors located at varying depths within the body. To address this limitation, a series of implanted NIR illumination sources are described for the specific heating of gold nanorod-containing tissues. Through computational modeling and ex vivo studies, a candidate device is identified and validated in a model of orthotopic ovarian cancer. As the therapeutic, imaging, and diagnostic applications of plasmonic nanomaterials progress, effective methods for NIR light delivery to challenging anatomical regions will complement ongoing efforts to advance plasmonic photothermal therapy toward clinical use.
Extraction of Any Angle Virtual Slice on 3D CT Image

The images from most medical imaging equipments such as CT, MRI must be along some fixed direction, but it can't satisfy the clinical inspection from arbitrary directions and angles. In view of this problem, the method of any angle extraction of virtual slice on 3D CT image is proposed in this paper. VC++6.0 with VTK are adopted to reconstruct the 3D images using the 2D CT image sequence in DICOM format. The normal vector and interior point are calculated to form the virtual clipping plane, which in turn is used to incise the 3D object. And the information of virtual slice is obtained, in the mean while the virtual slice images are displayed on the screen. By simple interactive operations like using mouse, the image scaling, translation and rotation can be realized in real time. Therefore, the method presented in this paper is an effective complement to present medical imaging equipments.
Density Functional Theory Calculations for Nitro Benzene Molecules Group

Electronic properties for nitrobenzene molecules have been studied using three parameters Lee-Yang-Parr density functional theory with 6-31G** basis sets. The optimized structures and electronic properties calculations for the studied molecules have been performed using Gaussian 03 program. This study includes benzene molecule calculations for comparison and study the addition effect of nitro as a side group on the electronic properties of benzene. The results show that the energy gaps for nitrobenzene molecules group is less than that for benzene.
Compressed video indexing based on object motion

Compressed video processing for the sake of content based retrieval saves time of the expensive decoding. In this paper, we process the compressed MPEG video data for the motion analysis of its contents. Two motion components are differentiated from each other. Firstly, the object's motion; the change in object's co-ordinates throughout consecutive frames. Secondly, the camera motion resulting from the camera effects such as zooming in and out, and panning right and left, . etc. A trajectory is constructed for each object and represented by a spatio-temporal representation. Video objects are indexed by the actual motion of the objects, independent from the moving camera motion.
Detection of aflatoxin B1 in serum samples of male Japanese subjects by radioimmunoassay and high-performance liquid chromatography.

Aflatoxin B1 (AFB1) was detected in serum samples of healthy Japanese males by radioimmunoassay and high-performance liquid chromatography. Blood samples were obtained from 20 subjects after fasting and from 80 subjects after lunch. The subjects ranged in age from 20 to 63 years of age. Measurement of AFB1 in the samples was performed by radioimmunoassay and was confirmed by high-performance liquid chromatography using a mu Porasil column and a C18-mu Bondapak column after the conversion of AFB1 to its water adduct AFB2a. AFB1 was detected in 5 of 20 fasting blood samples [20 to 56 pg/ml of serum; 33.6 +/- 14.6 (S.D.)] and in 29 of 80 serum samples taken after lunch (20 to 1169 pg/ml of serum; 218.1 +/- 268.3). Mass spectral analysis of the material obtained after high-performance liquid chromatography separation from serum samples confirmed the presence of AFB1.
An Appraisal of Human Mitochondrial DNA Instability: New Insights into the Role of Non-Canonical DNA Structures and Sequence Motifs

Mitochondrial DNA (mtDNA) deletion mutations are frequently observed in aged postmitotic tissues and are the cause of a wide range of human disorders. Presently, the molecular bases underlying mtDNA deletion formation remain a matter of intense debate, and it is commonly accepted that several mechanisms contribute to the spectra of mutations in the mitochondrial genome. In this work we performed an extensive screening of human mtDNA deletions and evaluated the association between breakpoint density and presence of non-canonical DNA elements and over-represented sequence motifs. Our observations support the involvement of helix-distorting intrinsically curved regions and long G-tetrads in eliciting instability events. In addition, higher breakpoint densities were consistently observed within GC-skewed regions and in the close vicinity of the degenerate sequence motif YMMYMNNMMHM. A parallelism is also established with hot spot motifs previously identified in the nuclear genome, as well as with the minimal binding site for the mitochondrial transcription termination factor mTERF. This study extends the current knowledge on the mechanisms driving mitochondrial rearrangements and opens up exciting avenues for further research.
High-Throughput Analysis and Characterization of Astragalus membranaceus Transcriptome Using 454 GS FLX

Astragalus membranaceus (Fisch.) Bge (AR), one of the most important medicinal plants in Asia, was found to exhibit various bioactivities. Due to limited genomic and transcriptomic data, the biosynthetic pathway of the major bioactive compound in AR, is currently unclear. In this study, 454 GS FLX technology was employed to produce a substantial expressed sequence tag (EST) dataset from the AR. In all, 742721 high-quality reads from the AR were produced using Roche GS FLX Titanium. A total of 9893 unique sequences were obtained and annotated by a similarity search against the public databases, and involved in the secondary metabolic pathway, which would facilitate deciphering the molecular mechanism of secondary metabolism in AR. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. GO revealed the unique sequences that could be assigned to 34 vocabularies. In the KEGG mapping, unique sequences were established as associated with 46 biochemical pathways. These results provided the largest EST collections in AR and will contribute to biosynthetic and biochemical studies that lead to drug improvement. With respect to the genes related to metabolism and biosynthesis pathway were also found. Our work demonstrated the utility of 454 GS FLX as a method for the rapid and cost-effective identification of AR transcriptome, and this EST dataset will be a powerful resource for further studies such as taxonomy, molecular breeding, and secondary metabolism in AR.
Pricing Tasks in Online Labor Markets

In this paper we present a mechanism for determining near-optimal prices for tasks in online labor markets, often used for crowdsourcing. In particular, the mechanisms are designed to handle the intricacies of markets like Mechanical Turk where workers arrive online and requesters have budget constraints. The mechanism is incentive compatible, budget feasible, and has competitive ratio performance and also performs well in practice. To demonstrate the mechanism's practical effectiveness we conducted experiments on the Mechanical Turk platform.