Miracle-dz/UniFAR-FTUs huggingface dataset:
Salmonella typhimurium pgtB mutants conferring constitutive expression of phosphoglycerate transporter pgtP independent of pgtC

PgtC is one of the three components of the atypical "two-component" pgt regulatory system. To investigate whether functional PgtC required for the induction of pgtP expression could be bypassed in the signal transduction process, we sought, and succeeded in isolating, intergenic suppressors arising in the low-copy mini-F plasmid, pSJ11, bearing the entire pgt system except for a 168-bp deletion near the end of the pgtC gene. By transport assays, these suppressors were found to confer constitutive pgtP expression. Intriguingly, all five mutations reside near the 5' end of the pgtB gene, at codons 19 and 21. One mutation alters Arg-19 to Gln, two alter Ala-21 to Thr, one alters Ala-21 to Val, and one alters Ala-21 to Ile. Appropriate strains in which the pgtP promoter was fused to lacZ and which bore the pgtB mutations with and without mutations in pgtC and pgtA genes were constructed, and the epistatic relationships of the wild-type pgtC allele, a mutant pgtA allele, and an essentially total deletion of pgtC to the constitutive pgtB mutations were determined. In the mutant strains bearing the Ala-21 --> Ile and Ala-21 --> Val substitutions, the level of constitutive pgtP-lacZ reporter expression was not affected by the presence of the wild-type pgtC allele, nor was it affected by the total absence of PgtC in the case of the Ala-21 --> Val alteration examined; however, in the mutant strains bearing the Ala-21 --> Thr and the Arg-19 --> Gln substitutions, the extent of constitutive pgtP-lacZ reporter expression was markedly enhanced by the presence of wild-type pgtC allele and, in the case of the Arg-19 -->Gln change examined, by the total absence of PgtC as well. These results indicate that PgtC contains no domain necessary for the kinase activity; that PgtB can be activated in the absence of PgtC mutational alterations of the protein itself; and that PgtB and PgtC interact in the signaling process, with PgtC functioning to activate and modulate the kinase activity of Pgtb. In all strains, the replacement of the wild type pgtA allele with a mutant pgtA allele completely abolished expression of the pgtP-lacZ reporter, indicating that functional pgtA is essential for the constitutivity. His-457 of PgtB, a potential site of autophosphorylation, is also required for the constitutivity because its change to Val drastically reduced pgtP-lacZ reporter expression. The structural basis for the activation of the altered PgtB is discussed in terms of putative structure of PgtB in the membrane.
Determinants of Success in University Careers: Findings from the German Academic Labor Market / Erfolgsfaktoren in der Wissenschaft – Ergebnisse aus einer Habilitiertenbefragung an deutschen Universitäten

Summary What factors determine the chances of being appointed to a chair in Germany? We propose to derive hypotheses from discrimination theory, social and human capital theory, and the signaling approach. In a survey we sampled scholars from mathematics, law and sociology who had completed their Habilitation (“second book”) from 1985 and 2005 at West German universities. A young age at the time of completion of the Habilitation is beneficial across all disciplines. In sociology, the number of publications included in the Science Citation Index is the most important factor in attaining a chair, and women are at an advantage when they face the same conditions as do men. In the field of law, parents’ years of education have a significant impact on success, as has having a highly respected mentor. In mathematics, the chances of getting a professorship increase significantly with high occupational prestige of the parents, the share of time spent in research, the specialty of applied mathematics, or having a mentor with a high reputation. Zusammenfassung Welche Faktoren beeinflussen in Deutschland die Chance, auf einen Lehrstuhl berufen zu werden? Die hierzu aus Diskriminierungs-, Sozial- und Humankapitaltheorie sowie dem Signaling-Ansatz abgeleiteten Hypothesen werden mittels einer Primarerhebung von Daten uber Personen untersucht, die sich zwischen 1985 und 2005 in Mathematik, Rechtswissenschaften oder Soziologie an einer westdeutschen Universitat habilitiert haben. Ein geringes Lebensalter zum Zeitpunkt der Habilitation wirkt sich in allen Disziplinen positiv aus. In der Soziologie hat die Anzahl der SCI-Publikationen den grcßten positiven Einfluss. Zudem haben Frauen bessere Chancen unter sonst gleichen Bedingungen wie Manner. In den Rechtswissenschaften steigt die Chance mit dem Vorhandensein hochgebildeter Eltern und einem Mentor bzw. einer Mentorin mit hoher Reputation und in der Mathematik mit hohem Berufsprestige der Eltern, einem hohen Anteil an Zeit fur Forschung, einer Spezialisierung in angewandter Mathematik oder einem Mentor bzw. einer Mentorin mit hoher Reputation.
(54) SINGLE STRANDED DNA APTAMERS

