Miracle-dz/UniFAR-FTUs huggingface dataset:
EVALUATION OF SIGNAL SEQUENCES FOR THE DELIVERY OF TRANSGENE PRODUCTS INTO THE XYLEM OF GRAPEVINE Project Leader

Xylella fastidiosa (Xf), a gram-negative bacterium, is the causative agent of Pierce’s disease (PD) in grapevines. Because Xf is xylem-limited, it will be essential that any anti-Xylella gene product be present in the xylem in an effective concentration. Work on understanding the mechanism of how proteins are targeted to this plant compartment will be relevant for the delivery of therapeutic proteins into the xylem. In addition, it will be a useful tool for Xylella and glassy-wing sharpshooter (GWSS) gene function studies. This is a continuing project that began in late 2005. In our earlier research we collected xylem exudates from grapevines and analyzed its protein composition by two-dimensional gel electrophoresis. Peptide spectrum and Blast analysis showed that the proteins found in the exudates are secreted proteins that share function similarities with proteins found in xylem exudates of other species. The corresponding cDNA sequences of five of them were found in the TIGR Vitis vinifera gene index. Two of these sequences for xylem proteins Chi1b and one similar to NtPRp27 were fused to the mature pear polygalacturonase inhibiting protein (pPGIP)-encoding gene. We also made three other constructs incorporating signal peptides from the xylem sap protein XSP30, the rice amylase protein Ramy3D that we have described in earlier reports along with pPGIP lacking a signal peptide as control. We have successfully transformed Vitis vinifera ‘Thompson Seedless’ (TS) grape with the five vectors and callus and embryo cultures for all five vectors have been obtained. The expression of these chimeric genes is being evaluated in permanent transformations in order to evaluate their ability to target pPGIP to the xylem. We have successfully obtained Chi1b and Nt transformed TS plants that are PCR positive for the transgene. Using a zone inhibition assay, we have determined that seven out of 15 plants tested so far are positive for polygalacturonase inhibiting activity. Micropropagation of promising transformants and bench grafting of transgenic rootstock to wildtype scions are currently underway. The results of this research will not only be applied in projects that test anti-Xylella gene products that should be delivered into the xylem but also in functional studies that are intended to target the products of Xf and GWSS genes to the xylem.
Characterization of the Molecular Determinants of Primary HIV-1 Vpr Proteins: Impact of the Q65R and R77Q Substitutions on Vpr Functions

Although HIV-1 Vpr displays several functions in vitro, limited information exists concerning their relevance during infection. Here, we characterized Vpr variants isolated from a rapid and a long-term non-progressor (LTNP). Interestingly, vpr alleles isolated from longitudinal samples of the LTNP revealed a dominant sequence that subsequently led to diversity similar to that observed in the progressor patient. Most of primary Vpr proteins accumulated at the nuclear envelope and interacted with host-cell partners of Vpr. They displayed cytostatic and proapoptotic activities, although a LTNP allele, harboring the Q65R substitution, failed to bind the DCAF1 subunit of the Cul4a/DDB1 E3 ligase and was inactive. This Q65R substitution correlated with impairment of Vpr docking at the nuclear envelope, raising the possibility of a functional link between this property and the Vpr cytostatic activity. In contradiction with published results, the R77Q substitution, found in LTNP alleles, did not influence Vpr proapoptotic activity.
STF behaviour in a CT ΔΣ modulator

In this paper we propose a topology for continuous time SigmaDelta modulators. Unlike the modulators presented until now, they exhibit no peaking in their signal transfer function. Instead it achieves a 'flat' STF with the desired anti-aliasing properties and with small internal nodes signal levels. Now, a simple filter, e.g. a first-order low-pass filter can precede the modulator to prevent out of band signals corrupting the correct operation of the modulator.
An ongoing OO software engineering measurement experiment

