Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways

In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels relative to a mock treatment were measured. One hundred ninety two genes were found to have significantly altered expression between the compatible and incompatible reactions. Among those were genes involved in photosynthesis, the production of reactive oxygen species, ubiquitination, signal transduction, as well as in the shikimate/phenylpropanoid pathway. These data indicate that various metabolic pathways are affected, some of which might be used by RL6003 to mount a coordinated defense against an incompatible fungal pathogen.
International Conference on Information Systems ( ICIS ) 1-1-2008 More Than Just Friends ? Facebook , Disclosive Ethics and the Morality of Technology

Social networking sites have become increasingly popular destinations for people wishing to chat, play games, make new friends or simply stay in touch. Furthermore, many organizations have been quick to grasp the potential they offer for marketing, recruitment and economic activities. Nevertheless, counterclaims depict such spaces as arenas where deception, social grooming and the posting of defamatory content flourish. Much research in this area has focused on the ends to which people deploy the technology, and the consequences arising, with a view to making policy recommendations and ethical interventions. In this paper, we argue that tracing where morality lies is more complex than these efforts suggest. Using the case of a popular social networking site, and concepts about the morality of technology, we disclose the ethics of Facebook as diffuse and multiple. In our conclusions we provide some reflections on the possibilities for action in light of
Necessary and sufficient conditions for bounded distributed mean square tracking of multi‐agent systems with noises

This paper is concerned with the distributed control problem of second‐order agents under directed network topology. The control input of each agent only depends on its own state and the states of its neighbors corrupted by white noises. By using the algebraic graph theory and stochastic analysis method, necessary and sufficient conditions are presented for mean square bounded tracking. Finally, several simulation examples are given to illustrate the results. Copyright © 2015 John Wiley & Sons, Ltd.
Growth Factors Quantification of human cells in NOD / SCID mice by duplex real-time polymerase-chain reaction

ANDREAS NITSCHE,* MICHAEL BECKER,° ILSE JUNGHAHN,° JUTTA AUMANN,° OLFERT LANDT,# IDUNA FICHTNER,° BURGHARDT WITTIG,@ WOLFGANG SIEGERT* *Klinik für Innere Medizin m.S. Hämatologie und Onkologie, Charité Campus, Virchow Klinikum, Humboldt Universität zu Berlin; °Department of Experimental Pharmacology, MaxDelbrück-Center for Molecular Medicine, Berlin; #TIB Molbiol, Berlin; @Institut für Molekularbiologie und Biochemie und Centrum Somatische Gentherapie, UKBF, FU Berlin, Germany original paper
Assessment of systemic and pulmonary arterial remodelling in women with systemic sclerosis

Objectives: Systemic sclerosis (SSc) leads to pulmonary circulation dysfunctionand there are some indications of systemic circulation impairment. We evaluated the influence of SSc on the elastic properties of large systemic arterial walls and potential correlations between systemic and pulmonary circulation involvement. Method: We examined 75 consecutive women (mean age 53.13 ± 10.1 years) with confirmed SSc [mean disease duration (DD) 7.1 ± 9.1 years] and 21 age-matched female volunteers (mean age 52.6 ± 8.3 years, ns). Pulse wave velocity (PWV) and transthoracic echocardiography were performed. SSc patients were divided into two groups according to the median of DD: ≤ 3 years (39 patients) and > 3 years (36 patients). Results: Patients with DD > 3 years had higher PWV than those with DD ≤ 3 years and controls (log PWV: 2.23 ± 0.23 vs. 2.13 ± 0.16 and vs. 2.11 ± 0.16 m/s; p = 0.028 and 0.029, respectively). In addition, echocardiographic indices showed impaired right ventricular (RV) function in the patients with DD > 3 years. Also in these SSc patients, PWV correlated with clinical and echocardiographic parameters of pulmonary circulation: age (r = 0.64, p < 0.0001), acceleration time of pulmonary ejection (AcT; r = −0.38, p = 0.021), and tricuspid regurgitation peak gradient (TRPG; r = 0.34, p = 0.04). Multiple linear regression analysis showed that PWV was independently associated with DD (β = 0.22, p = = 0.02), AcT (β = −0.215, p = 0.03), and age (β = 0.44, p < 0.001). Conclusions: In patients with SSc lasting more than 3 years, the disease is characterized by increased stiffness of the large systemic arteries. Longer duration of SSc leads simultaneously to the increased stiffness of the large systemic arteries and to the progressive impairment of RV function and its coupling to the pulmonary arterial bed.
Synchronization Dynamics in Response to Plaid Stimuli in Monkey V1