Addona, Terri A. , et al., “Multi-Site Assessment of the Precision and Reproducibility of Multiple Reaction Monitoring-Based Measure ments of Proteins in Plasma,” Nat. Biotechnol. 27(7), Jul. 2009, pp. 633-641. Akagi, Tsuyoshi, et al., Refractory Nature of Normal Human Diploid Fibroblasts with Respect to Oncogene-Mediated Transformation, PNAS, Nov. 11, 2003, vol. 100, No. 23, pp. 13567-13572. Akira, Shizuo, et al., “Pathogen Recognition and Innate Immunity. ” Cell, Feb. 24, 2006, 124, pp. 783-801. Barnes, Peter J., et al., “Nuclear Factor-KB A Pivotal Transcription Factor in Chronic Inflammatory Diseases. ” The New England Journal of Medicine, Apr. 10, 1997, vol. 336, No. 15, pp. 1066-1071. Bassett, Suzanne E. , et al., “Combinatorial Selection and Edited Combinatorial Selection of Phosphorothioate Aptamers Targeting Human Nuclear Factor-KB RelA/p50 and RelA/RelA. ” Biochemis try, 11 pages. Beg, Amer A. et al., “The IKB Proteins: Multifunctional Regulators of Rel/NF-KBTranscription Factors. ” Genes & Development, 1993, T2064-2070. Berezovski, Maxim V. , et al., "Aptamer-Facilitated Biomarker Dis covery (AptaBID). ” J. Am. Chem. Soc. , 2008 130:9137-9143. Bosisio, Daniela, et al., “A Hyper-Dynamic Equilibrium Between Promoter-Bound and Nucleoplasmic Dimers Controls NF-KB-De pendent Gene Activity. ” The EMBOJournal, 2006, vol. 25, No. 4, pp. 798-810.
Analysis of Carbon Tax on Selected European Countries: Does Carbon Tax Reduce Emissions?

Since the first days of its existence, the humanity had been using natural resources to meet its needs. Especially along with the globalization period as a result of the Industrial Revolution and the rapid development of communication technologies within the last fifty years, the production has increased significantly in the world and has created negative effects on the environment. The leading adverse effects involve the emission of greenhouse gases and the global warming, which stem from the energy supply of fossil fuels as the main inputs of production. The global warming can be described as an increase in temperature worldwide. Irreversibility is the most important feature of the global warming. Therefore, in the absence of objective measures, the future costs would be much higher than the current ones. For this reason, governments need to take various measures to reduce the volume of emissions. The most important of these measures is carbon taxes. Carbon taxation encourages individuals to use fewer fossil fuels and to find new sources of energy by increasing the cost of using fossil fuels that cause carbon dioxide emissions through the price mechanism. To this end, the impacts of carbon tax levied in 18 selected European countries on economic growth, urbanization, natural gas and petroleum usage, and CO2 emissions are examined by panel data analysis for the 1995-2015 period. The analysis results indicate that a 1% increase in environmental taxes reduces carbon dioxide emissions by 0.9%. Furthermore, it is reported that a 1% increase in natural gas and petroleum consumption among the variables included in the analysis increased carbon dioxide emissions by 0.1% and 0.7%, respectively; while a 1% increase in urbanization reduced carbon dioxide emissions by 0.9%.
Use case driven object modeling with UML: a practical approach

