Miracle-dz/UniFAR-FTUs huggingface dataset:
The Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids

Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal infections often harbor plasmids encoding fitness traits such as resistance and virulence determinants that are of clinical importance. We determined the complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E. coli EC302/04 which was isolated from the tracheal aspirate of a patient in Malaysia. In addition, we also performed comparative sequence analyses of 18 related IncFIIA plasmids to determine the phylogenetic relationship and diversity of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The plasmid is self-transmissible with a complete transfer region. pEC302/04 also carries antibiotic resistance genes such as blaTEM−1 and a class I integron containing sul1, cml and aadA resistance genes, conferring multidrug resistance (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e., PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system, ParAB, and PsiAB, which are important for plasmid maintenance were also found. Comparative plasmid analysis revealed only one conserved gene, the repA1 as the core genome, showing that there is an extensive diversity among the IncFIIA plasmids. The phylogenetic relationship of 18 IncF plasmids based on the core regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were separated into two distinct groups. These plasmids, which carry highly diverse genetic contents, are also mosaic in nature. The atypical combination of genetic materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a single ExPEC plasmid is rare but of clinical importance. Such phenomenon is bothersome when the plasmids are transmissible, facilitating the spread of virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA systems are more commonly found in particular ExPEC plasmid types, indicating the possible relationships between certain TA systems and ExPEC pathogenesis.
An Efficient Load Frequency Control Technique for Two-Area, Multi-source Interconnected Power Systems Considering Renewables

This paper suggests an efficient load frequency control (LFC) based on a tilted-integral-derivative (TID) controller to approach the frequency stability of multi-area interconnected power systems that contain renewable energy sources (RESs). The studied power system includes two equal areas, each of which contains conventional power plants; reheat-thermal, hydraulic, and gas power plants, and RESs; solar, and wind power plants. Moreover, the proposed TID controller is established with the help of a new optimizer known as the dandelion optimizer (DO). To evaluate the superiority of the proposed DO algorithm, its responses and results are compared with other new optimization algorithms such as the sperm swarm optimizer and black widow optimization algorithm. Furthermore, the superiority and robustness of the proposed TID controller depending on the DO algorithm is confirmed by comparing it with other controllers used in the literature such as the proportional-integral-derivative (PID) controller and fractional-order PID (FOPID) controller. The simulation results of the system response carried out by the software MATLAB show that the proposed TID controller based on the DO algorithm is viable and reliable under a range of load fluctuations and random power generated by RESs.
Assessing the Security of a Navigation System : A Case Study using Enhanced Loran

Global Navigation Satellite Systems (GNSS) has become increasingly interwoven into the fabric of our infrastructure and economic system. However, as GNSS becomes more important for safety of life and economically critical infrastructure, subversive elements will be increasingly tempted to deny or spoof its signals. The fact that GNSS has vulnerabilities is well known and it is becoming recognized that back ups to GNSS are necessary [1]. Indeed, we are hopefully moving to a more comprehensive approach to position, navigation and timing (PNT) architecture. An element that should be central to the consideration is security. This paper examines the security capabilities of Loran as a case study for examining both a secure navigation system and a secure back up to GNSS. Loran, in particular the next generation Enhanced Loran (eLoran), has many properties that make it a good complement to GNSS. It has similar outputs and performance as GNSS. As it is an area navigation (RNAV) system, it can be used to drive the same interfaces as GNSS. eLoran is being developed to provide performance levels that can support non precision approach (NPA), harbor entrance approach (HEA), and stratum 1 frequency and precise timing. At the same time, it is an independent system and has failure modes that differ from GNSS. The attractiveness of Loran as part of a full PNT architecture has been recognized by the US Department of Homeland Security (DHS). In 2008, the DHS announced that eLoran will be implemented to provide “an independent national positioning, navigation and timing system that complements the Global Positioning System (GPS) in the event of an outage or disruption in service [2]. ” Europe has also recognized this with the General Lighthouse Authority (GLA) of England, Ireland, and Scotland also promulgating the development of eLoran for maritime use [3].
Complex Interpersonal Conflict Behaviour: Theoretical Frontiers