Gamma synchronization has generally been associated with grouping processes in the visual system. Here, we examine in monkey V1 whether gamma oscillations play a functional role in segmenting surfaces of plaid stimuli. Local field potentials (LFPs) and spiking activity were recorded simultaneously from multiple sites in the opercular and calcarine regions while the monkeys were presented with sequences of single and superimposed components of plaid stimuli. In accord with the previous studies, responses to the single components (gratings) exhibited strong and sustained gamma-band oscillations (30–65 Hz). The superposition of the second component, however, led to profound changes in the temporal structure of the responses, characterized by a drastic reduction of gamma oscillations in the spiking activity and systematic shifts to higher frequencies in the LFP (∼10% increase). Comparisons between cerebral hemispheres and across monkeys revealed robust subject-specific spectral signatures. A possible interpretation of our results may be that single gratings induce strong cooperative interactions among populations of cells that share similar response properties, whereas plaids lead to competition. Overall, our results suggest that the functional architecture of the cortex is a major determinant of the neuronal synchronization dynamics in V1.
Correction for “ Lipopeptide nanoparticles for potent and selective siRNA delivery in rodents and nonhuman primates

ENGINEERING Correction for “Lipopeptide nanoparticles for potent and selective siRNA delivery in rodents and nonhuman primates,” by Yizhou Dong, Kevin T. Love, J. Robert Dorkin, Sasilada Sirirungruang, Yunlong Zhang, Delai Chen, Roman L. Bogorad, Hao Yin, Yi Chen, Arturo J. Vegas, Christopher A. Alabi, Gaurav Sahay, Karsten T. Olejnik, Weiheng Wang, Avi Schroeder, Abigail K. R. Lytton-Jean, Daniel J. Siegwart, Akin Akinc, Carmen Barnes, Scott A. Barros, Mary Carioto, Kevin Fitzgerald, Julia Hettinger, Varun Kumar, Tatiana I. Novobrantseva, June Qin, William Querbes, Victor Koteliansky, Robert Langer, and Daniel G. Anderson, which appeared in issue 11, March 18, 2014, of Proc Natl Acad Sci USA (111:3955–3960; first published February 10, 2014; 10.1073/pnas.1322937111). The authors note that they omitted additional funding sources in the Acknowledgments. The corrected Acknowledgments section should instead appear as “The authors thank the Koch Institute Swanson Biotechnology Center for technical support, specifically Flow Cytometry Core. This work was supported by the National Cancer Institute Center of Cancer Nanotechnology Excellence at MIT-Harvard (U54-CA151884), the National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), as a Program of Excellence in Nanotechnology (PEN) Award, Contract #HHSN268201000045C, as well as by Alnylam Pharmaceuticals and the NIH Grants R01-EB000244–27, 5-R01-CA132091–04, and R01-DE016516–03. Y.D. acknowledges support from the National Institute of Biomedical Imaging and Bioengineering for his postdoctoral fellowship 1F32EB017625. ”
Modeling the role of the basal ganglia in motor control and motor programming

