bluuebunny/crossref_metadata_2025 huggingface dataset:
Escherichia coli
O104:H4 Pathogenesis: an Enteroaggregative
E. coli
/Shiga Toxin-Producing
E. coli
Explosive Cocktail of High Virulence
Authors: Navarro-Garcia Fernando
Published: May 2015

A major outbreak caused by
Escherichia coli
of serotype O104:H4 spread throughout Europe in 2011. This large outbreak was caused by an unusual strain that is most similar to enteroaggregative
E. coli
(EAEC) of serotype O104:H4. A significant difference, however, is the presence of a prophage encoding the Shiga toxin, which is characteristic of enterohemorrhagic
E. coli
(EHEC) strains. This combination of genomic features, associating characteristics from both EAEC and EHEC, represents a new pathotype. The 2011
E. coli
O104:H4 outbreak of hemorrhagic diarrhea in Germany is an example of the explosive cocktail of high virulence and resistance that can emerge in this species. A total of 46 deaths, 782 cases of hemolytic-uremic syndrome, and 3,128 cases of acute gastroenteritis were attributed to this new clone of EAEC/EHEC. In addition, recent identification in France of similar O104:H4 clones exhibiting the same virulence factors suggests that the EHEC O104:H4 pathogen has become endemically established in Europe after the end of the outbreak. EAEC strains of serotype O104:H4 contain a large set of virulence-associated genes regulated by the AggR transcription factor. They include, among other factors, the pAA plasmid genes encoding the aggregative adherence fimbriae, which anchor the bacterium to the intestinal mucosa (stacked-brick adherence pattern on epithelial cells). Furthermore, sequencing studies showed that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga toxin-producing EAEC O104:H4 strain that caused the German outbreak. This article discusses the role these virulence factors could have in EAEC/EHEC O104:H4 pathogenesis.
Overview and Historical Perspectives
Authors: Kaper James B. , O'Brien Alison D.
Published: May 2015

In this overview, we describe the history of Shiga toxin (Stx)-producing
Escherichia coli
(STEC) in two phases. In phase one, between 1977 and 2011, we learned that
E. coli
could produce Shiga toxin and cause both hemorrhagic colitis and the hemolytic-uremic syndrome in humans and that the prototype STEC—
E. coli
O157:H7—adheres to and effaces intestinal epithelial cells by a mechanism similar to that of enteropathogenic
E. coli
. We also recognized that the genes for Stx are typically encoded on a lysogenic phage; that STEC O157:H7 harbors a large pathogenicity island that encodes the elements needed for the characteristic attaching and effacing lesion; and that the most severe cases of human disease are linked to production of Stx type 2a, not Stx type 1a. Phase two began with a large food-borne outbreak of hemorrhagic colitis and hemolytic-uremic syndrome in Germany in 2011. That outbreak was caused by a novel strain consisting of enteroaggregative
E. coli
O104:H4 transduced by a Stx2a-converting phage. From this outbreak we learned that any
E. coli
strain that can adhere tightly to the human bowel (either by a biofilm-like mechanism as in
E. coli
O104:H4 or by an attaching and effacing mechanism as in
E. coli
O157:H7) can cause severe diarrheal and systemic illness when it acquires the capacity to produce Stx2a. This overview provides the basis for the review of current information regarding these fascinating and complex pathogens.
c-di-GMP and its Effects on Biofilm Formation and Dispersion: a
Pseudomonas Aeruginosa
Review
Authors: Ha Dae-Gon , O'Toole George A.
Published: May 2015

