Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic networks controlling retinal injury.

PURPOSE The present study defines genomic loci underlying coordinate changes in gene expression following retinal injury. METHODS A group of acute phase genes expressed in diverse nervous system tissues was defined by combining microarray results from injury studies from rat retina, brain, and spinal cord. Genomic loci regulating the brain expression of acute phase genes were identified using a panel of BXD recombinant inbred (RI) mouse strains. Candidate upstream regulators within a locus were defined using single nucleotide polymorphism databases and promoter motif databases. RESULTS The acute phase response of rat retina, brain, and spinal cord was dominated by transcription factors. Three genomic loci control transcript expression of acute phase genes in brains of BXD RI mouse strains. One locus was identified on chromosome 12 and was highly correlated with the expression of classic acute phase genes. Within the locus we identified the inhibitor of DNA binding 2 (Id2) as a candidate upstream regulator. Id2 was upregulated as an acute phase transcript in injury models of rat retina, brain, and spinal cord. CONCLUSIONS We defined a group of transcriptional changes associated with the retinal acute injury response. Using genetic linkage analysis of natural transcript variation, we identified regulatory loci and candidate regulators that control transcript levels of acute phase genes.
An evaluation of methods for encoding multiple 2D spatial data

Datasets over a spatial domain are common in a number of fields, often with multiple layers (or variables) within data that must be understood together via spatial locality. Thus one area of long-standing interest is increasing the number of variables encoded by properties of the visualization. A number of properties have been demonstrated and/or proven successful with specific tasks or data, but there has been relatively little work comparing the utility of diverse techniques for multi-layer visualization. As part of our efforts to evaluate the applicability of such visualizations, we implemented five techniques which represent a broad range of existing research (Color Blending, Oriented Slivers, Data-Driven Spots, Brush Strokes, and Stick Figures). Then we conducted a user study wherein subjects were presented with composites of three, four, and five layers (variables) using one of these methods and asked to perform a task common to our intended end users (GIS analysts). We found that the Oriented Slivers and Data-Driven Spots performed the best, with Stick Figures yielding the lowest accuracy. Through analyzing our data, we hope to gain insight into which techniques merit further exploration and offer promise for visualization of data sets with ever-increasing size.
Cloning and Expression of Beta Subunit Gene of Phycocyanin From Spirulina platensis in Escherichia coli

Background: C-Phycocyanin (C-PC) from blue-green algae such as Spirulina has been reported to have various pharmacological characteristics, including anti-inﬂammatory and anti-tumor activities. Recombinant β-subunit of C-PC (C-PC/β) is an inhibitor of cell proliferation and an inducer of cancer cell apoptosis. Objectives: Since C-PC/β has a big potential to be used as a promising cancer prevention or therapy agent, the purpose of this study was to clone and express Spirulina platensis cpcB gene in a bacterial expression system. This is a significant step for the production of this compound. Materials and Methods: The cpcB gene was amplified using specific primers and cloned in a bacterial expression vector, namely pET43.1a+. Gene expression of cpcB was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and the dot blotting technique. Results: The SDS-PAGE analysis and dot blotting confirmed the production of recombinant C-PC/β in the bacterial expression system. Over-expression of cpcB gene was optimized in induction by 1 mM Isopropyl-β-D-Thiogalactoside (IPTG), after four hours of inoculation at 30°C. Conclusions: Over-expression of the synthetic CPC/β protein in the bacterial system (Escherichia coli BL-21) showed that E. coli can be used as a basis for further research to produce this desired protein in large quantities.
Effects of Seasonal Variation in Prey Abundance on Field Metabolism, Water Flux, and Activity of a Tropical Ambush Foraging Snake