This paper reports on an ongoing software measurement experiment which has been set up to monitor and evaluate team based student projects building object-oriented software. In this experiment, students are building the same system, in two languages (Eiffel and Smalltalk). Our process, called the Software Assessment Through Ongoing Profile Sheets (SATOPS) is being used in a project management framework to provide: a more objective feedback to improve students' learning; a method for measuring their understanding for grading purposes; and an instrument for making software engineering metrics measurements. We argue that SATOPS is the basis for reproducible software engineering experiments in a university environment.
Thermal-aware memory mapping in 3D designs

DRAM is usually used as main memory for program execution. The thermal behavior of a memory block in a 3D SIP is affected not only by the power behavior but also the heat dissipating ability of that block. The power behavior of a block is related to the applications run on the system while the heat dissipating ability is determined by the number of tier and the position the block locates. Therefore, a thermal-aware memory allocator should consider the following two points. First, allocator should consider not only the power behavior of a memory block but also the physical location during memory mapping, second, the changing temperature of a physical block during execution of programs. In this paper, we will propose a memory mapping algorithm taking into consideration the above-mentioned two points. Our technique can be classified as static thermal management to be applied to embedded software designs. Experiments show that our method can reduce temperature of memory system by 17.2°C as compared to a straightforward mapping in the best case, and 13.4°C in average.
Information technology acceptance: evolving with the changes in the network environment

The existing models of information technology (IT) acceptance were developed with the concept of the static individual computing environment in mind. As such, in today's rapidly changing IT environment, they do not serve as adequate indicators of an individual's IT usage behavior. The author addresses this problem by first carefully observing the changing needs of a user, and discussing network (distributed computing) trends of the IT environment. He enhances the existing models of IT by introducing several factors, including internal personal belief factors, external social belief factors, and other relevant determinants based on network externality and complementarity that influence an individual to use IT. He begins with the review of what other researchers have done on the topics of the adoption and diffusion of IT. He does this by reexamining and recognizing the theoretical contributions and empirical findings of various researchers. He discusses the key determinants of IT use and diffusion in a distributed network computing environment. He integrates the factors into his model by carefully evaluating their applicability. Lastly, he discusses the contribution of the model for future empirical research in the field. In all, he proposes a more enriched model of IT acceptance by combining the behavioral models of IT acceptance and the models of IT diffusion from various other disciplines (i.e., marketing, economics, etc).
Sulfide as a signaling molecule in autophagy

Hydrogen sulfide is already recognized as an important signaling molecule in mammalian systems, and emerging data suggest that H2S is a signaling molecule just as important as nitric oxide (NO) and H2O2 in plants. Although sulfide is generated in chloroplasts and mitochondria, it is present predominantly in the charged HS- form due to the basic pH inside both organelles, thus requiring an active transporter, which is yet to be identified, to be released. In Arabidopsis, we found that the cytosolic L-cysteine desulfhydrase DES1 is involved in the degradation of cysteine, and therefore responsible for the generation of H2S in this cellular compartment. DES1 deficiency leads to the induction of autophagy. Moreover, we have demonstrated that sulfide in particular exerts a general effect on autophagy through negative regulation, in a way unrelated to nutrient deficiency. The mechanisms of H2S action and its molecular targets are largely unknown, although in animal systems, protein S-sulfhydration has been proposed as a mechanism for sulfide-mediated signaling.
Astaxanthin Suppresses MPP+-Induced Oxidative Damage in PC12 Cells through a Sp1/NR1 Signaling Pathway