Since its initial discovery as an allosteric factor regulating cellulose biosynthesis in
Gluconacetobacter xylinus
, the list of functional outputs regulated by c-di-GMP has grown. We have focused this article on one of these c-di-GMP-regulated processes, namely, biofilm formation in the organism
Pseudomonas aeruginosa
. The majority of diguanylate cyclases and phosphodiesterases encoded in the
P. aeruginosa
genome still remain uncharacterized; thus, there is still a great deal to be learned about the link between c-di-GMP and biofilm formation in this microbe. In particular, while a number of c-di-GMP metabolizing enzymes have been identified that participate in reversible and irreversible attachment and biofilm maturation, there is a still a significant knowledge gap regarding the c-di-GMP output systems in this organism. Even for the well-characterized Pel system, where c-di-GMP-mediated transcriptional regulation is now well documented, how binding of c-di-GMP by PelD stimulates Pel production is not understood in any detail. Similarly, c-di-GMP-mediated control of swimming, swarming and twitching also remains to be elucidated. Thus, despite terrific advances in our understanding of
P. aeruginosa
biofilm formation and the role of c-di-GMP in this process since the last version of this book (indeed there was no chapter on c-di-GMP!) there is still much to learn.
Everyman's Guide to Bacterial Insertion Sequences
Authors: Siguier Patricia , Gourbeyre Edith , Varani Alessandro , Ton-Hoang Bao , Chandler Mick
Published: May 2015

The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.

In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.
Tyrosine Recombinase Retrotransposons and Transposons
Authors: Poulter Russell T. M. , Butler Margi I.
Published: May 2015

Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold
Dictyostelium discoideum
. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.
Sleeping Beauty
Transposition
Authors: Ivics Zoltán , Izsvák Zsuzsanna
Published: May 2015

Sleeping Beauty
(
SB
) is a synthetic transposon that was constructed based on sequences of transpositionally inactive elements isolated from fish genomes.
SB
is a Tc1/
mariner
superfamily transposon following a cut-and-paste transpositional reaction, during which the element-encoded transposase interacts with its binding sites in the terminal inverted repeats of the transposon, promotes the assembly of a synaptic complex, catalyzes excision of the element out of its donor site, and integrates the excised transposon into a new location in target DNA.
SB
transposition is dependent on cellular host factors. Transcriptional control of transposase expression is regulated by the HMG2L1 transcription factor. Synaptic complex assembly is promoted by the HMGB1 protein and regulated by chromatin structure.
SB
transposition is highly dependent on the nonhomologous end joining (NHEJ) pathway of double-strand DNA break repair that generates a transposon footprint at the excision site. Through its association with the Miz-1 transcription factor, the
SB
transposase downregulates cyclin D1 expression that results in a slowdown of the cell-cycle in the G1 phase, where NHEJ is preferentially active. Transposon integration occurs at TA dinucleotides in the target DNA, which are duplicated at the flanks of the integrated transposon.
SB
shows a random genome-wide insertion profile in mammalian cells when launched from episomal vectors and “local hopping” when launched from chromosomal donor sites. Some of the excised transposons undergo a self-destructive autointegration reaction, which can partially explain why longer elements transpose less efficiently.
SB
became an important molecular tool for transgenesis, insertional mutagenesis, and gene therapy.
Ty3, a Position-specific Retrotransposon in Budding Yeast
Authors: Sandmeyer Suzanne , Patterson Kurt , Bilanchone Virginia
Published: May 2015

Long terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element ofSaccharomyces cerevisiaeis one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3–Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3–Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3–Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.
An Unexplored Diversity of Reverse Transcriptases in Bacteria
Authors: Zimmerly Steven , Wu Li
Published: May 2015

Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.
Topological Behavior of Plasmid DNA
Authors: Higgins N. Patrick , Vologodskii Alexander V.
Published: May 2015

The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing
in vivo
and
in vitro
reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
Plasmid Detection, Characterization, and Ecology
Authors: Smalla Kornelia , Jechalke Sven , Top Eva M.
Published: May 2015

Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
Risk factors for injury in sport climbing and bouldering: a systematic review of the literature
Authors: Woollings Kaikanani Y , McKay Carly D , Emery Carolyn A
Published: May 2015

Background

Rock climbing is an increasingly popular sport worldwide, as a recreational activity and a competitive sport. Several disciplines including sport climbing and bouldering have developed, each employing specific movements and techniques, leading to specific injuries.

Objective

To examine risk factors and prevention measures for injury in sport climbing and bouldering, and to assess the methodological quality of existing studies.

Methods

12 electronic databases and several other sources were searched systematically using predetermined inclusion and exclusion criteria. Eligible articles were peer-reviewed, based on primary research using original data; outcome measures included injury, morbidity or mortality in rock climbing, and included one or more potential risk factor or injury prevention strategy. Two independent reviewers assessed the methodology of research in each study using the Downs and Black Quality Index. The data extracted is summarised, and appraisals of the articles are presented with respect to the quality of evidence presented.

