Miracle-dz/UniFAR-FTUs huggingface dataset:
A DNA Sequence Recognition Loop on APOBEC3A Controls Substrate Specificity

APOBEC3A (A3A), one of the seven-member APOBEC3 family of cytidine deaminases, lacks strong antiviral activity against lentiviruses but is a potent inhibitor of adeno-associated virus and endogenous retroelements. In this report, we characterize the biochemical properties of mammalian cell-produced and catalytically active E. coli-produced A3A. The enzyme binds to single-stranded DNA with a Kd of 150 nM and forms dimeric and monomeric fractions. A3A, unlike APOBEC3G (A3G), deaminates DNA substrates nonprocessively. Using a panel of oligonucleotides that contained all possible trinucleotide contexts, we identified the preferred target sequence as TC (A/G). Based on a three-dimensional model of A3A, we identified a putative binding groove that contains residues with the potential to bind substrate DNA and to influence target sequence specificity. Taking advantage of the sequence similarity to the catalytic domain of A3G, we generated A3A/A3G chimeric proteins and analyzed their target site preference. We identified a recognition loop that altered A3A sequence specificity, broadening its target sequence preference. Mutation of amino acids in the predicted DNA binding groove prevented substrate binding, confirming the role of this groove in substrate binding. These findings shed light on how APOBEC3 proteins bind their substrate and determine which sites to deaminate.
Under Consideration for Publication in J. Functional Programming Web Programming in Scheme - the Laml Approach

Functional programming fits well with the use of descriptive markup in HTML and XML. There is also a good fit between S-expressions in Lisp and the means of expression in HTML and XML. These similarities are exploited in LAML (Lisp Abstracted Markup Language) which is a software package for Scheme. LAML supports exact mirrors of different versions of HTML. In the mirrors each HTML element is represented by a named Scheme function. The mirror functions guarantee that the generated HTML code is valid. LAML has been used for both server side CGI programming and programmatic authoring of non-trivial static web materials. The programmatic LAML author can use the power of functional programming for the production of everyday web documents. Equally important, it is straightforward to define domain-specific web languages in Scheme syntax which parallel the advantages of XML.
Measurement of pedagogical content knowledge: students' knowledge and conceptions

Almost 30 years ago, Shulman categorized the knowledge of teachers by several categories including the pedagogical content knowledge (PCK): "It represents the blending of content and pedagogy into an understanding of how particular topics, problems, or issues are organized, represented and adapted to the diverse interests and abilities of learners. " [10]. The interest in research results dealing with this competency has increased in the last years. Several research projects have operationalized and measured the PCK for different subjects with notable results. They have shown discrepancies in teacher education, which need to be considered and overcome. Due to the young age of the subject computer science it will be interesting to obtain corresponding results in computer science education. In this article we present examples for test items measuring computer science teachers' PCK with main focus on the field of students' tasks and conceptions. They were developed on the base of the test instrument of the MoKoM project which was used in a large study investigating students' knowledge in computer science. Furthermore we will give an outlook on the setting of the assessment we are planning to conduct with these test items.
Grade/CPN: Semi-automatic Support for Teaching Petri Nets by Checking Many Petri Nets Against One Specification

Grading dozens of Petri net models manually is a tedious and error-prone task. In this paper, we present Grade/CPN, a tool supporting the grading of Colored Petri nets modeled in CPN Tools. The tool is extensible, con? gurable, and can check static and dynamic properties. It automatically handles tedious tasks like checking that good modeling practise is adhered to, and supports tasks that are di? cult to automatize, such as checking model legibility. We propose and support the Britney Temporal Logic which can be used to guide the simulator and to check temporal properties. We provide our experiences with using the tool in a course with 100 participants.
Mean-Entropy Models for Uncertainty Portfolio Selection

Uncertainty theory is a branch of axiomatic mathematics based on normality, monotonicity, self-duality, countable subadditivity, and product measure axioms. In this paper, portfolio selection problems in uncertainty environment is solved using uncertainty programming methods. The concept of quadratic entropy is introduced in the model to measure risk of securities. Furthermore, a hybrid intelligent algorithm based on the 99-method and Genetic Algorithm is presented to solve the meanquadratic entropy model.
Inflation in Developing Asia: Pass-Through from Global Food and Oil Price Shocks

The world economy experienced a sharp spike in food and oil prices during 2007 and 2008. In light of developing Asia's dependence on imported oil and food, we can expect higher global food and oil prices to result in higher domestic consumer prices in the region. However, the actual impact of the global commodity shocks on consumer price inflation in developing Asia depends on a number of other factors, including government policy measures. The objective of this paper is to examine empirically the extent of the pass-through of global food and oil prices to domestic consumer prices in nine countries in the region. The main empirical result is that the magnitude of the pass-through has been limited. Government policy measures, for example, subsidies and price controls, played a role in reducing or delaying the pass-through of oil and food price increases to domestic prices.
Remote monitoring using sensor in greenhouse agriculture