Objective: To investigate astaxanthin (ATX) neuroprotection, and its mechanism, on a 1-methyl-4-phenyl-pyridine ion (MPP+)-induced cell model of Parkinson’s disease. Methods: Mature, differentiated PC12 cells treated with MPP+ were used as an in vitro cell model. The MTT assay was used to investigate cell viability after ATX treatment, and western blot analysis was used to observe Sp1 (activated transcription factor 1) and NR1 (NMDA receptor subunit 1) protein expression, real-time PCR was used to monitor Sp1 and NR1 mRNA, and cell immunofluorescence was used to determine the location of Sp1 and NR1 protein and the nuclear translocation of Sp1. Results: PC12 cell viability was significantly reduced by MPP+ treatment. The expression of Sp1 and NR1 mRNA and protein were increased compared with the control (p < 0.01). Following co-treatment with ATX and MPP+, cell viability was significantly increased, and Sp1 and NR1 mRNA and protein were decreased, compared with the MPP+ groups (p < 0.01). In addition, mithracycin A protected PC12 cells from oxidative stress caused by MPP+ by specifically inhibiting the expression of Sp1. Moreover, cell immunofluorescence revealed that ATX could suppress Sp1 nuclear transfer. Conclusion: ATX inhibited oxidative stress induced by MPP+ in PC12 cells, via the SP1/NR1 signaling pathway.
Building and Optimizing MRAM-Based Commodity Memories

Emerging non-volatile memory technologies such as MRAM are promising design solutions for energy-efficient memory architecture, especially for mobile systems. However, building commodity MRAM by reusing DRAM designs is not straightforward. The existing memory interfaces are incompatible with MRAM small page size, and they fail to leverage MRAM unique properties, causing unnecessary performance and energy overhead. In this article, we propose four techniques to enable and optimize an LPDDRx-compatible MRAM solution: ComboAS to solve the pin incompatibility; DynLat to avoid unnecessary access latencies; and EarlyPA and BufW to further improve performance by exploiting the MRAM unique features of non-destructive read and independent write path. Combining all these techniques together, we boost the MRAM performance by 17% and provide a DRAM-compatible MRAM solution consuming 21% less energy.
Effects of a Caffeine-Containing Energy Drink on Simulated Soccer Performance

Background To investigate the effects of a caffeine-containing energy drink on soccer performance during a simulated game. A second purpose was to assess the post-exercise urine caffeine concentration derived from the energy drink intake. Methodology/Principal Findings Nineteen semiprofessional soccer players ingested 630±52 mL of a commercially available energy drink (sugar-free Red Bull®) to provide 3 mg of caffeine per kg of body mass, or a decaffeinated control drink (0 mg/kg). After sixty minutes they performed a 15-s maximal jump test, a repeated sprint test (7×30 m; 30 s of active recovery) and played a simulated soccer game. Individual running distance and speed during the game were measured using global positioning satellite (GPS) devices. In comparison to the control drink, the ingestion of the energy drink increased mean jump height in the jump test (34.7±4.7 v 35.8±5.5 cm; P<0.05), mean running speed during the sprint test (25.6±2.1 v 26.3±1.8 km · h−1; P<0.05) and total distance covered at a speed higher than 13 km · h−1 during the game (1205±289 v 1436±326 m; P<0.05). In addition, the energy drink increased the number of sprints during the whole game (30±10 v 24±8; P<0.05). Post-exercise urine caffeine concentration was higher after the energy drink than after the control drink (4.1±1.0 v 0.1±0.1 µg · mL−1; P<0.05). Conclusions/significance A caffeine-containing energy drink in a dose equivalent to 3 mg/kg increased the ability to repeatedly sprint and the distance covered at high intensity during a simulated soccer game. In addition, the caffeinated energy drink increased jump height which may represent a meaningful improvement for headers or when players are competing for a ball.
What you Sculpt is What you Get: Modeling Physical Interactive Devices with Clay and 3D Printed Widgets