Results

19 studies met the inclusion criteria, and introduced 35 possible risk factors or injury prevention measures in climbing. Age, increasing years of climbing experience, highest climbing grade achieved (skill level), high climbing intensity score (CIS) and participating in lead climbing are potential risk factors. Results regarding injury prevention measures remain inconclusive.

Discussion

This field is relatively new and, as such, the data are not as robust as for more established sports with a larger research foundation. The key need is establishing modifiable risk factors using prospective studies and high quality methodology, such that injury prevention strategies can be developed. The CIS may be a useful measure in this field of research.
Extra Physiotherapy in Critical Care (EPICC) Trial Protocol: a randomised controlled trial of intensive versus standard physical rehabilitation therapy in the critically ill
Authors: Thomas Kirsty , Wright Stephen E , Watson Gillian , Baker Catherine , Stafford Victoria , Wade Clare , Chadwick Thomas J , Mansfield Leigh , Wilkinson Jennifer , Shen Jing , Deverill Mark , Bonner Stephen , Hugill Keith , Howard Philip , Henderson Andrea , Roy Alistair , Furneval Julie , Baudouin Simon V
Published: May 2015

Introduction

Patients discharged from Critical Care suffer from excessive longer term morbidity and mortality. Physical and mental health measures of quality of life show a marked and immediate fall after admission to Critical Care with some recovery over time. However, physical function is still significantly reduced at 6 months. The National Institute for Health and Care Excellence clinical guideline on rehabilitation after critical illness, identified the need for high-quality randomised controlled trials to determine the most effective rehabilitation strategy for critically ill patients at risk of critical illness-associated physical morbidity. In response to this, we will conduct a randomised controlled trial, comparing physiotherapy aimed at early and intensive patient mobilisation with routine care. We hypothesise that this intervention will improve physical outcomes and the mental health and functional well-being of survivors of critical illness.

Methods and analysis

308 adult patients who have received more than 48 h of non-invasive or invasive ventilation in Critical Care will be recruited to a patient-randomised, parallel group, controlled trial, comparing two intensities of physiotherapy. Participants will be randomised to receive either standard or intensive physiotherapy for the duration of their Critical Care admission. Outcomes will be recorded on Critical Care discharge, at 3 and 6 months following initial recruitment to the study. The primary outcome measure is physical health at 6 months, as measured by the SF-36 Physical Component Summary. Secondary outcomes include assessment of mental health, activities of daily living, delirium and ventilator-free days. We will also include a health economic analysis.

Ethics and dissemination

The trial has ethical approval from Newcastle and North Tyneside 2 Research Ethics Committee (11/NE/0206). There is a Trial Oversight Committee including an independent chair. The results of the study will be submitted for publication in peer-reviewed journals and presented at national and international scientific meetings.

Trial registration number

ISRCTN20436833.
Discrete element modeling of fluid injection–induced seismicity and activation of nearby fault
Authors: Yoon Jeoung Seok , Zimmermann Günter , Zang Arno , Stephansson Ove
Published: May 2015

Enhanced geothermal systems, shale gas, and geological carbon sequestration all require underground fluid injection in high-pressure conditions. Fluid injection creates fractures, induces seismicity, and has the potential to reactivate nearby faults that can generate a large magnitude earthquake. Mechanisms of fluid injection–induced seismicity and fault reactivation should be better understood to be able to mitigate larger events triggered by fluid injection. This study investigates fluid injection, induced seismicity, and triggering of fault rupture using hydromechanical-coupled discrete element models. Results show that a small amount of fluid pressure perturbation can trigger fault ruptures that are critically oriented and stressed. Induced seismicity by rock failure shows in general higher b-values (slope of magnitude–frequency relation) compared to seismicity triggered by the fault fracture slip. Numerical results closely resemble observations from geothermal and shale-gas fields and demonstrate that discrete element modeling has the potential to be applied in the field as a tool for predicting induced seismicity prior to in situ injection.
Cell Assembly Signatures Defined by Short-Term Synaptic Plasticity in Cortical Networks
Authors: Carrillo-Reid Luis , Lopez-Huerta Violeta G. , Garcia-Munoz Marianela , Theiss Stephan , Arbuthnott Gordon W.
Published: May 2015