The basal ganglia (BG) are a group of highly interconnected nuclei buried deep in the brain. They are involved in an important range of brain functions, including both lower-level movement control and higher-level cognitive decision making. Dysfunction of the BG has been linked to the human neurological disorders such as Parkinson's disease, Huntington's disease, and schizophrenia. This thesis proposes a uniied functional model of the BG, called multi-input multi-output adaptive switching (MIMOAS) model that attempts to account for the role of the BG in both higher-level rote behavior and lower-level motor control. In the model, BG circuitry eeectively implements a large set of parallel noncompetitive logical OR and NOR circuits that can be driven by speciic patterns of cortical activity. These aaord selective gating of target thalamocortical neurons. This process can be viewed as a general mapping between binary context and response vectors. The mapping is proved to be learnable via a reinforcement mechanism that is consistent with actions commonly proposed for nigro-striatal dopaminergic pathways in the striatum and homeostasis in synaptic physiology. It appears that the cortico-striatal connections provide a biologically plausible realization of winner-take-all dynamics that is diierent from many engineering alternatives implementing the same function. With the winner-take-all units as functioning as a hidden layer, using corticostriatal weights as the only tunable parameters, the adaptive BG network can develop the capacity to perform universal binary mappings. In this way, the model can simulate important features of procedural learning in human experiments. At the same time, it can be shown that derangement of the winner-take-all dynamics could underlie the tremor and rigidity seen in Parkinson's disease. Title: Associate Professor of Aeronautics and Astronautics 3 4 Acknowledgments First I would like to express my deepest gratitude to my two advisors and Ph.D. thesis supervisors, Prof. Eric Feron and Prof. Steve Massaquoi. Eric is such a caring mentor to me. It is his strongest support, both intellectual and emotional, that have helped me through these unforgettable seven years at MIT (Eric was also my Masters thesis supervisor). I beneeted greatly from his wild and insightful imagination and constant enthusiasm in research. He is my perfect role model in academia as well as in life. Steve is my rst and, by all means, best teacher of neuroengineering. He introduced me to this fantastic world of brain research, and this thesis grew out of his original idea on the basal ganglionic function. …
A multi-level secure file sharing server and its application to a multi-level secure cloud

Contemporary cloud environments are built on low-assurance components, so they cannot provide a high level of assurance about the isolation and protection of information. A “multi-level” secure cloud environment thus typically consists of multiple, isolated clouds, each of which handles data of only one security level. Not only are such environments duplicative and costly, data “sharing” must be implemented by massive, wasteful copying of data from low-level domains to high-level domains. The requirements for certifiable, scalable, multi-level cloud security are threefold: 1) To have trusted, high-assurance components available for use in creating a multi-level secure cloud environment; 2) To design a cloud architecture that efficiently uses the high-assurance components in a scalable way, and 3) To compose the secure components within the scalable architecture while still verifiably maintaining the system security properties. This paper introduces a trusted, high-assurance file server and architecture that satisfies all three requirements. The file server is built on mature technology that was previously certified and deployed across domains from TS/SCI to Unclassified and that supports high-performance, low-to-high and high-to-low file sharing with verifiable security.
Comparison of Virtualization Algorithms and Topologies for Data Center Networks

Data centers are core infrastructure of cloud computing. Network virtualization in these centers is a promising solution that enables coexistence of multiple virtual networks on a shared infrastructure. It offers flexible management, lower implementation cost, higher network scalability, increased resource utilization, and improved energy efficiency. In this paper, we consider switch-centric data center network topologies and evaluate their use for network virtualization by comparing Deterministic (D-ViNE) and Randomized (R-ViNE) Virtual Network Embedding, Global Resource Capacity (GRC), and Global Resource Capacity-Multicommodity (GRC-M) Flow algorithms.
Characterizing home wireless performance: The gateway view

In this paper, we analyze a large dataset of passive wireless measurements and obtain insights about wireless performance. We monitor 167 homes continuously for 4 months from the vantage point of the gateway, which allows us to capture all the activity on the home wireless network. We report on the makeup of the home wireless network, traffic activity, and performance characteristics. We find that in most homes, a small number of devices account for most of the observed traffic volume and the bulk of this traffic activity occurs in the evenings. Studying link performance, we find that overall, the vast majority of transmissions are carried out at high data rates and the wireless networks have good coverage. We find a small number of episodes where performance is poor; a few homes have a disproportionate number of poor performance reports. Investigating further, we observe that most of these are not caused by poor coverage (pointing to network interference). Our results significantly add to the understanding of home wireless networks and will help ISPs to understand their subscriber networks.
Relevancy based semantic interoperation of reuse repositories

