Miracle-dz/UniFAR-FTUs huggingface dataset:
Standard for the Electronic Distribution of SBOLv Diagrams

A common method for publicly distributing design diagrams on the Web would enhance understanding of the mechanisms and intended function of synthetic DNA constructs. We aim to improve the usefulness of the depicted design to readers by establishing a systematic scheme for linking diagrams of synthetic biological mechanisms to reference information on the Registry of Standard Biological Parts [1]. Through the use of standard diagrams based on SBOL-visual (BBF RFC 16) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. This standard applies the use of the established SBOLv symbols on the Web to clearly represent synthetic constructs. Linking these diagrams using http URLs to reference information at the Registry provides a method to retrieve contextual reference information about components of DNA constructs. Use of standardized diagrams in engineering promotes fast and accurate communication between researchers, which in turn promotes effective re-use of biological parts.
A collaborative filtering recommendation algorithm using user implicit demographic information

With development of network technology and society, people enjoy the e-commerce shopping convenience while also deeply troubled by the "information overload" problem. Recommendation systems help the customers find suitable products they need from a large number of commodities. Among the recommendation systems, the most widely used algorithm is collaborative filtering (CF) recommendation algorithm. In order to improve the recommendation quality, many scholars combined demographic information with CF algorithm, but they did not take into account the user implicit demographic information. However, there is a gap between explicit demographic information and implicit demographic information. To solve this problem, we propose a way to mine the user implicit demographic information. Then we introduce uncertain multiple attribute decision making method into our algorithm to find out a set of initial items. Finally, we recommend items users might like in the set of initial items according to the similarity. Experiments show that this method is more reasonable and more accurate to make recommendations for the target users.
Measuring flow as concept for detecting game fun in the Pac-Man game

Popular games often have a high-quality graphic design but quite simple-minded non player characters (NPC). Recently, Computational Intelligence (CI) methods have been discovered as suitable methods to revive NPC, making games more interesting, challenging, and funny. We present a fairly large study of human players on the simple arcade game Pac-Man, controlling the ghosts behaviors by simple strategies, neural networks or evolutionary algorithms. The playerpsilas fun is of course a subjective experience, but we presume that it is related to the psychological flow concept. We deal with the question whether flow is a more reliable measure than asking human players directly for the fun experienced during the game. In order to detect flow, we introduce a measure based on the interaction time fraction between the human-controlled Pac-Man and the ghosts, and compare the outcome to the results of a fun measure suggested by Yannakakis and Hallam [1].
Low Levels of Polymorphisms and No Evidence for Diversifying Selection on the Plasmodium knowlesi Apical Membrane Antigen 1 Gene

Infection with Plasmodium knowlesi, a zoonotic primate malaria, is a growing human health problem in Southeast Asia. P. knowlesi is being used in malaria vaccine studies, and a number of proteins are being considered as candidate malaria vaccine antigens, including the Apical Membrane Antigen 1 (AMA1). In order to determine genetic diversity of the ama1 gene and to identify epitopes of AMA1 under strongest immune selection, the ama1 gene of 52 P. knowlesi isolates derived from human infections was sequenced. Sequence analysis of isolates from two geographically isolated regions in Sarawak showed that polymorphism in the protein is low compared to that of AMA1 of the major human malaria parasites, P. falciparum and P. vivax. Although the number of haplotypes was 27, the frequency of mutations at the majority of the polymorphic positions was low, and only six positions had a variance frequency higher than 10%. Only two positions had more than one alternative amino acid. Interestingly, three of the high-frequency polymorphic sites correspond to invariant sites in PfAMA1 or PvAMA1. Statistically significant differences in the quantity of three of the six high frequency mutations were observed between the two regions. These analyses suggest that the pkama1 gene is not under balancing selection, as observed for pfama1 and pvama1, and that the PkAMA1 protein is not a primary target for protective humoral immune responses in their reservoir macaque hosts, unlike PfAMA1 and PvAMA1 in humans. The low level of polymorphism justifies the development of a single allele PkAMA1-based vaccine.
Parallel Matching Algorithms of Publish/Subscribe System

Publish/subscribe systems form an important communication paradigms in distributed systems. However, how to leverage current chip multi-processors to increase throughput and reduce the matching time still need further research. In this paper, we present and implement two types of parallel matching algorithms. Experiments show that relatively independent matching algorithm produces similar throughput as complete independent matching algorithm and the average matching time of collaborative matching algorithm is reduced by approximately 77% as the number of threads increases from one to six.
Introduction to the SI Library of unit-based computation