Preface. Theory, in Practice. The Premise. Acknowledgments. 1. Introduction. A Walk (Backwards) Through the ICONIX Process. Key Features of the ICONIX Process. Process Fundamentals. The Process in a Nutshell. 2. Domain Modeling The Key Elements of Domain Modeling. The Top 10 Domain Modeling Errors. Exercises. 3. Use Case Modeling. The Key Elements of Use Case Modeling. The Top 10 Use Case Modeling Errors. Exercises. 4. Requirements Review. The Key Elements of Requirements Review. The Top 10 Requirements Review Errors. 5. Robustness Analysis. The Key Elements of Robustness Analysis. The Top 10 Robustness Analysis Errors. Exercises. 6. Preliminary Design Review (PDR). The Key Elements of Preliminary Design Review (PDR). The Top 10 PDR Errors. 7. Sequence Diagrams. The Key Elements of Sequence Diagrams. The Top 10 Sequence Diagramming Errors. Exercises. 8. Critical Design Review (CDR). The Key Elements of Critical Design Review (CDR). The Top 10 CDR Errors. Appendix. Index. 0201432897T04092002
IDS for Node Replicas at Distributed & Centralized Levels in Mobile WSN

Wireless Sensor Networks (WSNs) consist of sensor nodes, deployed in hostile environments where they are often vulnerable to physical capture and compromise. Once a sensor node is compromised, the adversary can extract cryptographic secrets from node, replicate the compromised node and distribute the clones at strategic positions in the network for malicious attacks. This is known as node replication attack. So it is critical to ensure the security of sensor networks. Existing detection schemes for node clone attacks are mainly focused on static networks which rely on the witness-finding strategy, which cannot be applied to mobile networks. In this paper, Distributed & Centralized Level (DCL) method is proposed to detect node replicas in mobile sensor networks. The security and performance analysis indicate that this method can identify clone attacks with a high detection probability at the cost of low energy consumption. Our simulation results show that our method achieves effective and robust replica detection capability.
Fairness in a data center

Fairness in a data center by Mikkel Hagen University of New Hampshire, December, 2012 Existing data centers utilize several networking technologies in order to handle the performance requirements of different workloads. Maintaining diverse networking technologies increases complexity and is not cost effective. This results in the current trend to converge all traffic into a single networking fabric. Ethernet is both cost-effective and ubiquitous, and as such it has been chosen as the technology of choice for the converged fabric. However, traditional Ethernet does not satisfy the needs of all traffic workloads, for the most part, due to its lossy nature and, therefore, has to be enhanced to allow for full convergence. The resulting technology, Data Center Bridging (DCB), is a new set of standards defined by the IEEE to make Ethernet lossless even in the presence of congestion. As with any new networking technology, it is critical to analyze how the different protocols within DCB interact with each other as well as how each protocol interacts with existing technologies in other layers of the protocol stack. This dissertation presents two novel schemes that address critical issues in DCB networks: fairness with respect to packet lengths and fairness with respect to flow control and bandwidth utilization. The Deficit Round Robin with Adaptive Weight Control (DRRAWC) algorithm actively monitors the incoming streams and adjusts the scheduling weights of the outbound port. The algorithm was implemented on a real DCB switch and shown to increase fairness for traffic consisting of mixed-length packets. Targeted Priority-based Flow Control (TPFC) provides a hop-by-hop flow control mechanism that restricts the flow of aggressor streams while allowing victim streams to continue unimpeded. Two variants
Acceleration of Packet Classification Using Adjacency List of Rules

Packet classification is used to determine the behavior of packets incoming to network devices. Since it is achieved using linear search on a classification rule list, a large number of rules leads to longer communication latency. To decrease this latency, the problem is generalized as optimal rule ordering (ORO), which aims to identify the order of rules that minimizes the classification latency caused by packet classification while preserving the classification policy. Since ORO is known to be NP-complete, various heuristics for ORO have been proposed. Sub-graph merging (SGM) is the state-of-the-art heuristic algorithm for ORO. However, the SGM algorithm does not terminate in most cases because of inappropriate updates of the array that stores the number of reachable rules. Moreover, since SGM uses the adjacent matrix to maintain the preceding relation on the rules, a considerable amount of time is consumed when the preceding relation is complex. In this paper, we propose a correction for SGM that can terminate for any instance. The proposed algorithm decreases reordering time by about 99\% compared to SGM. Furthermore, we propose a reordering algorithm that selects sub-graphs more comprehensively than SGM. Doing so decreases the latency in comparison with SGM. We show the efficiency of the algorithms through experiments.
STUDY ON MANAGEMENT ALTERNATIVES ON AGILE METHOD BASED FINANCIAL SECURITY SOFTWARE PROJECT 1

