bluuebunny/crossref_metadata_2025_split huggingface dataset:
TH‐EF‐BRA‐09: CT Number and Size Variations of Well‐Known Mobile Targets in Deformable Image Registration Algorithms in CT Images with Motion Artifacts Induced by Controlled Motion Patterns
Authors: Jaskowiak J , Alsbou N , Algan O , Ahmad S , Ali I 
Published: June 2015

Purpose:To evaluate quantitatively the performance of different deformable image registration algorithms using a mobile thorax phantom with well‐defined targets and controlled motion‐patterns imaged with helical, axial and cone‐beam CT. Materials andMethods:A thorax phantom was scanned using helical, axial and cone‐beam CT imaging while it is moving and stationary. The phantom system was moved using cyclic motion with adjustable motion amplitude (0–40 mm) and frequency (0.125–0.5Hz). Several water equivalent targets (small, medium and large) with known sizes were inserted in the middle of low‐density foam. The CT images of the mobile phantom were registered with the images of the stationary phantom with different deformable image registration algorithms using the DIRART software. The performance of different deformable image registration algorithms were evaluated in terms of reducing image artifact and reproducing the shape, size and CT‐number level of well‐defined targets.Results:The image artifacts induced by phantom motion which included deformation and spread‐out of the targets increased with motion amplitude. The deformable image registration improved image‐quality from artifacts induced by motion in the deformed CT images. The CT‐number profiles showed that the deformable image registration algorithms were able to reproduce the shape and size of the mobile targets where the spread‐out artifacts were eliminated. However, the CT‐numbers deviated from the corresponding values for the stationary targets. The discrepancy between the CT‐number level from the deformed CT images and that from the stationary CT images increased with motion amplitude.Conclusion:The performance of the deformable image registration depends on several parameters that include: motion artifacts, deformable image registration algorithm, and imaging modes. The deformable image registration algorithms reproduced size and shape of mobile targets with different motion‐patterns. However, they did not reproduce the CT‐number value which deviated strongly from the actual value of the stationary CT images with increasing motion amplitude.
In Vitro
Activities of 21 Antimicrobial Agents Alone and in Combination with Aminoglycosides or Fluoroquinolones against Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolates Causing Bacteremia
Authors: Cha Min Kyeong , Kang Cheol-In , Kim So Hyun , Cho Sun Young , Ha Young Eun , Wi Yu Mi , Chung Doo Ryeon , Peck Kyong Ran , Song Jae-Hoon ,   on behalf of the Korean Network for Study on Infectious Diseases (KONSID)
Published: June 2015

ABSTRACT

We evaluated the
in vitro
activity of various antimicrobials alone and in combination against 291 extended-spectrum-β-lactamase-producing
Escherichia coli
(ESBL-EC) isolates causing bacteremia in South Korean hospitals. Ceftazidime, cefepime, and piperacillin-tazobactam in combination with amikacin showed greater activity than found in combination with ciprofloxacin. In settings with a high prevalence of ESBL-producing pathogens, combination aminoglycoside antimicrobial therapy, especially with amikacin, may be considered for empirical therapy against suspected Gram-negative sepsis as a carbapenem-saving strategy.
Retroviral DNA Transposition: Themes and Variations
Authors: Skala Anna Marie 
Published: June 2015

ABSTRACT
Retroviruses and LTR retrotransposons are transposable elements that encapsidate the RNAs that are intermediates in the transposition of DNA copies of their genomes (proviruses), from one cell (or one locus) to another. Mechanistic similarities in DNA transposase enzymes and retroviral/retrotransposon integrases underscore the close evolutionary relationship among these elements.

The retroviruses are very ancient infectious agents, presumed to have evolved from Ty3/Gypsy LTR retrotransposons (
1
), and DNA copies of their sequences can be found embedded in the genomes of most, if not all, members of the tree of life. All retroviruses share a specific gene arrangement and similar replication strategies. However, given their ancestries and occupation of diverse evolutionary niches, it should not be surprising that unique sequences have been acquired in some retroviral genomes and that the details of the mechanism by which their transposition is accomplished can vary.