To address current deplorable practices in numeric computation, we set out to develop a software subsystem to provide a convenient means of expressing, computing with, and displaying numeric values with attached units, thus obtaining the well-known bene#12;ts of type safety consistent with recommended unit-based practices of long standing. An additional requirement of this project was to ensure strict compile-time type-checking without run-time overhead (i.e., at no run-time cost in time or in space). More speci#12;cally, we sought 1. application of current software technology to numeric physical concepts, 2. convenience of expression in such application, 3. general utility rooted in existing standards, 4. use of nomenclature from our problem domain, and 5. no attendant performance penalties! The present project, known as The SI Library of Unit-based Computation, has succeeded in addressing these requirements. The resulting software module (known hereinafter as the SI Library or, simply, the Library ) meets (and, in many respects, greatly exceeds! ) all its goals and is intended for contribution (for non-commercial use) to the FPCLTF (\Zoom") project library at Fermilab.
Adaptive named entity recognition based on conditional random fields with automatic updated dynamic gazetteers

This paper presents a hybrid model which combines conditional random fields (CRFs) with dynamic gazetteers (DGs) for the task of Chinese named entity recognition (NER). In the previous work of NER, gazetteers were widely used. But their gazetteers were all static ones which cannot adapt themselves to the new domains and new out-of-vocabulary named entities (OOVNEs). In this work, we build and maintain DGs to solve the problems and propose a method to automatically update DGs along with the recognition process of the named entities (NEs). With this method, the DGs can be updated to contain more and more new NEs and features of NEs that are not found in the training data. These newly added items make the DGs become more aware of the knowledge about new domains and hence be more adaptive to new domains for the recognition of OOVNEs. Experiments on the People's Daily corpus demonstrate that our method is effective, and can improve the average F-score by 1%~2%.
A Particle Swarm Optimizer with Chaotic Self-Feedback for Global Optimization of Multimodal Functions

This paper proposes an improved particle swarm optimization utilizing iterative chaotic map with infinite collapses (ICMIC) perturbations (ICMICPSO) for global optimization of multimodal functions. The chaotic perturbation generated by the ICMIC is incorporated into the particle's velocity updating rule to make the particles have a larger potential space to fly. With the coefficient of chaotic perturbation decaying, the dynamics of ICMICPSO algorithm is a chaotic dynamics first and then a steepest descent dynamics. The proposed ICMICPSO method as hybrid optimization is tested on several widely used multimodal functions. Numerical results are compared with that of some other chaotic PSO methods available in the usual literature. The performance studies demonstrate that the effectiveness and efficiency of the proposed ICMICPSO approach are comparably to or better than that of the other CPSO variants in this paper.
The Role of Organizational Culture, Leadership, and Infrastructure in Knowledge Creation

Knowledge management systems provide opportunities for organizations to obtain and manipulate their knowledge in order to impact their strategic initiatives. As these systems become more prevalent within organizational structures, the benefits of KM systems can be enhanced by reviewing the impact of organizational culture, organizational leadership, and organizational infrastructure components on the KM system and its processes. In this paper, the focus is on the current research regarding these components, their connection to the process of knowledge creation, and areas for future research agendas. Although there has been extensive research in knowledge processes, there is potential for researchers to continue contributing to future studies of the connection between organizational influences and the process of knowledge creation.
School enrollment in Indonesia

The objective of this paper is to relate children's school enrollment and level of educational attainment to their household socioeconomic characteristics and the availability of schools. For primary school enrollment, two issues are explored. The first concerns the characteristics of those children who do not attend school, given the relative availability of facilities. The second concerns household expenditures on education, particularly in relation to the availability of facilities and households' ability and willingness to pay for education. The study, based on data, shows that education in Indonesia, especially beyond the primary level, is very much an income-related phenomenon. Education is also strongly influenced by attitudes as implied by the evidence that the relatively rich and well-educated shun vocational training, even though it appears to yield a comparable return in the market to general training. In addition, the fact that girls do not receive more schooling may be related to parents' attitudes, although their behavior may also be influenced by the lower market returns to girls' education. The data clearly show that availability of facilities promotes school attendance and educational attainment. Yet, household considerations should not be disregarded.
Security of ADS-B: State of the Art and Beyond

Automatic dependent surveillance-broadcast (ADS- B) is the communications protocol currently being rolled out as part of next generation air transportation systems. As the heart of modern air traffic control, it will play an essential role in the protection of two billion passengers per year, besides being crucial to many other interest groups in aviation. The inherent lack of security measures in the ADS-B protocol has long been a topic in both aviation circles as well as the academic community. Due to recently published proof-of-concept attacks, the topic is becoming ever more pressing, especially with the deadline for mandatory implementation in most airspaces fast approaching. This survey first summarizes the attacks and problems that have been reported in relation to ADS-B security. Thereafter, we survey both the theoretical and practical efforts which have been conducted previously concerning these issues, including possible countermeasures proposed in the literature. In addition, the survey seeks to go beyond the current state of the art and gives a detailed assessment of security measures which have been developed more generally for related wireless networks such as sensor networks and vehicular ad hoc networks, including a taxonomy of all considered approaches. Index Terms—ADS-B; aviation; security; wireless; privacy; broadcast
The Iowa Continuity of Care study: Background and methods.