The cell assembly (CA) hypothesis has been used as a conceptual framework to explain how groups of neurons form memories. CAs are defined as neuronal pools with synchronous, recurrent and sequential activity patterns. However, neuronal interactions and synaptic properties that define CAs signatures have been difficult to examine because identities and locations of assembly members are usually unknown. In order to study synaptic properties that define CAs, we used optical and electrophysiological approaches to record activity of identified neurons in mouse cortical cultures. Population analysis and graph theory techniques allowed us to find sequential patterns that represent repetitive transitions between network states. Whole cell pair recordings of neurons participating in repeated sequences demonstrated that synchrony is exhibited by groups of neurons with strong synaptic connectivity (concomitant firing) showing short-term synaptic depression (STD), whereas alternation (sequential firing) is seen in groups of neurons with weaker synaptic connections showing short-term synaptic facilitation (STF). Decreasing synaptic weights of a network promoted the generation of sequential activity patterns, whereas increasing synaptic weights restricted state transitions. Thus in simple cortical networks of real neurons, basic signatures of CAs, the properties that underlie perception and memory in Hebb's original description, are already present.
Online Epileptic Seizure Prediction Using Wavelet-Based Bi-Phase Correlation of Electrical Signals Tomography
Authors: Vahabi Zahra , Amirfattahi Rasoul , Shayegh Farzaneh , Ghassemi Fahimeh
Published: May 2015

Considerable efforts have been made in order to predict seizures. Among these methods, the ones that quantify synchronization between brain areas, are the most important methods. However, to date, a practically acceptable result has not been reported. In this paper, we use a synchronization measurement method that is derived according to the ability of bi-spectrum in determining the nonlinear properties of a system. In this method, first, temporal variation of the bi-spectrum of different channels of electro cardiography (ECoG) signals are obtained via an extended wavelet-based time-frequency analysis method; then, to compare different channels, the bi-phase correlation measure is introduced. Since, in this way, the temporal variation of the amount of nonlinear coupling between brain regions, which have not been considered yet, are taken into account, results are more reliable than the conventional phase-synchronization measures. It is shown that, for 21 patients of FSPEEG database, bi-phase correlation can discriminate the pre-ictal and ictal states, with very low false positive rates (FPRs) (average: 0.078/h) and high sensitivity (100%). However, the proposed seizure predictor still cannot significantly overcome the random predictor for all patients.
Triangulations and quadrangulations of the sphere
Authors: Sağlam İsmail
Published: May 2015

Thurston proved that the space of non-negatively curved triangulations of the 2-sphere can be parametrized by a quotient of a lattice by a group. We prove his result by a new method. Also we prove similar results for some different families of triangulations and quadrangulations of the 2-sphere.
Study of Biomolecules Imaging Using Molecular Dynamics Simulations
Authors: Kheirodin Mohsen , Pishkenari Hossein Nejat , Moosavi Ali , Meghdari Ali
Published: May 2015

The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip–sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a graphene sheet is used as the substrate. The effects of CNT's geometric parameters such as the CNT height, the diameter, the tilt angle, the flexibility and the number of layers on the image quality have been evaluated.
Colored Petri nets
Authors: Jensen Kurt , Kristensen Lars M.
Published: May 2015

Formal executable models enable systematic evaluation of system designs prior to implementation and deployment.
Evaluation without ground truth in social media research
Authors: Zafarani Reza , Liu Huan
Published: May 2015

Even without it, some ingenious methods can be developed to help verify users' social media behavioral patterns.
Investigating Task Coordination in Globally Dispersed Teams
Authors: Sutanto Juliana , Kankanhalli Atreyi , Yian Tan Bernard Cheng
Published: May 2015

