Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication of Herpes Simplex Virus DNA*

Herpes simplex virus type 1 (HSV-1) is a member of the herpes group of viruses, the Herpesviridiae, which includes the important human pathogens herpes simplex virus type 2, cytomegalovirus, varicella zoster virus, Epstein-Barr virus, human herpesviruses 6 and 7, and Kaposi’s associated herpesvirus, human herpesvirus 8 (reviewed in Ref. 1). Of these, HSV-1 has been the most extensively studied. The HSV-1 genome is a 153-kilobase linear duplex with 75 open reading frames. It consists of two unique regions, UL (unique long), comprising 82% and the US (unique short) comprising 18%, flanked by the repeated regions a, b, and c (Fig. 1). As a consequence of recombination through the a sequences, the HSV-1 genome actually exists as an equimolar mixture of four isomeric forms generated by inversion of the UL and US sequences relative to each other. An interesting but poorly understood aspect of the HSV-1 life cycle, in fact, the life cycle of all the herpesviruses, is the ability to enter latency, a state in which no infectious progeny are produced and only limited transcription of viral genes occurs. Upon presentation of the appropriate stimulus, the latently infected cells enter a lytic phase with the resultant production of infectious viral particles (1). In the lytic phase, following penetration of the nucleus, a temporally regulated program of viral gene expression mediated by RNA polymerase II begins. A virion protein, VP16, acts in trans together with the cellular octamer DNA-binding protein, Oct-1, to induce the a or immediate early genes, the first set of HSV-1 genes to be expressed. These serve as transactivators of b or early gene expression. Their synthesis peaks at 2–4 h, postinfection. Functional a proteins are required for the synthesis of all the virally encoded proteins. Synthesis of the b class of proteins reaches peak rates 5–7 h and is detectable as early as 3 h postinfection. The b proteins include the enzymes that are required for replication of the viral genome: a DNA polymerase, a single-strand DNA-binding protein, a primosome or helicase-primase, an origin-binding protein, and a set of enzymes involved in DNA repair and in deoxynucleotide metabolism. Homologues of these proteins are found in virtually all herpesviruses (1, 2). Viral DNA synthesis begins shortly after the appearance of the b proteins and is detectable as early as 3 h and continues up to 15 h postinfection, with the bulk of the DNA synthesized during the latter part of the period. The temporal program of viral gene expression ends with the appearance of the g or late proteins, which constitute the structural proteins of the virus (1).
Leadership Without Easy Answers

Five sub principles of the razor’s edge: A. Identify the adaptive challengesDiagnose the situation with light of the values at stake, and unbundled the issues that come with. B. Keep the level of distress within a tolerable range for doing adaptive work. C. Focus attention on the ripening issues and not on stress reducing distractions. D. Give the work back to the people, but at a rate they can stand. E. Protect the voices of leadership without authority.
Application of image registration techniques in breast dynamic contrast-enhanced magnetic resonance imaging

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a relatively new, promising technique for breast cancer diagnostics. A few series of images of the same body region are rapidly acquired before, during and after injection of paramagnetic contrast agent. Propagation of the contrast agent causes modification of MR signal over time. Its analysis provides information on tissue properties, including tumour status, that is not available with the regular MRI. If a patient unintentionally changes position during the examination, then the consecutive image series are not properly aligned and their analysis is difficult, inaccurate or even impossible. The purpose of this work is to design a registration scheme that could be applied to solve the problem in a routine manner, in standard hospital conditions. The proposed registration framework, composed of B-spline transformation, mean squares metric and LBFGSB optimizer, is able to produce satisfactory results within reasonable time.
Detection of PrPCWD in mule deer by immunohistochemistry of lymphoid tissues