Software reuse is a promising solution to the software crisis. Reuse repositories are the basic infrastructure for software reuse. During the past decade, various academic, commercial, governmental, and industrial organizations have developed many Internet-enabled reuse repositories to provide access to software components and related resources. It has necessitated semantic interoperation to allow distributed maintenance and management of these repositories while enabling users to efficiently and conveniently access resources from multiple reuse repositories via a single representation view. In this paper, we have proposed an approach to enhancing the semantic interoperability of reuse repositories, called the improved relevancy matching and ranking (IRMR) method, based on analyzing the correlation of terms in representation methods of the repositories. A prototype system, the Virtual Repository supporting Semantic Interoperation (VRSI), is presented to illustrate the application of this approach to support the semantic interoperation of reuse repositories. Experimental results on real world reuse repositories demonstrated significant improvement in terms of searching effectiveness.
Unrelated umbilical cord blood transplantation and unrelated bone marrow transplantation in children with hematological disease: A meta‐analysis

Abstract: UCB has been used as an alternative source of HSC. Both unrelated donor BM and UCB are available as potential options for transplantation. However, there have been limited comparisons of the outcomes of unrelated donor UCBT vs. UBMT in the unrelated setting. Our aim is to observe the therapeutic efficacy of UCBT and UBMT for treatment of pediatric hematological diseases. We electronically searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and critically appraised all relevant articles (1989.1–2008.5). Comparative studies were carried out on clinical therapeutic effect of UCBT and UBMT with research on stem cells engraftment, complications, earlier mortality, and survival rate. We performed a meta‐analysis using review manager 5.0 software (RevMan, The Nordic Cochrane Center, The Cochrane Collaboration) and adopted funnel plot regression to assess the publication bias. We obtained 324 records. Seven trials totaling 1453 patients have been assessed. Pooled comparisons of studies of UCBT and UBMT in children found that the incidence of engraftment failure and earlier transplantation‐related mortality were higher with UCBT because of its delay of hematological recovery [OR = 4.96, 95% CI (3.25, 7.59), p < 0.00001 and OR = 2.36, 95% CI (1.79, 3.11), p < 0.00001 respectively], but CMV infection didn’t increase obviously. There was no difference in long disease‐free survival rate [OR = 0.85, 95% CI (0.65, 1.01), p = 0.06] between UCBT and UBMT due to the decrease of GVHD in UCBT [OR = 0.45, 95% CI (0.34, 0.60), p < 0.0001]. Our meta‐analysis confirmed that UCBT in children is also an effective way to treat children with hematological disease and has equivalent survival outcomes compared with UBMT.
An enhanced user authentication solution for mobile payment systems using wearables

As technology continues to evolve, banks and other enterprises are restructuring their businesses to provide services to customers anywhere and anytime. However, it is challenging to move from conventional payment systems toward digital wallets across a range of payment services. Mobile devices are easily lost or stolen, so the rapid adoption of mobile devices for payment systems requires protection against unauthorized access to private applications and data. When mobile devices communicate with merchant point-of-sale systems, there is a risk of data leakage because third party applications in point-of-sale systems might access private data stored on the device without the user's knowledge or permission. We thus propose the use of wearable devices to store partial private data for the user and to participate in the user authentication. In this paper, we design a practical user authentication solution for mobile payment systems, and the main idea is to split the user's private data, such as credit card and banking information, and then store them across two separate devices e.g., a smartphone and a wearable device. Our solution can improve the security of existing mobile payment systems that utilize user biometrics as an authentication factor, such as Apple Pay and Samsung Pay. Copyright © 2016 John Wiley & Sons, Ltd.
The Description-Experience Gap in Risky Choice: The Role of Sample Size and Experienced Probabilities