We present a method for fabricating prototypes of interactive computing devices from clay sculptures without requiring the designer to be skilled in CAD software. The method creates a "what you sculpt is what you get" process that mimics the "what you see is what you get" processes used in interface design for 2D screens. Our approach uses clay for modeling the basic shape of the device around 3D printed representations, which we call "blanks", of physical interaction widgets such as buttons, sliders, knobs and other electronics. Each blank includes 4 fiducial markers uniquely arranged on a visible surface. After scanning the sculpture, these fiducial marks allow our software to identify widget types and locations in the scanned model. The software then converts the scan into a printable prototype by positioning mounting surfaces, openings for the controls and a splitting plane for assembly. Because the blanks fit in the sculpted shape, they will reliably fit in the interactive prototype. Creating an interactive prototype requires about 30 minutes of human effort for sculpting, and after scanning, involves a single button click to use the process.
Causal reasoning on biological networks: interpreting transcriptional changes

MOTIVATION The interpretation of high-throughput datasets has remained one of the central challenges of computational biology over the past decade. Furthermore, as the amount of biological knowledge increases, it becomes more and more difficult to integrate this large body of knowledge in a meaningful manner. In this article, we propose a particular solution to both of these challenges. METHODS We integrate available biological knowledge by constructing a network of molecular interactions of a specific kind: causal interactions. The resulting causal graph can be queried to suggest molecular hypotheses that explain the variations observed in a high-throughput gene expression experiment. We show that a simple scoring function can discriminate between a large number of competing molecular hypotheses about the upstream cause of the changes observed in a gene expression profile. We then develop an analytical method for computing the statistical significance of each score. This analytical method also helps assess the effects of random or adversarial noise on the predictive power of our model. RESULTS Our results show that the causal graph we constructed from known biological literature is extremely robust to random noise and to missing or spurious information. We demonstrate the power of our causal reasoning model on two specific examples, one from a cancer dataset and the other from a cardiac hypertrophy experiment. We conclude that causal reasoning models provide a valuable addition to the biologist's toolkit for the interpretation of gene expression data. AVAILABILITY AND IMPLEMENTATION R source code for the method is available upon request.
Analysis of watermarking systems in the frequency domain and its application to design of robust watermarking systems

This paper aims to design robust watermarking systems in the frequency domain. We first present the general model of watermark embedding and extracting processes and carry out their analysis. Then we examine the robustness of the watermarking system against common image processing and clarify the reason why detection errors occur in the watermark extracting process. Based on the result, we improve the watermark extracting process and design the robust watermarking systems. The improvement is accomplished using deconvolution filter and neural network techniques. Numerical experiments using the DCT-based watermarking system show good performance as we expected.
The design and evaluation of a high-performance soft keyboard

The design and evaluation of a high performance soft keyboardfor mobile systems are described. Using a model to predict theupper-bound text entry rate for soft keyboards, we designed akeyboard layout with a predicted upper-bound entry rate of 58.2wpm. This is about 35% faster than the predicted rate for a QWERTYlayout. We compared our design (OPTI) with a QWERTY layout in alongitudinal evaluation using five participants and 20 45-minutesessions of text entry. Average entry rates for OPT1 increased from17.0 wpm initially to 44.3 wpm at session 20. The average ratesexceeded those for the QWERTY layout after the 10 session (about 4hours of practice). A regression equation (R = .997) in the form ofthe power-law of learning predicts that our upper-bound predictionwould be reach at about session 50.
IDH1/IDH2 Mutations Define the Prognosis and Molecular Profiles of Patients with Gliomas: A Meta-Analysis