Task coordination poses significant challenges for globally dispersed teams (GDTs). Although various task coordination mechanisms have been proposed for such teams, there is a lack of systematic examination of the appropriate coordination mechanisms for different teams based on the nature of their task and the context under which they operate. Prior studies on collocated teams suggest matching their levels of task dependence to specific task coordination mechanisms for effective coordination. This research goes beyond the earlier work by also considering additional contextual factors of GDT (i.e., temporal dispersion and time constraints) in deriving their optimal IT-mediated task coordination mechanisms. Adopting the structural contingency theory, we propose optimal IT-mediated task coordination portfolios to fit the different levels of task dependence, temporal dispersion, and perceived time constraint of GDTs. The proposed fit is tested through a survey and profile analysis of 95 globally dispersed software development teams in a large financial organization. We find, as hypothesized, that the extent of fit between the actual IT-mediated task coordination portfolios used by the surveyed teams and their optimal portfolios proposed here is positively related to their task coordination effectiveness that in turn impacts the team's efficiency and effectiveness. The implications for theory and practice are discussed.
Future internets escape the simulator
Authors: Berman Mark , Demeester Piet , Lee Jae Woo , Nagaraja Kiran , Zink Michael , Colle Didier , Krishnappa Dilip Kumar , Raychaudhuri Dipankar , Schulzrinne Henning , Seskar Ivan , Sharma Sachin
Published: May 2015

Future Internet testbeds permit experiments not possible in today's public Net or commercial cloud services.
Efficient Fault-Tolerant Topology Reconfiguration Using a Maximum Flow Algorithm
Authors: Ren Yu , Liu Leibo , Yin Shouyi , Han Jie , Wei Shaojun
Published: May 2015

With an increasing number of processing elements (PEs) integrated on a single chip, fault-tolerant techniques are critical to ensure the reliability of such complex systems. In current reconfigurable architectures, redundant PEs are utilized for fault tolerance. In the presence of faulty PEs, the physical topologies of various chips may be different, so the concept of virtual topology from network embedding problem has been used to alleviate the burden for the operating systems. With limited hardware resources, how to reconfigure a system into the most effective virtual topology such that the maximum repair rate can be reached presents a significant challenge. In this article, a new approach using a maximum flow (MF) algorithm is proposed for an efficient topology reconfiguration in reconfigurable architectures. In this approach, topology reconfiguration is converted into a network flow problem by constructing a directed graph; the solution is then found by using the MF algorithm. This approach optimizes the use of spare PEs with minimal impacts on area, throughput, and delay, and thus it significantly improves the repair rate of faulty PEs. In addition, it achieves a polynomial reconfiguration time. Experimental results show that compared to previous methods, the MF approach increases the probability to repair faulty PEs by up to 50% using the same redundant resources. Compared to a fault-free system, the throughput only decreases by less than 2.5% and latency increases by less than 4%. To consider various types of PEs in a practical application, a cost factor is introduced into the MF algorithm. An enhanced approach using a minimum-cost MF algorithm is further shown to be efficient in the fault-tolerant reconfiguration of heterogeneous reconfigurable architectures.
IllumiRoom
Authors: Jones Brett R. , Benko Hrvoje , Ofek Eyal , Wilson Andrew D.
Published: May 2015

IllumiRoom is a proof-of-concept system that surrounds a television with projected light, bringing video games, and film experiences out of the TV screen and into the real world. IllumiRoom uses 3D scanning and projected light to change the appearance of the room, induce apparent motion, extend the field of view, and enable entirely new gaming experiences. Our system is entirely self-calibrating and is designed to work in any room. We present a detailed exploration of the design space of possible projected visualizations and we demonstrate ways to trigger and drive these visualizations from gaming content. We also contribute specific feedback from two groups of target users (10 gamers and 15 game designers); providing insights for enhancing game and film experiences beyond the TV.
Integrating Transactions into BPEL Service Compositions
Authors: Sun Chang-Ai , Zhang Xin , Shang Yan , Aiello Marco
Published: May 2015