PURPOSE The background and methods of an ongoing study to determine the effects of hospital pharmacists' enhanced communication with patients and their community providers are described. SUMMARY The Iowa Continuity of Care study is a randomized, prospective trial enrolling 1000 patients with selected medical conditions admitted to one large Midwest hospital. Patients will be randomized to a control group (usual care), minimal intervention, or enhanced intervention. For the intervention groups, a pharmacist case manager (PCM) will provide admission medication verification with the patients' community pharmacists, medication teaching, and discharge counseling. Patients in the enhanced intervention group will have a discharge care plan faxed to their outpatient physician and community pharmacist and will receive a follow-up phone call from the PCM three to five days after discharge; the PCM will continue to facilitate communication between the patient and community providers until all medication problems are resolved. A blinded research nurse will collect data, including adverse drug event (ADE) data, at admission and 30 and 90 days after discharge. The primary outcome measures include medication appropriateness, ADEs, emergency department visits, unscheduled office visits, and rehospitalizations. Data will be collected from the inpatient electronic medical record, outpatient physician medical records, and community pharmacist records and directly from patients. A cost-effectiveness analysis will be performed. CONCLUSION This study will address the value of a PCM in improving communication of care plans between the inpatient and community settings and thereby optimizing medication use.
Abstract 356: Krueppel-Like Factor 15 Regulates Wnt/β-Catenin Transcription and Controls Cardiac Progenitor Cell Fate in the Postnatal Heart

Wnt/β-catenin signaling controls adult heart remodeling partly by regulating cardiac progenitor cell (CPC) differentiation. We now identified and characterized a novel cardiac interaction of the transcription factor Krueppel-like factor 15 (KLF15) with the Wnt/β-catenin signaling on adult CPCs. In vitro mutation, reporter gene assays and co-localization studies revealed that KLF15 requires two distinct domains for nuclear localization and for repression of β-catenin-mediated transcription. KLF15 had no effect on β-catenin stability or cellular localization, but interacted with its co-factor TCF4, which is required for activation of β-catenin target gene expression. Moreover, increased TCF4 ubiquitination was induced by KLF15. In line with this finding we found KLF15 to interact with the Nemo-like kinase, which was shown to phosphorylate and target TCF4 for degradation. In vivo analyses of adult Klf15 functional knock-out (KO) vs. wild-type (WT) mice showed a cardiac β-catenin-mediated transcriptional activation and reduced TCF4 degradation along with cardiac dysfunction assessed by echocardiography (n=10). FACS analysis of the CPC enriched-population of KO vs. WT mice revealed a significant reduction of cardiogenic-committed precursors identified as Sca1+/αMHC+ (0.8±0.2% vs. 1.8±0.1%) and Tbx5+ (3.5±0.3% vs. 5.2±0.5%). In contrast, endothelial Sca1+/CD31+ cells were significantly higher in KO mice (11.3±0.4% vs. 8.6±0.4%; n≥9). In addition, Sca1+ isolated cells of Klf15 KO showed increased RNA expression of endothelial markers von Willebrand Factor, CD105, and Flk1 along with upregulation of β-catenin target genes. CPCs co-cultured on adult fibroblasts resulted in increased endothelial Flk1 cells and reduction of αMHC and Hand1 cardiogenic cells in KO vs. WT CPCs (n=9). Treating these co-cultures with Quercetin, an inhibitor of nuclear β-catenin, resulted in partial rescue of the observed phenotype. This study uncovers a critical role of KLF15 for the maintenance of cardiac tissue homeostasis. Via inhibition of β-catenin transcription, KLF15 controls cardiomyogenic cell fate similar to embryonic cardiogenesis. This knowledge may provide a tool for activation of endogenous CPCs in the postnatal heart.
De‐shadowing of satellite/airborne imagery

A de‐shadowing technique is presented for multispectral and hyperspectral imagery over land acquired by satellite/airborne sensors. The method requires a channel in the visible and at least one spectral band in the near‐infrared (0.8–1 µm) region, but performs much better if bands in the short‐wave infrared region (around 1.6 and 2.2 µm) are available as well. The algorithm consists of these major components: (i) calculation of the covariance matrix and zero‐reflectance matched filter vector, (ii) derivation of the unscaled and scaled shadow function, (iii) histogram thresholding of the unscaled shadow function to define the core shadow areas, (iv) region growing to include the surroundings of the core shadow areas for a smooth shadow/clear transition, and (v) de‐shadowing of the pixels in the final shadow mask. The critical parameters of the method are discussed. Example images from different climates and landscapes are presented to demonstrate the successful performance of the shadow removal process over land surfaces.
Simplified exhaust pipe noise radiation modelling using the Fourier PSTD method