References CORNWELL, H. J. C. , ANDERSON, S. S. , THOMPSON, P. M. , MAYER, S. J., ROSS, H. M. , POMEROY, P. P. & MUNRO, R. (1992) The serologic response of the common seal (Phoca vituilina) and the grey seal (Halichoerus grypus) to phocine distemper virus as measured by a canine distemper virus neutralisation test. Science of the Total Environmnent 115, 99-116 CORPE, H. M. , THOMPSON, P. M. & PORTER, L. J. (1998) A rapid noninvasive technique for distinguishing harbor seals (Phoca vitulina) in their first year from older age classes. Marine Mammal Science 14, 372-379 GRENFELL, B. T. , LONERGAN, M. E. & HARWOOD, J. (1992) Quantitative investigations of the epidemiology of phocine distemper virus in European common seal populations. Science of the Total Envirotitnent 115, 15-29 HARDER, T. C. , STEDE, M. , WILLHAUS, T. , SCHWARZ, J., HEIDEMANN, G. & LIESS, B. (1993) Morbillivirus antibodies of maternal origin in harbour seal pups (Phoca vittulina). Veterinary Record 132, 632-633 HARDING, K. C. , HARKONEN, T. & CASWELL, H. (2002) The 2002 European seal plague: epidemiology and population consequences. Ecology Letters 5, 1-6 HEIDE-JORGENSEN, M-P., HARKONEN, T. & ABERG, P. (1992a) Long-term effects of epizootic in harbour seals in the Kattegat-Skagerrak and adjacent areas. Ambio 21, 511-516 HEIDE-JORGENSEN, M-P., HARKONEN, T. , DIETZ, R. & THOMPSON, P. M. (1992b) Retrospective of the 1988 European seal epizootic. Diseases of Aquiatic Organismts 13, 37-62 HUGHES, D. E. , CARTER, S. D. , ROBINSON, I. , CLARKE, D. D. & CLARKE, C. J. (1992) Anti-canine distemper virus antibodies in common and grey seals. Veterinary Record 130, 449-450 JENSEN, T. , VAN DE BILDT, M. , DIETZ, H. H. , ANDERSEN, T. H. , HAMMER, A. S. , KUIKEN, T. & OSTERHAUS, A. (2002) Another phocine distemper outbreak in Europe. Science 297, 209 REINEKING, B (2002) Status report 37. cwss.www. de/news/news/Seals/01seal-news.html. Accessed October 3, 2002, November 8, 2002 SWINTON, J., HARWOOD, J., GRENFELL, B. T. & GILLIGAN, C. A. (1998) Persistence thresholds for phocine distemper virus infection in harbour seal Phoca vitulina metapopulations. Journal ofAnimal Ecology 67, 54-68 THOMPSON, P. M. , CORNWELL, H. J. C. , ROSS, H. M. & MILLER, D. (1992) Serologic study of phocine distemper in a population of harbour seals in Scotland. Joturnal of Wildlife Diseases 28, 21-27 VISSER, 1. K. G. , VEDDER, E. J., VOS, H. W. , VAN DE BILDT, M. W. G. & OSTERHAUS, A. D. M. E. (1993) Continued presence of phocine distemper virus in the Dutch Wadden Sea seal population. Veterinary Record 133, 320-322
Automatic Transliteration of Judeo-Arabic Texts into Arabic Script