Part I: Introduction. Preview. Part II: Description. First Step: Description of Behavioural Components. Second Step: Descriptive Dimensions. Part III: Explanation. Third Step: Explanatory Dimensions. Fourth Step: Complexity Explanations. Part IV: Conclusion. Renewed View. Thirty-four Propositions. References. Glossary. Indices.
The Development and Validation of a Revised Version of the Mathematics Anxiety Rating Scale

A 24-item shortened version of the 98-item Mathematics Anxiety Rating Scale (MARS) was developed to provide a more efficient index of statistics or mathematics course-related anxiety. The revised scale, which yielded a coefficient alpha reliability estimated at . 98, was correlated . 97 with a full scale MARS. It shows a pattern of relationships with state, trait, and test anxiety parallel to that of full scale MARS. Further, the relationship with mathematics achievement was consistent for both the revised and full scale MARS. A principal axes factor analysis of revised MARS identified two clear factors, labeled "Learning Mathematics Anxiety" and "Mathematics Evaluation Anxiety. " Revised MARS appears to be an attractive substitute for full scale MARS for statistical or mathematical course-related uses.
Development of Immunocompetent Lymphocytes In Vivo From Murine Umbilical Cord Blood Cells

Background. Reports concerning the immunological functions of lymphocytes derived from umbilical cord blood cell (UCBC) have been limited. Methods. In murine syngeneic transplantation system using green fluorescent protein transgenic donors, UCBC-derived lymphocytes were studied for their immunological competence. Results. Hematopoietic stem cells (HSC) among UCBC differentiated in the recipients into phenotypically mature T and B lymphocytes. The T lymphocytes were capable of specific recognition of major histocompatibility complex/peptide complex and of the subsequent activation. The antigen-induced CD4+ T cells produced lymphokine upon in vitro antigen stimulation. CD8+ T cells simulated in the mixed lymphocyte culture could lyze specific target cells. Furthermore, RAG2(−/−) mice reconstituted with UCBC mounted specific antibody responses to T-dependent antigen comparable to those by bone marrow chimeras and also rejected allogeneic skin grafts. Conclusion. Collectively the data indicated that T and B lymphocytes derived from UCBC-HSC are fully competent in immunological terms.
Higher biodiversity is required to sustain multiple ecosystem processes across temperature regimes

Biodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1–4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive‐based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment.
Text mining for the biocuration workflow

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.
Supporting Computing Element Heterogeneity in P2P Grids

We propose resource discovery and load balancing techniques to accommodate computing nodes with many types of computing elements, such as multi-core CPUs and GPUs, in a peer-to-peer desktop grid architecture. Heterogeneous nodes can have multiple types of computing elements, and the performance and characteristics of each computing element can be very different. Our scheme takes into account these diverse aspects of heterogeneous nodes to maximize overall system throughput. However, straightforward methods of handling diverse computing elements that differ on many axes can result in high overheads, both in local state and in communication volume. We describe approaches that minimize messaging costs without sacrificing the failure resilience provided by an underlying peer-to-peer overlay network. Simulation results show that our scheme's load balancing performance is comparable to that of a centralized approach, that communication costs are reduced significantly compared to the existing system, and that failure resilience is not compromised.
The Role of PET/CT for Evaluating Breast Cancer

Positron emission tomography combined with computed tomography (PET/CT) has been receiving increasing attention during the recent years for making the diagnosis, for determining the staging and for the follow-up of various malignancies. The PET/CT findings of 58 breast cancer patients (age range: 34-79 years old, mean age: 50 years) were retrospectively compared with the PET or CT scans alone. PET/CT was found to be better than PET or CT alone for detecting small tumors or multiple metastases, for accurately localizing lymph node metastasis and for monitoring the response to chemotherapy in breast cancer patients.
Formation Modelling and 6DOF Spacecraft Coordination Control