The noise, radiated from the tailpipe of automotive exhaust ducts, is affected by the jet flow leaving the exhaust and by its surrounding geometry. The current work extends existing studies of sound radiation from a jet pipe with radiation over a rigid ground surface and relies on a numerical study. A simplified approach is used where the mean flow properties behind the tailpipe are calculated by solving the Reynolds averaged Navier-Stokes equations (RANS). The extended Fourier pseudospectral time-domain (PSTD) method is then utilized to compute the sound propagation in the tailpipe geometry by solving the linearized Euler equations (LEE). As the vorticity modes in the shear layer behind the tailpipe may turn unstable using the LEE, additional calculations with the LEE with applied high wave number dissipation and the LEE with mean flow gradient terms suppressed (LEE-GTS) are carried out. Results are validated by analytical expressions in free field and the necessity of solving the LEE rather than the LEE-GTS in the current application is shown. Finally, a calculation of tailpipe noise radiation over a ground surface is performed.
Correlation between the administrative leadership style and inclination towards organizational learning in local administrative organizations

The aim of the paper was to conduct a preliminary verification of theoretical postulates on correlation between the administrative leadership style and learning processes in local administrative organizations. The basic research hypothesis is that administrative leadership style is positively correlated with inclination to organizational learning in local administrative organizations, notwithstanding other organizational and contextual variables, such as internal organizational structure, number of employees, ruling political party and its continuity. In order to construct an empirical study, a cross-sectional study among three Croatian city governments has been applied. The main variables have been measured on the basis of civil servants’ perception of administrative leadership style and inclination to organizational learning in each organization. The results of correlation analysis between administrative leadership style, on one hand, and, each level of learning in organization and each process of learning across the levels, on the other, are presented in the paper. On the basis of the results obtained and consequent discussion, some general conclusions and recommendations for administrative organizations are provided.
Testing for Individual Effects in Dynamic Models Using Panel Data

This note presents a simple, linear test for individual effects in dynamic models using panel data; building upon the techniques of Holtz-Eakin, Newey, and Rosen (HNR) [198S] for estimating vector autoregressions using panel data. While implementing estimators which are consistent in the presence of individual effects is straightforward, there is no guarantee that this form of heterogeneity is an -important feature of the data. Moreover, there are advantages to avoiding an individual v effects specification. Thus, it is useful to have a test for the existence of individual effects. The test focuses on sample moment conditions implied by the presence of individual effects and is particularly suited for dynamic models using panel data. The calculations follow directly from linear, instrumental variable techniques which are computationally straightforward. Moreover, the test statistics follows directly from the estimation of autoregressive models.
Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

The fundamental biological and clinical importance of integral membrane proteins prompted the development of a yeast-based system for the high-throughput identification of protein-protein interactions (PPI) for full-length transmembrane proteins. To this end, our lab developed the split-ubiquitin based Membrane Yeast Two-Hybrid (MYTH) system. This technology allows for the sensitive detection of transient and stable protein interactions using Saccharomyces cerevisiae as a host organism. MYTH takes advantage of the observation that ubiquitin can be separated into two stable moieties: the C-terminal half of yeast ubiquitin (Cub) and the N-terminal half of the ubiquitin moiety (Nub). In MYTH, this principle is adapted for use as a 'sensor' of protein-protein interactions. Briefly, the integral membrane bait protein is fused to Cub which is linked to an artificial transcription factor. Prey proteins, either in individual or library format, are fused to the Nub moiety. Protein interaction between the bait and prey leads to reconstitution of the ubiquitin moieties, forming a full-length 'pseudo-ubiquitin' molecule. This molecule is in turn recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor, and subsequent induction of reporter gene expression. The system is highly adaptable, and is particularly well-suited to high-throughput screening. It has been successfully employed to investigate interactions using integral membrane proteins from both yeast and other organisms.
Sniffing Behaviours in Guenons

In Old World monkeys (OWM), the olfactory sense is thought to be less important than in other primate taxa. However, during the last decade experimental studies have shown that OWM possess much better olfactory capabilities than suspected. Here, we investigate for the very first time sniffing behaviours in three guenon species (Diana, de Brazza's and owl-faced monkeys) held in the Leipzig Zoo, Germany. We recorded frequencies and contexts of sniffing. The sniff index was used to allow comparisons across species. It was found that individuals sniffed 6.12 ± 7.69 times per hour. Most sniffing occurred in food-related contexts. Furthermore, Diana monkeys sniffed less often than de Brazza's and owl-faced monkeys. Thus, natural selection may drive the differences in using the olfactory sense in closely related primate species.