The responses of animals to seasonal food shortages can have important consequences for population dynamics and the structure and function of food webs. We investigated how an ambush foraging snake, the northern death adder Acanthophis praelongus, responds to seasonal fluctuations in prey availability in its tropical environment. In the dry season, field metabolic rates and water flux, as measured by doubly labeled water, were significantly lower than in the wet season. Unlike some other reptiles of the wet‐dry tropics, death adders showed no seasonal difference in their resting metabolism. About 94% of the decrease in energy expended in the dry season was due to a decrease in activity and digestion, with lower body temperatures accounting for the remainder. In the dry season, death adders were less active and moved shorter distances between foraging sites than in the wet season. Analysis of energy expenditure suggested that adders fed no more than every 2–3 wk in the dry season but fed more frequently during the wet season. Unlike many lizards that cease feeding during the dry season, death adders remain active and attempt to maximize their energy intake year‐round.
Barrier to Autointegration Factor Becomes Dephosphorylated during HSV-1 Infection and Can Act as a Host Defense by Impairing Viral DNA Replication and Gene Expression

BAF (Barrier to Autointegration Factor) is a highly conserved DNA binding protein that senses poxviral DNA in the cytoplasm and tightly binds to the viral genome to interfere with DNA replication and transcription. To counteract BAF, a poxviral-encoded protein kinase phosphorylates BAF, which renders BAF unable to bind DNA and allows efficient viral replication to occur. Herein, we examined how BAF phosphorylation is affected by herpes simplex virus type 1 (HSV-1) infection and tested the ability of BAF to interfere with HSV-1 productive infection. Interestingly, we found that BAF phosphorylation decreases markedly following HSV-1 infection. To determine whether dephosphorylated BAF impacts HSV-1 productive infection, we employed cell lines stably expressing a constitutively unphosphorylated form of BAF (BAF-MAAAQ) and cells overexpressing wild type (wt) BAF for comparison. Although HSV-1 production in cells overexpressing wtBAF was similar to that in cells expressing no additional BAF, viral growth was reduced approximately 80% in the presence of BAF-MAAAQ. Experiments were also performed to determine the mechanism of the antiviral activity of BAF with the following results. BAF-MAAAQ was localized to the nucleus, whereas wtBAF was dispersed throughout cells prior to infection. Following infection, wtBAF becomes dephosphorylated and relocalized to the nucleus. Additionally, BAF was associated with the HSV-1 genome during infection, with BAF-MAAAQ associated to a greater extent than wtBAF. Importantly, unphosphorylated BAF inhibited both viral DNA replication and gene expression. For example, expression of two regulatory proteins, ICP0 and VP16, were substantially reduced in cells expressing BAF-MAAAQ. However, other viral genes were not dramatically affected suggesting that expression of certain viral genes can be differentially regulated by unphosphorylated BAF. Collectively, these results suggest that BAF can act in a phosphorylation-regulated manner to impair HSV-1 transcription and/or DNA replication, which is similar to the antiviral activity of BAF during vaccinia infection.
Design and analysis of a magnetic-geared electronic-continuously variable transmission system using finite element method

This paper proposes a new electronic-continuously variable transmission (E-CVT) system for power-split hybrid electric vehicles (HEVs). The key is to integrate two permanent magnet motor/generators (M/Gs) together with a coaxial magnetic gear (CMG). By designing the modulating ring of the CMG to be rotatable, this integrated machine can achieve both power splitting and mixing, and therefore, can seamlessly match the vehicle road load to the engine optimal operating region. With the one-side-in and one- side-out structure and the non-contact transmission of the CMG, all the drawbacks aroused by the mechanical gears and chain existing in the traditional E-CVT system can be overcome. Moreover, the proposed E-CVT system possesses the merits of small size and light weight, which are vitally important for extending the full-electric drive range of HEVs. The working principle and the design details are elaborated. By using the flnite element method (FEM), the electromagnetic characteristics are analyzed.
Artifact-free JPEG Decompression with Total Generalized Variation