In this paper we present a 6DOF Euler-Lagrange model formulation of relative translation and rotation in a leader-follower spacecraft formation. To show the applicability of the model, we also present a solution to the problem of relative translational and rotational tracking, using the concept of vectorial integrator backstepping. The controller solution utilizes the quaternion representation to achieve a shorter rotation path on commanded attitude changes, and the equilibrium points in the closed-loop system are proved to be uniformly asymptotically stable. Finally, simulation results are presented to show the performance of the derived control law, together with the impact of orbital perturbations when these are left uncompensated.
Measuring insect rarity: practical issues, pragmatic approaches

Rarity is often considered an indication of species extinction risk, and rarity measures are used as important tools to predict species vulnerability and hence to establish conservation priorities. For these reasons, rarity is among the most important issues involved in conservation programs. A number of studies have attempted to investigate relationships between rarity and extinction risk in plants and vertebrates, whereas only few papers have investigated similar issues in invertebrate taxa. This has limited the use of standardized rarity measures in invertebrate conservation studies. Assessing rarity is especially important when other pieces of information are difficult, or even definitively impossible, to obtain, as commonly found for most insects. Four broad categories of rarity are commonly recognized: geographical, ecological, population and phylogenetic rarity. On the basis of this framework, we present here a short review of the rarity forms most frequently investigated in insect studies, and their relationships with the main species traits related to extinction risk (such as body size, mobility, trophic level, host specificity, larval and adult behaviours, etc.). We discuss what they mean, how they can be measured, which type of data (field collections, museum data, literature information) are needed and how to avoid the most common pitfalls associated with rarity studies, with indications for pragmatic approaches in data analysis.
Akt Determines Cell Fate Through Inhibition of the PERK-eIF2α Phosphorylation Pathway

Inhibition of a stress-response pathway renders tumor cells more susceptible to death induced by inhibitors of phosphoinositide 3-kinase signaling. Increasing the Chances of Death Regulation of mRNA translation affects cell growth, proliferation, and differentiation and involves several eukaryotic initiation factors (eIFs). Cells respond to various stresses by blocking the initiation of translation through the phosphorylation of the eIF2α subunit by a number of kinases, including PERK. Increased signaling by the kinases phosphoinositide 3-kinase (PI3K) and Akt is commonly observed in human cancers and leads to the phosphorylation of several proteins involved in the regulation of cell survival and proliferation. Mounir et al. found that the activity of PERK and the amount of phosphorylated eIF2α (eIF2αP) were increased in cells deficient in Akt signaling. The authors showed that Akt-mediated phosphorylation of PERK inhibited its activity and blocked the phosphorylation of eIF2α. In cells undergoing oxidative or endoplasmic reticulum stress, the PERK-eIF2αP pathway antagonized the activity of Akt. Finally, blocking the PERK-eIF2αP pathway rendered tumor cells more susceptible to death after treatment with inhibitors of PI3K-Akt signaling. These data suggest that Akt can control protein synthesis through the PERK-eIF2αP pathway and that inactivation of PERK and eIF2αP may improve the efficacy of therapies that target PI3K-Akt signaling. Metazoans respond to various forms of environmental stress by inducing the phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α) at serine-51, a modification that leads to global inhibition of mRNA translation. We demonstrate induction of the phosphorylation of eIF2α in mammalian cells after either pharmacological inhibition of the phosphoinositide 3-kinase (PI3K)–Akt pathway or genetic or small interfering RNA–mediated ablation of Akt. This increase in the extent of eIF2α phosphorylation also occurred in Drosophila cells and depended on the endoplasmic reticulum (ER)–resident protein kinase PERK, which was inhibited by Akt-dependent phosphorylation at threonine-799. The activity of PERK and the abundance of phosphorylated eIF2α (eIF2αP) were reduced in mouse mammary gland tumors that contained activated Akt, as well as in cells exposed to ER stress or oxidative stress. In unstressed cells, the PERK-eIF2αP pathway mediated survival and facilitated adaptation to the deleterious effects of the inactivation of PI3K or Akt. Inactivation of the PERK-eIF2αP pathway increased the susceptibility of tumor cells to death by pharmacological inhibitors of PI3K or Akt. Thus, we suggest that the PERK-eIF2αP pathway provides a link between Akt signaling and translational control, which has implications for tumor formation and treatment.
Synthesizing Java expressions from free-form queries