This paper proposes a monitoring system that can remotely monitor and predict changes of humidity and temperature level in the greenhouse atmosphere. The objective of the research project is to implement an agro-environmental remote monitoring system using wired sensor and issue SMS notification. The system will includes active measurements, which capable of detecting degradation level for humidity and temperature; and be equipped with an alert mechanism to notify workers about the atmosphere quality in the greenhouse so that precaution steps can be taken promptly. Hypothetical -Deductive method will be used as development methodology because it serves as the typical method in similar research field. With development of this Remote Monitoring System, it is hope that it will benefit farmers in term of bringing new technical innovation in collecting data and monitoring greenhouse.
A review of the application of event studies in marketing

This paper provides a critique of the application of the event study methodology to the marketing field, reviews past research, identifies various strategies for improvement in the use of this methodology, and identifies future directions for research. This review is in three sections. The first section presents the findings of a comprehensive search not only of the marketing literature, but also of marketing studies using the event study methodology that are published in a large number of business, economics, and finance journals. The identified studies are categorized into a number of research fields. The event studies are organized chronologically and reviewed in terms of their specific research focus and empirical findings. In the second section, studies published in marketing journals between 2001 and 2007 are examined more closely to determine how well more recent research meets several best practice guidelines being proposed by various authors around the application of the methodology. The third part of the review explores how the event study methodology might be applied to existing areas of research, in addition to its potential application to a wider range of marketing issues. These include theory development in terms of the application of more specific or appropriate theory to justify the research predictions; replication and extension of studies either due to changes in social attitudes, government legislation or methodological issues that challenge previous research findings; the development of new areas of research interest including the links between advertising and childhood obesity, drugs, and sport, the impact of new technological developments, and the effects of advances in internet marketing and satellite advertising; and advancing the use of the methodology to marketing challenges in the rapidly expanding regions such as China and India. It is expected that the use of the event study methodology in marketing will continue to gain momentum due to continuing demand for marketing actions and assets to be evaluated in financial terms in order to illustrate the return on investment.
Simultaneously vanishing point detection and radial lens distortion correction from single wide-angle images

Radial lens distortion often exists in common cameras, which makes the taken images violate the assumption of pinhole camera model. The prestigious division model for radial distortion with just a single parameter is presented by Fitzgibbon. Lines in 3D space may be projected onto curves in the image plane due to radial distortion. Alemán et al. utilized Hough transform with three parameters, one parameter coming from the division model, and the other two arising from the corrected image line, to automatically and simultaneously correct radial lens distortion and detect multiple image lines. The score function used in the method of Alemán et al. is the total weighted length of all peaks greater than some threshold in Hough space, namely, the image lines greater than some preset length. However, the corrected results from some distorted images are not very satisfactory using the method proposed by Alemán et al. In this paper, we present a novel score function which combines statistical quantities with grouping based on vanishing points from multiple line images. The experimental results validated the proposed method.
A classification of interactions with information

A faceted classification of interactions with information is proposed, based on an empirical study of knowledge workers in their ordinary work environments. The purpose of the classification is to inform the design of information retrieval systems which can support, within a single framework, the whole variety of interactions with information that people engage in during the course of information seeking. The classification scheme has five major facets, by combination of which it is claimed that all those interactions of people with information which are related to information seeking can be described.
Instruction-Based Voltage Scaling for Power Reduction in SIMD-Based MPSoCs

Power reduction in Multiprocessor System-on-Chip (MPSoC) is a key design challenge today. In this paper, we present an approach to power reduction for homogeneous SIMD MPSoC platforms. The technique involves the use of dynamic voltage scaling and power management of voltage islands. The basic idea is to have different supply voltage for different instructions: slow instructions run at the higher voltage levels while fast instructions run at lower voltages to save on power. We use a reconfigurable MPSoC architecture, namely MorphoSys, as a vehicle to demonstrate the approach, although the methods are suitable for other SIMD MPSoC architectures. A number of image processing benchmarks are manually mapped to the hardware to demonstrate the power reduction. The results show energy savings from 12% up to 24% for the specified benchmarks using the proposed approach.
The Copycat project: a model of mental fluidity and analogy-making

concept (as opposed to the instance thereof found inside the string xyz). Many people, eager to construct a successor to Platonic z, invoke the commonplace notion of circularity, thus conceiving of a as the successor of z, much as January can be considered the successor of December, the digit Ό' the successor of the digit '9', an ace the successor of a king, or, in music, the note A the successor of the noteG. Invoking circularity in this way to deal with Problem 6 is a small type of creative leap, and not to be looked down upon. However, the general notion of circularity is not available to the program, as it is to people, for borrowing and insertion into the alphabet world. In fact, for important reasons, 5 The current version of Copycat is not able to create two simultaneous bonds between two given objects (e.g., both the alphabetical and numerical successorship bonds between г and ss), so the program is at present unable to get what many people consider to be the best answer—namely,
Dealing with anonymity in wireless sensor networks