The concept of software as a service has been increasingly adopted to develop distributed applications. Ensuring the reliability of loosely coupled compositions is a challenging task because of the open, dynamic, and independent nature of composable services; this is especially true when the execution of a service-based process relies on independent but correlated services. Transactions are the prototypical case of compositions spanning across multiple services and needing properties to be valid throughout the whole execution. Although transaction protocols and service composition languages have been proposed in the past decade, a true viable and effective solution is still missing. In this article, we propose a systematic aspect-based approach to integrating transactions into service compositions, taking into account the well-known protocols: Web Service Transaction and Business Process Execution Language (BPEL). In our approach, transaction policies are first defined as a set of aspects. They are then converted to standard BPEL elements. Finally, these transaction-related elements and the original BPEL process are weaved together, resulting in a transactional executable BPEL process. At runtime, transaction management is the responsibility of a middleware, which implements the coordination framework and transaction protocols followed by the transactional BPEL process and transaction-aware Web services. To automate the proposed approach, we developed a supporting platform called
Salan
to aid the tasks of defining, validating, and weaving aspect-based transaction policies, and of deploying the transactional BPEL processes. By means of a case study, we demonstrate the proposed approach and evaluate the performance of the supporting platform. Experimental results show that this approach is effective in producing reliable business processes while reducing the need for direct human involvement.
Constructing semantic interpretation of routine and anomalous mobility behaviors from big data
Authors: Fuchs Georg , Stange Hendrik , Hecker Dirk , Andrienko Natalia , Andrienko Gennady
Published: May 2015

Annually organized VAST Challenges provide a unique opportunity to analyze complex data with available ground truth. In 2014, one of the tasks was to interpret routine and anomalous patterns of human mobility based on big data: trajectories of cars and credit card transactions.

We describe a scalable visual analytics approach to solving this problem. Repeatedly visited personal and public places were extracted from trajectories by finding spatial clusters of stop points. Temporal patterns of people's presence in the places resulted from spatio-temporal aggregation of the data by the places and hourly intervals within the weekly cycle. Based on these patterns, we identified the meanings or purposes of the places: home, work, breakfast, lunch and dinner, etc. Meanings of some places could be refined using the credit card transaction data. By representing the place meanings as points on a 2D plane, we built an abstract semantic space and transformed the original trajectories to trajectories in the semantic space, i.e., performed
semantic abstraction
of the data. Spatio-temporal aggregation of the transformed trajectories into flows between the semantic places and subsequent clustering of time intervals by the similarity of the flow situations allowed us to reveal and analyze the routine movement behaviors. To detect anomalies, we (a) investigated the visits to the places with unknown meanings, and (b) looked for unusual presence times or visit durations at different semantic places.

The analysis is scalable since all tools and methods can be applied to much larger data. Moreover, the semantic data abstraction can serve as a tool for protecting the personal privacy.
New Research Directions in Knowledge Discovery and Allied Spheres
Authors: Nica Anisoara , Suchanek Fabian M. , Varde Aparna S.
Published: May 2015

The realm of knowledge discovery extends across several allied spheres today. It encompasses database management areas such as data warehousing and schema versioning; information retrieval areas such as Web semantics and topic detection; and core data mining areas, e.g., knowledge based systems, uncertainty management, and time-series mining. This becomes particularly evident in the topics that Ph.D. students choose for their dissertation. As the grass roots of research, Ph.D. dissertations point out new avenues of research, and provide fresh viewpoints on combinations of known fields. In this article we overview some recently proposed developments in the domain of knowledge discovery and its related spheres. Our article is based on the topics presented at the doctoral workshop of the ACM Conference on Information and Knowledge Management, CIKM 2011.
Pyogenes Riesengranulom bei einer Patientin mit chronischer lymphatischer Leukämie
Authors: Plovanich Molly , Tsibris Hillary C. , Lian Christine G. , Mostaghimi Arash
Published: May 2015

Das pyogene Granulom, auch als lobuläres kapilläres Hämangiom bezeichnet, ist eine häufige, gutartige, proliferative vaskuläre Läsion, die in jedem Alter auf der Haut oder den Schleimhäuten auftreten kann. Die meisten Läsionen werden nicht größer als 2 cm, es liegen jedoch auch Berichte über vereinzelte Fälle von riesenhaften pyogenen Granulomen der Haut vor, meist bei Patienten mit zugrunde liegender Funktionsstörung des Immunsystems. Hier berichten wir erstmals über ein pyogenes Riesengranulom bei einer Patientin mit einer malignen hämatologischen Erkrankung, in diesem Fall mit chronischer lymphatischer Leukämie.
Xenopus Cytogenetics and Chromosomal Evolution
Authors: Krylov Vladimir , Tlapakova Tereza
Published: May 2015