We present a new code assistance tool for integrated development environments. Our system accepts as input free-form queries containing a mixture of English and Java, and produces Java code expressions that take the query into account and respect syntax, types, and scoping rules of Java, as well as statistical usage patterns. In contrast to solutions based on code search, the results returned by our tool need not directly correspond to any previously seen code fragment. As part of our system we have constructed a probabilistic context free grammar for Java constructs and library invocations, as well as an algorithm that uses a customized natural language processing tool chain to extract information from free-form text queries. We present the results on a number of examples showing that our technique (1) often produces the expected code fragments, (2) tolerates much of the flexibility of natural language, and (3) can repair incorrect Java expressions that use, for example, the wrong syntax or missing arguments.
Distributed Storage to Support User Interactivity in Peer-to-Peer Video Streaming

Providing random access function in peer-to-peer on-demand video streaming is a challenging task, due to not only the asynchronous user interactivity but also the unpredictability of group dynamics. In this paper, we propose VMesh, a distributed peer-to-peer video-on-demand (VoD) streaming scheme which efficiently supports random seeking functionality. In VMesh, videos are divided into segments and stored in peers in a distributed manner. An overlay mesh is built upon peers to support jumping forward/backward, pause and restart during playback. Our scheme utilizes the large total storage capacity of peers to improve the segment supply so as to support interactive commands in a scalable manner. Through simulation, we show that our system outperforms a recent work, P2VoD. VMesh also has low segment missing rate under random member join/leave. In addition, the system achieves low joining and seeking latencies which are crucial requirements in an interactive VoD system.
Spectrum refarming for OFDMA small cells overlaying CDMA cellular networks

In this paper, a novel spectrum refarming (SR) system is proposed in which the Orthogonal Frequency Division Multiple Access (OFDMA) small cells overlay the Code Division Multiple Access (CDMA) cellular networks in the same legacy CDMA spectrum. In order to predict and control the interferences from the OFDMA small cells to the CDMA macrocell, the OFDMA downlink transmissions in the small cells are arranged to be synchronous with the CDMA uplink transmission in the macrocell. We first analyze the interferences between the OFDMA small cells and CDMA macrocell, then formulate the OFDMA resource allocation problem for this proposed SR system. Through assigning the interference margins to each OFDMA small cell, a new resource allocation algorithm is proposed to solve the formulated problem efficiently. Simulation results are given to validate the effectiveness of the proposed algorithm and evaluate the performance of the proposed SR system.
Introduction to General Linear Models

In this chapter, we introduce general linear models (GLM) that have been widely used in brain imaging applications. The GLM is a very flexible and general statistical framework encompassing a wide variety of fixed effect models such as the multiple regressions, the analysis of variance (ANOVA), the multivariate analysis of variance (MANOVA), the analysis of covariance (ANCOVA) and the multivariate analysis of covariance (MANCOVA) [5]. Note that the term linear is misleading in a sense that the model can also include mathematically nonlinear model terms such as the higher degree polynomials. This chapter is mainly based on [2]. The GLM provides a framework for testing various associations and hypotheses while accounting for nuisance covariates in the model in a straightforward fashion. The effect of age, sex, brain size and possibly IQ can have severe confounding effects on the final outcome of many anatomical and functional imaging studies. Older population’s reduced functional activation could be the consequence of age-related atrophy of neural systems [3]. Brain volumes are significantly larger for children with autism 12 years old and younger compared with normally developing children [1]. Therefore, it is desirable to account for various confounding factors such as age and sex in the model. This can be done using GLM. The parameters of the GLM are mainly estimated by the least squares estimation and has been implemented in many statistical packages such as R (www.r-project.org) or Splus [4] and brain imaging packages such as SPM (www.fil.ion.ucl.ac.uk/spm) and fMRISTAT (www.math.mcgill.ca/keith/fmristat).