Background Isocitrate dehydrogenase isoforms 1 and 2 (IDH1 and IDH2) mutations have received considerable attention since the discovery of their relation with human gliomas. The predictive value of IDH1 and IDH2 mutations in gliomas remains controversial. Here, we present the results of a meta-analysis of the associations between IDH mutations and both progression-free survival (PFS) and overall survival (OS) in gliomas. The interrelationship between the IDH mutations and MGMT promoter hypermethylation, EGFR amplification, codeletion of chromosomes 1p/19q and TP53 gene mutation were also revealed. Methodology and Principal Findings An electronic literature search of public databases (PubMed, Embase databases) was performed. In total, 10 articles, including 12 studies in English, with 2,190 total cases were included in the meta-analysis. The IDH mutations were frequent in WHO grade II and III glioma (59.5%) and secondary glioblastomas (63.4%) and were less frequent in primary glioblastomas (7.13%). Our study provides evidence that IDH mutations are tightly associated with MGMT promoter hypermethylation (P<0.001), 1p/19q codeletion (P<0.001) and TP53 gene mutation (P<0.001) but are mutually exclusive with EGFR amplification (P<0.001). This meta-analysis showed that the combined hazard ratio (HR) estimate for overall survival and progression-free survival in patients with IDH mutations was 0.33 (95% CI: 0.25–0.42) and 0.38 (95% CI: 0.21–0.68), compared with glioma patients whose tumours harboured the wild-type IDH. Subgroup analyses based on tumour grade also revealed that the presence of IDH mutations was associated with a better outcome. Conclusion Our study suggests that IDH mutations, which are closely linked to the genomic profile of gliomas, are potential prognostic biomarkers for gliomas.
Investigating the impact of network topology on the processing times of SDN controllers

Software Defined Networking (SDN) introduces the concept of logically-centralized controllers in charge of managing the forwarding behavior of network elements. The new possibilities enabled through the centralization of control logic come with a certain risk: The controller might become a performance bottleneck. Therefore, ensuring sufficient controller performance is one of the crucial tasks prior to a successful SDN deployment. Furthermore, fine-grained traffic engineering, e.g., to achieve higher link utilization, results in a higher frequency of requests that are sent to the controller, which leads to an increased controller load. It is therefore important to analyze the capabilities of SDN controllers prior to deployment. This paper investigates two software implementations, the OpenDaylight and Ryu controllers. The control message throughput of different controllers has been studied several times already; however, it is not yet known what influence the number and topology of connected switches have. This paper investigates this influence in detail for a fat-tree data center topology and a WAN topology as well as 261 topologies with varying characteristics from the Internet Topology Zoo.
An Investigation of Tourists' Patterns of Obligation to Protect the Environment

The environmental sustainability of the local tourism industry is increasingly a concern. Authors have proposed a demand-driven approach to sustainable destination management as complementary to traditional supply-side interventions. However, little empirical evidence supports the feasibility of such a demand-driven approach. This study contributes to this gap by investigating whether individuals who feel morally obliged to behave in an environmentally friendly manner represent useful target segments for destination management aiming to improve the ecological sustainability of the local tourism industry. Results indicate that distinctly different moral obligation segments exist that differ in pro-environmental behavior and attitudes. These segments are associated with distinctly different vacation preferences and can consequently be used by destination management for target marketing. Gaps between people's pro-environmental behavior at home and at the destination systematically differ across segments, leading to the conclusion that different combinations of demand and supply-side measures may be suitable to reduce the environmental footprint of different segments.
LSOD: Local Sparse Orthogonal Descriptor for Image Matching

We propose a novel method for feature description used for image matching in this paper. Our method is inspired by the autoencoder, an artificial neural network designed for learning efficient codings. Sparse and orthogonal constraints are imposed on the autoencoder and make it a highly discriminative descriptor. It is shown that the proposed descriptor is not only invariant to geometric and photometric transformations (such as viewpoint change, intensity change, noise, image blur and JPEG compression), but also highly efficient. We compare it with existing state-of-the-art descriptors on standard benchmark datasets, the experimental results show that our LSOD method yields better performance both in accuracy and efficiency.
Sentence Induced Transformations in "Conceptual" Spaces

The proposed work illustrates how "primitive concepts" can be automatically induced from a text corpus. The primitive concepts are identified by the orthonormal axis of a "conceptual" space induced by a methodology inspired tothe latent semantic analysis approach. The methodology represents a natural language sentence by means of a set of rotations of an orthonormal basis in the "conceptual"space. The rotations, triggered by the sequence of words composing the sentence and realized by means of geometric algebra rotors, allow to highlight "conceptual" relations that can arise among the primitive concepts.