In tandem with development of information technologies, telecommunication environment, infrastructure and device etc. are getting smarter and converged. As non-facing service transactions are expanded, financial institutions provide internet banking service, which customers are using with convenience. Accordingly, the information system market related with finance is anticipated to experience much changes in system setup due to change in business and financial environment, and upgrade or new development is continuously performed. However due to the development of informatized society, hacking and virus attack technics are becoming sophisticated and diversified, and also as the cases of infringement of personal privacy etc. are continuously occurring, much efforts are required to resolve these situations. Especially, the current attack paradigm on electronic financial service is concentrated on the customers using electronic finance, so the need for security system is ever increasing to resolve this situation. However, in pursuit of any effort to resolve such situation by proceeding financial security related project, mostly the time and cost incurred for the project is burdensome. Especially, most of such projects accompany numerous risks, and representatively any change in requirements of customers is exercising so heavy influence as to determine the success of the project. Any change in requirements related to financial security shall be immediately processed, but delay of project often occurs due to poor communication between developer and customer. In this regard, this thesis proposes the system to compose development team based on Agile Methods, to differentiate the role of team members and manage the project period, in case financial security software project is performed while development period and development cost is fixed. Also in order to verify the proposed system, actual project is implemented and comparison is made with the waterfall model which is the traditional development methodology. The result of verification shows effect of reduced number of 8% days required for development saving effect. By the proposed system, it is expected that successful progress of financial security related software project would be possible. In the future, subsequent studies on flexible expandability and systematic management methodology are necessary.
Robust, Fast and Accurate Solution of the Direct Position Analysis of Parallel Manipulators by Using Extra-Sensors

Parallel manipulators (PMs) are closed kinematic chains with one or more loops where only some pairs are actuated while the remaining are passive. In particular, they feature a fixed link (base) and an output moving link (platform) interconnected by at least two independent kinematic chains (legs) to form one loop. The most well known and commonly employed PMs (hereafter called UPS-PMs) feature n variable-length legs of type UPS (where U, P and S are for universal, spherical and prismatic pairs respectively). Equivalently, a revolute pair R could be used instead of the prismatic pair P in order to make the leg length variable (in this case the leg would be of type URS). These leg topologies provide the platform with six degrees of freedom with respect to the base. Although the definition of UPS-PMs requires n ≥ 2, in practice, neglecting overconstrained and redundantly-actuated manipulators, performance issues recommend 3 ≤ n ≤ 6. Indeed, UPS-PMs with only two UPS legs might exhibit a low stiffness against torques acting along the line joining the centers of the two spherical pairs, and their control would require the inseries placement of at least three actuators/sensors (one of them placed to control/measure at least one out of the three degrees of freedom of the spherical pairs) which reduces the overall manipulator dynamic and accuracy capabilities. On the other side, the use of more than six legs reduces the exploitable manipulator workspace for the increase of leg interference. Different sub-classes of manipulator architectures can be obtained according to the location of the centers of the U and S pairs in the base and in the platform respectively (Innocenti & Parenti-Castelli, 1994; Faugere & Lazard, 1995). General UPS-PM architectures feature distinct joint centers. Special architectures can be devised by setting some of the joint centers to be coincident. A schematic of a 6-DOF UPS-PM having six legs (n = 6) and general architecture is shown in Fig. 1. In the figure, the U pairs (connecting the legs to the base) and S pairs (connecting the legs to the platform) are depicted as grey and white dots respectively. Points Bi and Pi represent the centers of the U and S pairs of the i-th leg on the base and on the platform respectively. The six legs of type UPS are represented by the telescopic rods BiPi (i = 1, ., 6). Accordingly, the length of the i-th leg is defined as the distance li = ⎪Pi Bi⎪.
A comprehensive comparison and overview of R packages for calculating sample entropy