The Judeo-Arabic languages comprise a set of dialects spoken and written by Jewish communities living in Arab countries, mainly during the middle ages. Judeo-Arabic is typically written in Hebrew letters, enriched with various diacritic marks. The Judeo-Arabic spoken and written by any particular Jewish community is similar to the Arabic dialect used by their local Muslim community. In addition, Judeo-Arabic dialects borrow words from Aramaic and Hebrew, sometimes modified according to Arabic morphological rules. Since the Arabic alphabet is larger than the Hebrew one, additional diacritic marks are added to some Hebrew letters when rendering Arabic consonants that are lacking in the Hebrew alphabet. Judeo-Arabic authors often use different letters and diacritic marks to represent the same Arabic consonant. For example, some authors use ‫ג‬ to represent " and ‫ג׳‬ to represent $, while others reverse the two. This inconsistency increases the level of ambiguity of a given word, making the reading of Judeo-Arabic texts a challenging task even for an Arabic speaker. Such inconsistencies may be observed even in the same document. For instance, the letter ‫י‬ sometimes represents the letter &, such as in the word ‫פי‬ (" in " , ‫,)في‬ sometimes represents the letter (, such as in the word ‫סילת‬ (" I was asked " , (" on " / " to " / " at " , in Arabic ‫.)على‬ Currently, many works in Judeo-Arabic are being made available on the web. However, most Arabic speakers are unfamiliar with the Hebrew script, let alone the way it is used to render Judeo-Arabic. Therefore, there is a crucial need for automatic tools capable of transliterating Judeo-Arabic texts in Arabic letters. Since Judeo-Arabic texts usually contain some non-Arabic words, transliteration is only one step toward providing a full Arabic translation for a given Judeo-Arabic input. We are focusing mainly on the transliteration process, leaving Hebrew and Aramaic words in their original Hebrew script. As mentioned above, Judeo-Arabic is not a single language, but rather a set of dialects, each used by the local Jewish community in some of the Arab countries. Some texts are similar to Classical Arabic, the ancestor of the Modern Standard Arabic (MSA), which is widely used today in formal settings, while other texts are more similar to local Muslim dialects. We focus, for now, on the Judeo-Arabic version that is similar to MSA more than on the colloquial versions. We model …
NudgingPrivacy The Behavioral Economics of Personal Information

72 COPUBLISHED BY THE IEEE COMPUTER AND RELIABILITY SOCIETIES ■ 1540-7993/09/$26.00 © 2009 IEEE ■ NOVEMBER/DECEMBER 2009 revelation and protection, with satisfaction shared among the individual, organizations, and society as a whole. Research in this area isn’t new. The first explicit economic approaches to privacy appeared near the end of the 1970s, in particular via pioneering work from Chicago School economists such as Richard Posner and George Stigler. Research continued through the 1990s, thanks to contributions from economists keenly interested in information technologies (such as Hal Varian or Eli Noam) and researchers interested in the privacy “calculus” (such as Robert Laufer, Maxine Wolfe, Pamela Amstrong, or Mary Culnan). Theoretical and empirical studies in this area burgeoned after 2000 with the advent of the commercial Internet and the explosion of technologies for data dissemination, gathering, and analysis. However, the same technological advances that, in recent years, have vastly expanded information sharing and mining capabilities, have also made our privacy tradeoffs more difficult to navigate, exposing surprising dichotomies between our privacy attitudes and our actual behavior. In words, we’ve reacted to the new technological panopticon by demanding more privacy (surveys keep finding that privacy is one of American consumers’ largest concerns; see, for instance, the Consumer Union 2008 Consumer Reports Poll: “Americans Extremely Concerned gain fame and immortality. Today, like 2,000 years ago, many seek notoriety at the price of embarrassment, a tarnished reputation, or even infamy. In 2007, a new Facebook group came under media attention: 30 Reasons Girls Should Call It a Night counted “nearly 150,000 members and a collection of nearly 5,000 photos of young women passed out on the pavement, collapsed in shrubbery, peeing in bushes, and vomiting in toilets (or on themselves). ” Most of the subjects had uploaded the photos themselves. What is it that pushes us to seek fame by misconduct or publicity by sharing embarrassing information with strangers? How do we reconcile these desires with the apparent need for privacy that surveys keep finding so widespread among the American population? In short, what drives individuals to reveal, and to hide, information about themselves to and from others?
First-Order Algorithm for Content-Centric Sparse Multicast Beamforming in Large-Scale C-RAN