We propose a new model for the improved reconstruction of JPEG (Joint Photographic Experts Group) images. Given a JPEG compressed image, our method first determines the set of possible source images and then specifically chooses one of these source images satisfying additional regularity properties. This is realized by employing the recently introduced Total Generalized Variation (TGV) as regularization term and solving a constrained minimization problem. In order to obtain an optimal solution numerically, we propose a primaldual algorithm. We have developed a parallel implementation of this algorithm for the CPU and the GPU, using OpenMP and Nvidia’s Cuda, respectively. Finally, experiments have been performed, confirming a good visual reconstruction quality as well as the suitability for real-time application.
Multimedia Reasoning with Natural Language Support

In this paper we present an approach that combines multimedia reasoning and natural language processing for the semantic integration of automatic and manual image annotations based on domain ontologies. We discuss how to apply natural language processing to transform natural language descriptions and queries into an ontological representation that allows users to formulate formal semantics in an intuitive manner, without the need to cope with complex ontological structures and unwieldy user interfaces. Illustrative experimental examples demonstrate the added value.
Generating UML diagrams from task models

The importance of task analysis and modelling to software system development is well recognised. After all, the central mission for most software systems is to help users accomplish their tasks. However, while object-oriented analysis and design (OOAD) has been established as the major paradigm in the software industry, effectively incorporating task analysis and modelling into that process is still in the realm of research. In this paper, we propose a novel approach for integrating OOAD and Task Modelling. By exploiting the common semantic ground between task models and system behaviour models, we describe how UML diagrams, such as use cases, use case diagrams and scenario diagrams, can be automatically generated from task models represented in a semi-formal notation. We demonstrate our approach with a working example.
A Novel Complex, RUNX1-MYEF2, Represses Hematopoietic Genes in Erythroid Cells

ABSTRACT RUNX1 is known to be an essential transcription factor for generating hematopoietic stem cells (HSC), but much less is known about its role in the downstream process of hematopoietic differentiation. RUNX1 has been shown to be part of a large transcription factor complex, together with LDB1, GATA1, TAL1, and ETO2 (N. Meier et al., Development 133:4913–4923, 2006) in erythroid cells. We used a tagging strategy to show that RUNX1 interacts with two novel protein partners, LSD1 and MYEF2, in erythroid cells. MYEF2 is bound in undifferentiated cells and is lost upon differentiation, whereas LSD1 is bound in differentiated cells. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and microarray expression analysis were used to show that RUNX1 binds approximately 9,000 target sites in erythroid cells and is primarily active in the undifferentiated state. Functional analysis shows that a subset of the target genes is suppressed by RUNX1 via the newly identified partner MYEF2. Knockdown of Myef2 expression in developing zebrafish results in a reduced number of HSC.
Calmodulin Trapping by Calcium-Calmodulin-Dependent Protein Kinase

Multifunctional calcium-calmodulin-dependent protein kinase (CaM kinase) transduces transient elevations in intracellular calcium into changes in the phosphorylation state and activity of target proteins. By fluorescence emission anisotropy, the affinity of CaM kinase for dansylated calmodulin was measured and found to increase 1000 times after autophosphorylation of the threonine at position 286 of the protein. Autophosphorylation markedly slowed the release of bound calcium-calmodulin; the release time increased from less than a second to several hundred seconds. In essence, calmodulin is trapped by autophosphorylation. The shift in affinity does not occur in a site-directed mutant in which threonine at position 286 has been replaced by a non-phosphorylatable amino acid. These experiments demonstrate the existence of a new state in which calmodulin is bound to CaM kinase even though the concentration of calcium is basal. Calmodulin trapping provides for molecular potentiation of calcium transients and may enable detection of their frequency.
QoC-Based Context Data Caching for Disaster Area Scenarios

Disaster area scenarios are the consequence of sudden and unexpected disasters due to either human or natural causes, such as terrorist attacks and earthquakes. Towards the main goal of saving as many human lives as possible, context-aware services are emerging as standard-de-facto solutions to improve the coordination of involved rescue teams. Unfortunately, the scarce resources (communication bandwidth, memory, etc.) lead to very tough deployment scenarios to deal with. This paper presents our real-world quality-based context data distribution infrastructure for context-aware services in disaster areas. The main contribution is a quality-based caching solution that self-adapts by using quality requirements associated to close neighbors. Collected experimental results confirm that our proposal improves both system scalability and data availability.
Synthesis and testing of reversible Toffoli circuits