The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.
Serum Apolipoprotein-A1 and Cholesterol Levels in Nigerian Children with Plasmodium falciparum Infection
Authors: Orimadegun Adebola Emmanuel , Orimadegun Bose Etaniamhe
Published: May 2015

Objective: This study was carried out to determine whether or not Plasmodium falciparum malaria infection significantly affected apolipoprotein-A1 and cholesterol levels and if apolipoprotein-A1 correlated with the malaria severity in children younger than 5 years old. Subjects and Methods: Two hundred and fifty-five children, 170 of whom had microscopically confirmed P. falciparum infection, i.e. 85 cases of uncomplicated malaria (UM) and 85 of complicated malaria (CM), and 85 healthy controls were enrolled in this study. Serum levels of apolipoprotein-A1, total cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL) and triglycerides were determined. These levels were compared among the malaria and control groups, using ANOVA and post hoc analyses at p = 0.05. Results: There were significant differences in the mean serum levels of apolipoprotein-A1 (UM: 104.5 ± 38.1 mg/dl, CM: 90.9 ± 33.3 mg/dl and controls: 129.7 ± 48.3 mg/dl; p < 0.001), total cholesterol (UM: 138.8 ± 62.9 mg/dl, CM: 121.2 ± 55.2 mg/dl and controls: 155.1 ± 69.8 mg/dl; p = 0.002) and LDL (UM: 98.2 ± 55.5 mg/dl, CM: 84.3 ± 47.4 mg/dl and controls: 122.7 ± 69.4 mg/dl; p < 0.001). Post hoc analyses revealed that children with UM and CM had significantly lower levels of apolipoprotein-A1, cholesterol, HDL and LDL than controls but that there was no difference between the 2 malaria groups. Reductions in levels of lipids and apolipoprotein-A1 were worse in CM than in UM. Conclusion: Altered levels of serum lipids with CM were associated with a reduction in apolipoprotein-A1. These findings have potential diagnostic utility for the management of malaria.
Fatigue Is Associated with Increased Risk of Mortality in Patients on Chronic Hemodialysis
Authors: Bossola Maurizio , Di Stasio Enrico , Antocicco Manuela , Panico Loredana , Pepe Gilda , Tazza Luigi
Published: May 2015

Background: Little is known about the correlation between fatigue and survival in patients on chronic hemodialysis and whether fatigue is an independent predictor of outcome above and beyond the effects of depression. The aim of the present study was to determine if fatigue is a predictor of mortality in patients on chronic hemodialysis (CHP) and if this occurs independently of the symptoms of depression. Methods: CHP referring to the Hemodialysis Service of the Università Cattolica of Rome, Italy between November 2007 and January 2015 were studied. Demographic, clinical, and laboratory data were recorded for each patient at the moment of the inclusion in the study. Fatigue levels were assessed in patients using the Vitality Scale of SF-36 (SF-36 VS), functional ability by the activities of daily living (ADL) and instrumental activities of daily living (IADL), depressive symptoms through the Geriatric Depression Scale (GDS), cognitive function using the Mini Mental State Examination (MMSE), and comorbidity through the Charlson Comorbidity Index (CCI). Patients were grouped into four groups (quartiles): Quartile 1 (Q1), >65; Q2, ≥50 to <65; Q3, ≥35 to <50; Q4, <35. Results: We studied 126 patients: 11 were transplanted and 53 died. Patients who later died were older and had a worse cognitive performance, higher CCI and GDS scores, lower ADL, IADL and SF-36 VS scores, lower serum creatinine and albumin levels. Kaplan-Meier survival was significantly lower in Q4 than in Q1 (p = 0.0001). According to Cox regression analysis, higher fatigue (Q4) was associated with a higher risk of mortality (HR, 95% CI: 5.29, 2.2-12.73). Conclusion: Fatigue is associated with an increased risk of mortality in CHP, with the relationship independent of symptoms of depression. Fatigue should be assessed routinely and may be a potential target of interventions that aim to reduce mortality in CHP.
The Beginnings of Formal Logic: Deduction in Aristotle’s Topics vs. Prior Analytics
Authors: Malink Marko
Published: May 2015