In multimedia-rich communication scenarios, popular contents are requested by many users. This calls for the communication system design perspective transferring from user-centric to content-centric. To realize the content-centric paradigm, one of the dominant approaches is the multi-group multicast transmission. However, different content groups may cause interference with each other, and the quality of service is difficult to be guaranteed without coordination. Fortunately, a cloud radio access network (C-RAN) perfectly fills this gap as all the computations in the network are off-loaded to the computation center, making the central coordination possible. But a major challenge that C-RAN faces is that the resultant problem size could be extremely large, invalidating many existing second-order algorithms. In this paper, content-centric sparse multicast beamforming in a large-scale C-RAN is studied. In addition to the large-scale nature, this problem is further complicated by the discontinuity and non-convexity of the cost function and constraints. Despite the challenges, a first-order algorithm is proposed. Not only is the proposed algorithm guaranteed to converge to a critical point, but its complexity order is only linear with respect to the problem size. This is in sharp contrast to the cubic order of an existing solution, making the proposed algorithm indispensable for large-scale C-RAN with hundreds or thousands of users.
Smart and efficient multi-scenario SoC timing closure and ECO generator

Signoff timing analysis is still considered as a critical element in the SoC design flow. With the advancements of the leading edge technologies towards the deep sub-micron realms, the performance of a multi-million transistor SoC is challenged by the aggravation of process variations. Traditionally, the performance of an integrated circuit (IC) is characterized by the clock frequency at which it operates, and is evaluated considering only worst-case gate delays. This is a pessimistic approach, which highly underestimates the performance of the design in deep sub-micron. This pessimism drives the engineers to further optimize the design, eventually increasing the design cost drastically, as analysing such a design would require consumption of more resources, adding to increase in the number of iterations. With the aggravation of process variations, the main contributor to the delay of the circuit is dominated by the interconnect delays. Hence, the number of scenarios required to analyse and fix the design is enormous and ever increasing. Such a pessimism hampers with time-to-market window of product, which in worst case may be missed too. In world of large number of multi-scenarios, the engineering change order (ECO) becomes inevitable to achieve design timing closure with a low respin cost. This concern is attributed to the fact that, firstly, performing ECOs is an experimental process requiring an expert for each mode. The involvement of huge manual effort utilising their own respective scripts leads to significant amount of iterations to achieve its final goal. Secondly, timing violations under multi -scenario design exists even after the detailed routing. In the absence of such an implementation system, that can handle fixing of violations in multi-scenario design, without the involvement of manual effort, causes non-convergence of timing closure, making the design prone to the ping-pong effect. This becomes a bottleneck to the design cycle time. Additionally, this approach requires large memory usage and licensed CPU resources which are already very limited. This work presents a hierarchical approach to target the fixing of timing violations, gaining significant cycle time in overall timing closure. A complete solution for true hierarchical timing and crosstalk delay signoff is presented in this work. It explores the gaps in the current approach and provides a novel solution to address them. It discusses the smart and efficient Timing Closure Methodology which first identifies the Dominant Scenarios and then prioritizes the violations for fixing, in a manner which eliminates the danger of ping-pong effect, where fixing one set of violations can create hundreds of new violations. This iterative approach seamlessly integrates the steps of timing closure thereby reducing 90% of the manual effort.
Strut-tie method of design and possible serviceability problems: an exploration by NLFE

The strut and tie method presents a rational and consistent approach to the design of all parts in a reinforced concrete structure. With this approach, the load carrying mechanism of the structure is represented by approximating the compressive stress fields as struts, and tensile stress fields as ties. The stress in the struts and ties should not exceed the allowable compressive strength of the concrete or yield strength of the steel respectively. In the design of structures by this method there are two important issues to be addressed. The first issue is that of the visualization of an appropriate strut-tie model for a given structural system. In many structures there may be various load paths available and hence no unique strut-tie model exists. The second issue is that of validity of chosen models in relation to the serviceability and ultimate load characteristics of the resulting structure. It is important that the ductility of the structure should be maintained by insuring that crushing of concrete prior to yielding of steel is avoided at design loads. Since the strut and tie method involves a redistribution of the stresses from the elastic pattern, it is necessary to determine the extent to which that re-distribution can be allowed for, while preserving the required performance from the structure. In this work, visualization of strut-tie models was carried out using elastic finite element analysis. The resulting stress fields were used to design structures which were analysed using an in-house non-linear finite element program and also physically tested in the laboratory.
The design and testing of an indirect cabinet solar dryer, for thin layer drying of Rastrineobola argentea fish, under the climatic conditions of Maseno, Kenya