Abstract Sample entropy is a powerful tool for analyzing the complexity and irregularity of physiology signals which may be associated with human health. Nevertheless, the sophistication of its calculation hinders its universal application. As of today, the R language provides multiple open-source packages for calculating sample entropy. All of which, however, are designed for different scenarios. Therefore, when searching for a proper package, the investigators would be confused on the parameter setting and selection of algorithms. To ease their selection, we have explored the functions of five existing R packages for calculating sample entropy and have compared their computing capability in several dimensions. We used four published datasets on respiratory and heart rate to study their input parameters, types of entropy, and program running time. In summary, NonlinearTseries and CGManalyzer can provide the analysis of sample entropy with different embedding dimensions and similarity thresholds. CGManalyzer is a good choice for calculating multiscale sample entropy of physiological signal because it not only shows sample entropy of all scales simultaneously but also provides various visualization plots. MSMVSampEn is the only package that can calculate multivariate multiscale entropies. In terms of computing time, NonlinearTseries, CGManalyzer, and MSMVSampEn run significantly faster than the other two packages. Moreover, we identify the issues in MVMSampEn package. This article provides guidelines for researchers to find a suitable R package for their analysis and applications using sample entropy.
The Role of Adaptor Protein Complex-3 Delta-Mediated HIV-1 Gag Trafficking in HIV-1 Replication: A Dissertation

The process of HIV-1 particle production is a multi-step process directed by the viral structural protein Gag. As Gag is the only viral protein required to form virus-like particles, it presents a viable target for anti-viral therapeutics of which there are currently none. Although the functions of Gag during the particle assembly process have been well characterized, one of the least known parts of the assembly process is how Gag is targeted to the site of virus assembly. Two main virus assembly sites have been identified in cells that support HIV-1 replication: the plasma membrane or multivesicular bodies (MVBs). However the mechanism by which Gag is targeted to either of these sites remains unknown. The δ subunit of Adaptor Protein Complex 3 has previously been identified as a cellular co-factor for HIV-1 Gag and was reported to mediate Gag trafficking to MVBs, providing a mechanism for Gag targeting to this assembly site. Additionally, AP-3δ was reported to be required for HIV-1 production, suggesting that Gag to MVB targeting is also required for HIV-1 production. The work presented in this thesis further investigates the role of AP-3δ in Gag trafficking to MVBs and its role in HIV-1 production in previously unexplored host environments. Through the use of RNA interference-mediated depletion of AP-3δ, we determined that AP-3δ is dispensible for virus replication in infected HeLa cells, chronically infected HeLa-LAV cells and infected primary human monocyte-derived macrophages. We concomitantly disrupted AP-3 function by disrupting its association with membranes and observed no effect on virus production. Collectively, these results demonstrate that AP-3δ is not required for HIV-1 replication. However, AP-3δ was demonstrated to be required for Gag targeting to MVBs thus presenting a new model for the function of AP-3δ in the context of HIV-1 replication.
Moisture controls on Sphagnum growth and CO2 exchange on a cutover bog

Summary 1. Abandoned cutover peatlands are persistent sources of atmospheric CO2. Net ecosystem CO2 exchange and Sphagnum net primary production of an abandoned block-cut bog were measured in the field and in the laboratory using gas exchange techniques to determine the processes controlling CO2 exchange in these ecosystems. 2. Sphagnum net primary production was offset by peat respiration, resulting in the peatland becoming a net source of CO2 during the summer months. 3. Sphagnum photosynthesis was greatest at wet sites. In addition, sites with vascular plant cover photosynthesized at approximately twice the rate of sites where vascular plants were removed. 4. Laboratory results indicate that drying and wetting cycles negatively affect Sphagnum net primary production and net ecosystem CO2 exchange. Sphagnum and peat respiration increased 4–14-fold upon rewetting, whereas Sphagnum photosynthesis did not recover until 20 days of saturation. 5. Synthesis and applications. This research emphasizes the importance of stable moisture availability for the growth of Sphagnum and the eventual development of a new acrotelm on the cutover bog surface. Restoration techniques must therefore include companion species and a constant moisture supply above the minimum threshold for Sphagnum mosses.