Recently, researchers have been interested in reversible computing because of its ability to dissipate nearly zero heat and because of its applications in quantum computing and low power VLSI design. Synthesis and testing are two important areas of reversible logic. The thesis first presents an approach for the synthesis of reversible circuits from the exclusiveOR sum-of-products (ESOP) representation of functions, which makes better use of shared functionality among multiple outputs, resulting in up to 75% minimization of quantum cost compared to the previous approach. This thesis also investigates the previous work on constructing the online testable circuits and points out some design issues. A simple approach for online fault detection is proposed for a particular type of ESOP-based reversible circuit, which is also extended for any type of Toffoli circuits. The proposed online testable designs not only address the problems of the previous designs but also achieve significant improvements of up to 78% and 99% in terms of quantum cost and garbage outputs, respectively.
Disease Burden of Invasive Meningococcal Disease in the Netherlands Between June 1999 and June 2011: A Subjective Role for Serogroup and Clonal Complex.

BACKGROUND Several countries consider the implementation of a meningococcal serogroup B vaccine for young children and/or serogroup C or ACWY conjugate vaccine for adolescents. Representative information on clinical course of invasive meningococcal disease (IMD) is useful to evaluate cost-effectiveness of vaccination. Information on the relation between infecting meningococcal clonal complex (CC), disease course and outcome of IMD is scarce. METHODS A retrospective study using Dutch surveillance data on IMD from June 1999 to June 2011. Clinical information was retrieved from hospital records. The effect of age, comorbidity, clinical manifestation, serogroup, and CC on disease course and outcome was assessed in multivariable analyses. Meningococcal CCs were assessed by multilocus sequence typing. RESULTS Clinical information was retrieved for 879 IMD cases: 48% of patients presented with meningitis, 17% with septic shock, and 22% with septic shock plus meningitis. Development of septic shock was not related to CC or serogroup. Median (interquartile range) duration of hospital admission was 10 (8-13) days. Intensive care unit admittance (38%) was higher for patients aged ≥10 years and patients with septic shock (P-values ≤.001). Case-fatality rate (8%) and development of sequelae (29%) was dependent on age and clinical manifestation (P-values ≤.001) and not affected by comorbidity, CC, or serogroup. CONCLUSIONS IMD still coincides with a considerable disease burden and mortality. Disease course and outcome depend mainly on age and clinical manifestation and less on meningococcal CC or serogroup.
Lead exposure in pheochromocytoma cells induces persistent changes in amyloid precursor protein gene methylation patterns

It has been suggested that lead (Pb) exposure in early life may increase amyloid precursor protein (APP) expression and promote the pathogenesis of Alzheimer's disease in old age. The current study examined whether the DNA methylation patterns of APP gene in rat pheochromocytoma (PC12) cells changed after Pb acetate exposure. Undifferentiated PC12 cells were exposed to three doses of Pb acetate (50, 250, and 500 nM) and one control for 2 days or 1 week. The methylation patterns of APP promoter and global DNA methylation were analyzed. The DNA methyltransferase 1 (DNMT1) expression and the level of amyloid β peptide (Aβ) were also investigated. The results showed that the exposure of the three concentrations of Pb acetate could make the APP promoter hypomethylated. The global DNA methylation level and the expression of DNMT1 were changed in the 500 nM group after 2 days exposure and in the 250 and 500 nM group after 7 days exposure. Thus, Pb may exert neurotoxic effects through mechanisms that alter the global and promoter methylation patterns of APP gene. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.
Time-frequency analysis of heart rate variability for sleep and wake classification