In spite of the high global demand for fish which is a major source of animal protein, nearly 10% (13 million tons) of the world’s total fish production is lost through spoilage due to inadequate cold storage and poor marketing/distribution channels. Fish is a highly perishable product that is processed by freezing, canning, salting and drying. About 40% of fish landings in developing countries are preserved through traditional processing methods (smoking, drying and salting) organized at artisanal level. As a result of increased trade and co-operation among neighboring African countries over the past years, processed products from the artisanal sector now form a significant part of the small pelagic fish products traded intra-regionally. Lake Victoria provides about 95% of the total fish landings in Kenya, with Rasrineobola argentea (one of the pelagic species) being the second commercially important fish. It is harvested in very large quantities and is readily available at affordable price and widely used for both domestic and industrial purposes. Open-sun drying is the main preservation method employed by the fish farmers and involves spreading the fish on open ground where it is exposed to contamination, infestation and adverse weather conditions. It is estimated that post harvest losses of between 20 and 50% occur especially during rainy seasons. Although, the landings of R. argentea are higher as compared to other fish species, the value of the catch is often very low due to these huge losses. In an effort to curb these losses, a model of an indirect forced convection solar dryer was developed and tested for thin layer drying of R. argentea fish. The fish, in 10 kg batches were loaded onto the dryer and the moisture content reduced from an initial value of 73% (w. b.) to between 16 and 20% (w. b.) after 11 h of drying at average air flow rate of 0.017 kg/s, where open sun drying took 18 h. The mean efficiencies of collector and drying systems were 9.36 ± 3.95% and 11%, respectively. The drying rate constants of the fish in dryer were found to be: 0.146, 0.206 and 0.148 for the fish in the top, middle and bottom trays, respectively. Key words: Twin collector, indirect, forced convection, cabinet solar dryer, Rastrineobola argentea fish
Interactivity by design : creating & communicating with new media

What is interactivity? Introduction. I. INFORMATION DESIGN. Product definition. Audience and environment. What do users want? Development choices. Raw Materials. Planning. Organization. The flowchart. II. INTERACTION DESIGN. Orientation. Image maps and metaphors. Navigation. Usability. Functionality. The storyboard. III. PRESENTATION DESIGN. Digital media survival kit. Resolution. Anti-aliasing. Color and palettes. Compression is your friend. Laws of survival. Setting the style. How content defines style. Stylistic unity. Interface families. Layout. Layout conventions. Grids. Backgrounds. Windows and panels. Buttons and other controls. Images. Text. Video. Sound. Animating the screen. Putting it all together. The Prototype. Conclusion. Resource Guide. Credits. Index.
Middleware Layer for Replication between Relational and Document Databases

Effective and efficient data management is key to today’s competitive business environment. Data is a valuable asset for any organization. Data is information and information is knowledge. Today’s enterprise applications generate large amount of data especially because of high usage of the internet. As a result, enterprise applications should be able to scale out and perform as required. Otherwise, these applications will not be able to handle their data load, leading to trouble in business continuity. Data replication is one widely used phenomenon in distributed environments, where data is stored in multiple sites, within same or differing geographical areas. Thus enterprise applications will be able to scale out, so that they perform well. Many modern Database Management Systems (DBMSs) provide in-built methods for data replication. Replication is possible between heterogeneous database systems. In this research, the aim is to design and implement a middleware layer for data replication from RDBMS to document oriented DBMS. The middleware layer includes a Java program, source and destination DBMSs. The research approach is to capture DML/DDL changes in source relational DBMS and then convert and stores them in an intermediate XML format. Then the java program continuously looks for such data changes and then push them to the destination DBMS. A replication method like this can address the need of application scalability in situations where both types of DBMSs are used. In live environments, there are areas of possible performance improvements to the middleware layer, especially when dealing with large data volumes. Keywords— NoSQL, Document Databases, Relational Databases, Data Distribution, Replication