Nowadays Wireless Sensor Networks (WSN) are used in many application contexts. Data handled by WSN are required to be protected for privacy reasons since they can be directly or indirectly related to individuals. The problem of preventing the identification of individuals starting from their data, known as anonymity, is a fundamental requirement for privacy aware systems. This paper proposes a solution to guarantee anonymity for a wide spread type of WSN by means of privacy policies. The solution is based on a UML model that introduces the conceptual elements and guidelines that are needed to build privacy policies for WSN.
High-Throughput Irregular LDPC Decoder

This paper presents a high-throughput area-efficient decoder design for the irregular Quasi-Cyclic (QC) Low-Density Parity-Check (LDPC) codes. Two new techniques are proposed , including parallel layered decoding architecture (PLDA) and critical path splitting. PLDA enables parallel processing for all layers by establishing dedicated message passing paths among them . The decoder avoids crossbar-based large interconnect netw ork. Critical path splitting technique is based on articulate adjustment of the starting point of each layer to maximize the time intervals between adjacent layers, such that the critical path delay c an be split into pipelined stages. Furthermore, min-sum and losely coupled algorithms are employed to reduce chip area, and ear ly termination technique is applied to adjust the iterations.A rate1/2 2304-bit irregular LDPC decoder for 802.16e standard is implemented using ASIC design in 90nm CMOS process. The decoder can achieve the maximum throughput of 2.2Gbps at 10 iterations. The operating frequency is 950MHz and the chip area is only about 2.9mm.
Analysis of user influence in social network based on behavior and relationship

Online social network, has become an important platform for people to communicate and get information. Micro-blog, the convenient and quick platform showed strong development momentum. The paper provided an algorithm to analyze the micro-blog user's influence. Through sina weibo open platform to obtain the information of user relation data and the user data of the time published micro-blog. According to PageRank algorithm we can calculate user's influence. But all micro-blogging users are seen as the same and shared influence in the PageRank algorithm, not take into account the impact of user activity, which does not meet the actual situation of micro-blogging. Therefore we add the user activity to PageRank algorithm to obtain an improved PageRank algorithm. By comparing the experimental results of these two algorithms, we can see that when a user activity is high, even though he has little fans , it can also obtain a higher user influence value; on the contrary, when a user activity is low ,even though he has many fans, its user influence value is lower. It is proved that in the calculation of the influence of micro-blogging users, the improved algorithm is more realistic than the original algorithm.
Autocrine Activation of Neuronal NMDA Receptors by Aspartate Mediates Dopamine- and cAMP-Induced CREB-Dependent Gene Transcription

cAMP can stimulate the transcription of many activity-dependent genes via activation of the transcription factor, cAMP response element-binding protein (CREB). However, in mouse cortical neuron cultures, prior to synaptogenesis, neither cAMP nor dopamine, which acts via cAMP, stimulated CREB-dependent gene transcription when NR2B-containing NMDA receptors (NMDARs) were blocked. Stimulation of transcription by cAMP was potentiated by inhibitors of excitatory amino acid uptake, suggesting a role for extracellular glutamate or aspartate in cAMP-induced transcription. Aspartate was identified as the extracellular messenger: enzymatic scavenging of l-aspartate, but not glutamate, blocked stimulation of CREB-dependent gene transcription by cAMP; moreover, cAMP induced aspartate but not glutamate release. Together, these results suggest that cAMP acts via an autocrine or paracrine pathway to release aspartate, which activates NR2B-containing NMDARs, leading to Ca2+ entry and activation of transcription. This cAMP/aspartate/NMDAR signaling pathway may mediate the effects of transmitters such as dopamine on axon growth and synaptogenesis in developing neurons or on synaptic plasticity in mature neural networks.
Recent changes to the Federal Reserve's survey of terms of business lending