Risky prospects come in different forms. Sometimes options are presented with convenient descriptions summarizing outcomes and their respective likelihoods. People can thus make decisions from description. In other cases people must call on their encounters with such prospects, making decisions from experience. Recent studies report a systematic and large description-experience gap. One key determinant of this gap is people`s tendency to rely on small samples resulting in substantial sampling error. Here we examine whether this gap exists even when people draw on large samples. Although smaller, the gap persists. We use the choices of the present and previous studies to test a large set of candidate strategies that model decisions from experience, including 12 heuristics, two associative-learning models and the two-stage model of cumulative prospect theory. This model analysis suggests-as one explanation for the remaining description-experience gap in large samples-that people treat probabilities differently in both types of decisions. Copyright (c) 2008 John Wiley & Sons, Ltd.
DARSHANA: Detecting route hijacking for communication confidentiality

The Border Gateway Protocol (BGP) plays a critical role in the Internet providing connectivity to hosts across the world. Unfortunately, due to its limited security, attackers can hijack traffic by generating invalid routes. Some detection systems for route hijacking have been presented, but they require non-public information, high resources, or can easily be circumvented by attackers. We propose DARSHANA, a monitoring solution that detects route hijacking based solely on data-plane information, and has enough redundancy to prevent attacker countermeasures such as dropping of traceroute probes. DARSHANA uses active probing techniques that enable detection in near real-time. By using diverse methods, DARSHANA can still detect attacks even if the adversary manages to counter some techniques. We show that our solution allows effective detection of many hijacking attacks by emulating them using PlanetLab and Amazon AWS.
Chikungunya Fever: A Clinical and Virological Investigation of Outpatients on Reunion Island, South-West Indian Ocean

Background Chikungunya virus (CHIKV) is responsible for acute febrile polyarthralgia and, in a proportion of cases, severe complications including chronic arthritis. CHIKV has spread recently in East Africa, South-West Indian Ocean, South-Asia and autochthonous cases have been reported in Europe. Although almost all patients are outpatients, medical investigations mainly focused on hospitalised patients. Methodology/Principal Findings Here, we detail clinico-biological characteristics of Chikungunya (CHIK) outpatients in Reunion Island (2006). 76 outpatients with febrile arthralgia diagnosed within less than 48 hours were included by general practitioners during the CuraChik clinical trial. CHIK was confirmed in 54 patients and excluded in 22. A detailed clinical and biological follow-up was organised, that included analysis of viral intrahost diversity and telephone survey until day 300. The evolution of acute CHIK included 2 stages: the ‘viral stage’ (day 1–day 4) was associated with rapid decrease of viraemia and improvement of clinical presentation; the ‘convalescent stage’ (day 5–day 14) was associated with no detectable viraemia but a slower clinical improvement. Women and elderly had a significantly higher number of arthralgia at inclusion and at day 300. Based on the study clinico-biological dataset, scores for CHIK diagnosis in patients with recent febrile acute polyarthralgia were elaborated using arthralgia on hands and wrists, a minor or absent myalgia and the presence of lymphopenia (<1G/L) as major orientation criteria. Finally, we observed that CHIKV intra-host genetic diversity increased over time and that a higher viral amino-acid complexity at the acute stage was associated with increased number of arthralgia and intensity of sequelae at day 300. Conclusions/Significance This study provided a detailed picture of clinico-biological CHIK evolution at the acute phase of the disease, allowed the elaboration of scores to assist CHIK diagnosis and investigated for the first time the impact of viral intra-host genetic diversity on the disease course.
Video Segmentation Using Acoustic Analysis

Video segmentation is a key step for the long videos recorded from Television channels to be represented in the hierarchical structure. In this paper, a novel approach based on acoustic cues for automatic segmenting television stream into individual programs is proposed. This presented method is composed of the following steps: Several sets of repetitions in the audio track is detected by using silence detection and robust audio hashing; The found repetitions are treated as advertisements if the range of their length is from 5 seconds to 120 seconds; Programs are segmented from the recorded TV streams using the detected advertisements. Experiments on real-world TV recordings show the effectiveness of the proposed approach.