It is widely agreed that Aristotle’s Prior Analytics, but not the Topics, marks the beginning of formal logic. There is less agreement as to why this is so. What are the distinctive features in virtue of which Aristotle’s discussion of deductions (syllogismoi) qualifies as formal logic in the one treatise but not in the other? To answer this question, I argue that in the Prior Analytics—unlike in the Topics—Aristotle is concerned to make fully explicit all the premisses that are necessary to derive the conclusion in a given deduction.
Aristotle and Alexander on Perceptual Error
Authors: Johnstone Mark A.
Published: May 2015

Aristotle sometimes claims that (i) the perception of special perceptibles by their proper sense is unerring. This claim is striking, since it might seem that we quite often misperceive things like colours, sounds and smells. Aristotle also claims that (ii) the perception of common perceptibles (e.g. shape, number, movement) is more prone to error than the perception of special perceptibles. This is puzzling in its own right, and also places constraints on the interpretation of (i). I argue that reading Alexander of Aphrodisias on perceptual error offers an understanding of Aristotle that can help us to make good sense of both of Aristotle’s claims.
The Right to Travel for Abortion Services: A Case Study in Irish ‘Cross-border Reproductive Care’
Authors: Mulligan Andrea
Published: May 2015

Abortion is illegal in Ireland, except in very limited circumstances, but the Irish Constitution guarantees the right of women to travel abroad to obtain abortion services. Every year, large numbers of women travel to the uk to obtain abortions. This article argues that this can be regarded as an illustration of cross-border reproductive care (cbrc). cbrc is the phenomenon whereby people travel abroad to obtain assisted reproduction services that are illegal in their country of origin. A leading commentator, Guido Pennings, argues that cbrc is to be welcomed as a means by which society might compromise on issues of profound moral disagreement. Other commentators believe cbrc is highly problematic. This article argues that the Irish abortion example, when examined as an example of cbrc, illustrates both the advantages and disadvantages of cbrc identified by Pennings and his critics.
Understanding Russia’s Low Rate of Acquittal: Pretrial Screening and the Problem of Accusatorial Bias
Authors: Solomon Peter H.
Published: May 2015

The Soviet Union and post-Soviet Russia alike have had extremely low rates of acquittal in criminal cases, which conventional wisdom associates with an accusatorial bias. But other countries like Canada, Germany, The Netherlands, and France also have low rates of acquittal without the perception of bias. This article argues that the key difference lies in the presence or absence of pretrial screening—through the withdrawal of charges, diversion, and/or dispositions imposed by prosecutors. After a brief history of the low acquittal rate in Russia, the article documents the use of prosecutorial discretion to screen cases before trial in those four Western countries, especially through the exercise by prosecutors of quasi-judicial functions. The article goes on to demonstrate the absence of significant pretrial filtering of cases in Russia and to explore the implications for understanding the rate of acquittal.
Impact of Wind Direction, Wind Speed, and Particle Characteristics on the Collection Efficiency of the Double Fence Intercomparison Reference
Authors: Thériault Julie M. , Rasmussen Roy , Petro Eddy , Trépanier Jean-Yves , Colli Matteo , Lanza Luca G.
Published: May 2015

The accurate measurement of snowfall is important in various fields of study such as climate variability, transportation, and water resources. A major concern is that snowfall measurements are difficult and can result in significant errors. For example, collection efficiency of most gauge–shield configurations generally decreases with increasing wind speed. In addition, much scatter is observed for a given wind speed, which is thought to be caused by the type of snowflake. Furthermore, the collection efficiency depends strongly on the reference used to correct the data, which is often the Double Fence Intercomparison Reference (DFIR) recommended by the World Meteorological Organization. The goal of this study is to assess the impact of weather conditions on the collection efficiency of the DFIR. Note that the DFIR is defined as a manual gauge placed in a double fence. In this study, however, only the double fence is being investigated while still being called DFIR. To address this issue, a detailed analysis of the flow field in the vicinity of the DFIR is conducted using computational fluid dynamics. Particle trajectories are obtained to compute the collection efficiency associated with different precipitation types for varying wind speed. The results show that the precipitation reaching the center of the DFIR can exceed 100% of the actual precipitation, and it depends on the snowflake type, wind speed, and direction. Overall, this study contributes to a better understanding of the sources of uncertainty associated with the use of the DFIR as a reference gauge to measure snowfall.