The Federal Reserve's quarterly Survey of Terms of Business Lending, which has been conducted for more than twenty years, collects information on interest rates and other characteristics of commercial bank business loans. The survey has been changed from time to time to recognize innovations in bank lending practices and to improve the measurement of the desired information. The most recent changes took effect with the May 1997 survey. The major improvement was the addition of an item measuring loan risk. In addition, the reporting panel, which had been limited to domestically chartered commercial banks was expanded to include a sample of U.S. branches and agencies of foreign banks, which now account for a significant proportion of business lending to U.S. firms. This article discusses the most recent changes made to the survey and presents some information now available from the new items being reported. It also summarizes information about the use of loan risk ratings from consultations conducted with a sample of the survey respondents during the process of planning the revisions to the survey.
Specific association of the proto-oncogene product pp60c-src with an intracellular organelle, the PC12 synaptic vesicle

The protein product of the proto-oncogene c-src is a membrane- associated tyrosine kinase of unknown function. Identification of pp60c- src target membranes may elucidate the function of the c-src protein. The available evidence indicates that pp60c-src associates with distinct membranes within single cell types and has different distributions in different cell types. Our experiments demonstrate targeting of pp60c-src to an isolatable and biochemically identified membrane fraction in the neuroendocrine cell line PC12. The c-src protein was found to be specifically associated with synaptic vesicles since: (a) the pp60c-src immunofluorescent pattern overlapped with a synaptic vesicle marker, synaptophysin; (b) a significant proportion (44%) of the pp60c-src from PC12 but not fibroblast postnuclear supernatants was recovered in a small vesicle fraction; (c) an anti- synaptophysin cytoplasmic domain antibody immunodepleted all of the pp60c-src vesicles in this fraction, and (d) pp60c-src copurified during a 100-fold purification of PC12 synaptic vesicles. These results suggest a role for the c-src protein in the regulation of synaptic vesicle function.
On the efficiency of query-subquery nets: an experimental point of view

The aim of this paper is to analyze the efficiency of the QSQN method, which was proposed by us and Nguyen in [10] for evaluating queries to Horn knowledge bases. In order to compare QSQN with the well-known methods QSQR and the one based on the Magic-Set transformation, we have implemented all of these methods. We compare them using representative examples that appear in many articles on deductive databases. Our experimental results show that the QSQN method usually outperforms the two other methods. Apart from the experimental results, we also explain the reasons behind the good performance of QSQN.
Dynamic image fusion performance evaluation

This paper deals with the problem of objective evaluation of dynamic, multi-sensor image fusion. For this purpose an established static image fusion evaluation framework, based on gradient information preservation between the inputs and the fused image, is extended to deal with additional scene and object motion information present in multi-sensor sequences. In particular formulations for dynamic, multi-sensor information preservation models are proposed to provide space-time localised fusion performance estimates. Perceptual importance distribution models are derived to accommodate temporal data and provide a natural generalisation of localised performance estimates into both global and continuous dynamic fusion performance scores. The proposed system is described in detail and shown to exhibit better evaluation accuracy, robustness and sensitivity when compared to existing dynamic fusion metrics on an evaluation of several established image fusion algorithms applied to multi- sensor sequences from an array of dynamic fusion scenarios.
3PAR Fast RAID: High Performance Without Compromise

Document Abstract: 3PAR ® Fast RAID allows the 3PAR InServ ® Storage Server to deliver higher performance with less hardware, reducing storage costs compared to traditional storage arrays. This paper describes the components and specific benefits of 3PAR's improved implementation of RAID storage, then helps the reader evaluate and select the best RAID level for each volume. Built In are all trademarks or registered trademarks of 3PAR Inc. All other trademarks and registered trademarks are the property of their respective owners.
Site-Specific Phosphorylation of the DNA Damage Response Mediator Rad9 by Cyclin-Dependent Kinases Regulates Activation of Checkpoint Kinase 1

The mediators of the DNA damage response (DDR) are highly phosphorylated by kinases that control cell proliferation, but little is known about the role of this regulation. Here we show that cell cycle phosphorylation of the prototypical DDR mediator Saccharomyces cerevisiae Rad9 depends on cyclin-dependent kinase (CDK) complexes. We find that a specific G2/M form of Cdc28 can phosphorylate in vitro the N-terminal region of Rad9 on nine consensus CDK phosphorylation sites. We show that the integrity of CDK consensus sites and the activity of Cdc28 are required for both the activation of the Chk1 checkpoint kinase and its interaction with Rad9. We have identified T125 and T143 as important residues in Rad9 for this Rad9/Chk1 interaction. Phosphorylation of T143 is the most important feature promoting Rad9/Chk1 interaction, while the much more abundant phosphorylation of the neighbouring T125 residue impedes the Rad9/Chk1 interaction. We suggest a novel model for Chk1 activation where Cdc28 regulates the constitutive interaction of Rad9 and Chk1. The Rad9/Chk1 complex is then recruited at sites of DNA damage where activation of Chk1 requires additional DDR–specific protein kinases.