This paper describes a method to adapt the spectral features extracted from heart rate variability (HRV) for sleep and wake classification. HRV series can be derived from electrocardiogram (ECG) signals obtained from single-night polysomnography (PSG) recordings. Traditionally, the HRV spectral features are extracted from the spectrum of an HRV series with fixed boundaries specifying bands of very low frequency (VLF), low frequency (LF), and high frequency (HF). However, because they are fixed, they may fail to accurately reflect certain aspects of autonomic nervous activity, which in turn may limit their discriminative power when using HRV spectral features, e.g., in sleep and wake classification. This is in part related to the fact that the sympathetic tone (partially reflected in the LF band) and the respiratory activity (modulated in the HF band) will vary over time. In order to minimize the impact of these differences, we adapt the HRV spectral boundaries using time-frequency analysis. Experiments conducted on a dataset acquired from 15 healthy subjects show that the discriminative power of the adapted HRV spectral features are significantly increased when classifying sleep and wake. Additionally, this method also provides a significant improvement of the overall classification performance when used in combination with some other (non-spectral) HRV features.
Boosted multiple kernel learning for first-person activity recognition

Activity recognition from first-person (ego-centric) videos has recently gained attention due to the increasing ubiquity of the wearable cameras. There has been a surge of efforts adapting existing feature descriptors and designing new descriptors for the first-person videos. An effective activity recognition system requires selection and use of complementary features and appropriate kernels for each feature. In this study, we propose a data-driven framework for first-person activity recognition which effectively selects and combines features and their respective kernels during the training. Our experimental results show that use of Multiple Kernel Learning (MKL) and Boosted MKL in first-person activity recognition problem exhibits improved results in comparison to the state-of-the-art. In addition, these techniques enable the expansion of the framework with new features in an efficient and convenient way.
Clustering of static-adaptive correspondences for deformable object tracking

We propose a novel method for establishing correspondences on deformable objects for single-target object tracking. The key ingredient is a dissimilarity measure between correspondences that takes into account their geometric compatibility, allowing us to separate inlier correspondences from outliers. We employ both static correspondences from the initial appearance of the object as well as adaptive correspondences from the previous frame to address the stability-plasticity dilemma. The geometric dissimilarity measure enables us to also disambiguate keypoints that are difficult to match. Based on these ideas we build a keypoint-based tracker that outputs rotated bounding boxes. We demonstrate in a rigorous empirical analysis that this tracker outperforms the state of the art on a dataset of 77 sequences.
Memory as Social Glue: Close Interpersonal Relationships in Amnesic Patients

Memory may be crucial for establishing and/or maintaining social bonds. Using the National Social life, Health, and Aging Project questionnaire, we examined close interpersonal relationships in three amnesic people: K.C. and D.A. (who are adult-onset cases) and H.C. (who has developmental amnesia). All three patients were less involved than demographically matched controls with neighbors and religious and community groups. A higher-than-normal percentage of the adult-onset (K.C. and D.A.) cases’ close relationships were with family members, and they had made few new close friends in the decades since the onset of their amnesia. On the other hand, the patient with developmental amnesia (H.C.) had forged a couple of close relationships, including one with her fiancé. Social networks appear to be winnowed, but not obliterated, by amnesia. The obvious explanation for the patients’ reduced social functioning stems from their memory impairment, but we discuss other potentially important factors for future study.
A manipulation environment of virtual and real objects using a magnetic metaphor

This paper describes a method for the consolidated manipulation of virtual and real objects using a "magnetic metaphor". The method reduces the behavioral differences between the virtual and real objects. A limited number of physical laws are selected and simulated for the virtual objects; at the same time, limitations are placed on the physical laws for the real objects. Accordingly, a compromise can be found between the physical laws that operate on virtual objects and those which operate on real objects. Therefore, a system with this method enables a user to manipulate virtual and real objects in a similar manner by expecting the same responses and behaviors according to the same physical laws. Experimental results show that the proposed method improves the task performance in the manipulation of virtual and real objects existing in the same environment simultaneously.