While every step in the retrovirus lifecycle is, in some sense, relevant to transposition, this Chapter focuses mainly on the early phase of retroviral replication, during which viral DNA is synthesized and integrated into its host genome. Some of the initial studies that set the stage for current understanding are highlighted, as well as more recent findings obtained through use of an ever-expanding technological toolbox including genomics, proteomics, and siRNA screening. Persistence in the area of structural biology has provided new insight into conserved mechanisms as well as variations in detail among retroviruses, which can also be instructive.
Biology of Three ICE Families: SXT/R391, ICE
Bs1
, and ICE
St1
/ICE
St3
Authors: Carraro Nicolas , Burrus Vincent 
Published: June 2015

ABSTRACT
Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.
Recombination and Diversification of the Variant Antigen Encoding Genes in the Malaria Parasite
Plasmodium falciparum
Authors: Kirkman Laura A. , Deitsch Kirk W. 
Published: June 2015

ABSTRACT

The most severe form of human malaria is caused by the protozoan parasite
Plasmodium falciparum
. These parasites invade and replicate within the circulating red blood cells of infected individuals leading to numerous disease manifestations, including severe anemia, altered circulation, and tissue inflammation. Malaria parasites are also known for their ability to maintain a chronic infection through antigenic variation, the ability to systematically alter the antigens displayed on the surface of infected cells and thereby avoid clearance by the host’s antibody response. The genome of
P. falciparum
includes several large, multicopy gene families that encode highly variable forms of the surface proteins that are the targets of host immunity. Alterations in expression of genes within these families are responsible for antigenic variation. This process requires the continuous generation of new antigenic variants within these gene families, and studies have shown that new variants arise through extensive recombination and gene conversion events between family members. Malaria parasites possess an unusual complement of DNA repair pathways, thus the study of recombination between variant antigen encoding genes provides a unique view into the evolution of mobile DNA in an organism distantly related to the more closely studied model eukaryotes.
Programmed Rearrangement in Ciliates:
Paramecium
Authors: Betermier Mireille , Duharcourt Sandra 
Published: June 2015

ABSTRACT

Programmed genome rearrangements in the ciliate
Paramecium
provide a nice illustration of the impact of transposons on genome evolution and plasticity. During the sexual cycle, development of the somatic macronucleus involves elimination of ∼30% of the germline genome, including repeated DNA (e.g., transposons) and ∼45,000 single-copy internal eliminated sequences (IES). IES excision is a precise cut-and-close process, in which double-stranded DNA cleavage at IES ends depends on PiggyMac, a domesticated
piggyBac
transposase. Genome-wide analysis has revealed that at least a fraction of IESs originate from
Tc
/
mariner
transposons unrelated to
piggyBac
. Moreover, genomic sequences with no transposon origin, such as gene promoters, can be excised reproducibly as IESs, indicating that genome rearrangements contribute to the control of gene expression. How the system has evolved to allow elimination of DNA sequences with no recognizable conserved motif has been the subject of extensive research during the past two decades. Increasing evidence has accumulated for the participation of noncoding RNAs in epigenetic control of elimination for a subset of IESs, and in
trans
-generational inheritance of alternative rearrangement patterns. This chapter summarizes our current knowledge of the structure of the germline and somatic genomes for the model species
Paramecium tetraurelia
, and describes the DNA cleavage and repair factors that constitute the IES excision machinery. We present an overview of the role of specialized RNA interference machineries and their associated noncoding RNAs in the control of DNA elimination. Finally, we discuss how RNA-dependent modification and/or remodeling of chromatin may guide PiggyMac to its cognate cleavage sites.
Helitrons
, the Eukaryotic Rolling-circle Transposable Elements
Authors: Thomas Jainy , Pritham Ellen J. 
Published: June 2015

ABSTRACT

Helitrons
, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of
Helitrons
called
Helentrons
,
Proto-Helentron
, and
Helitron2
.
Helitrons
and
Helentrons
make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in
Drosophila
and many other animal genomes. The purpose of this review is to summarize what we have learned about
Helitrons
in the decade since their discovery. First, we describe the history of autonomous
Helitrons
, and their variants. Second, we explain the common coding features and difference in structure of canonical
Helitrons
versus the endonuclease-encoding
Helentrons
. Third, we review how
Helitrons
and
Helentrons
are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate
Helitrons
is carried out and how to validate candidate
Helitrons
. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where
Helitrons
are found, including discussions of vertical versus horizontal transfer, the propensity of
Helitrons
and
Helentrons
to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.
Adeno-associated Virus as a Mammalian DNA Vector
Authors: Salganik Max , Hirsch Matthew L. , Samulski Richard Jude 
Published: June 2015

ABSTRACT
In the nearly five decades since its accidental discovery, adeno-associated virus (AAV) has emerged as a highly versatile vector system for both research and clinical applications. A broad range of natural serotypes, as well as an increasing number of capsid variants, has combined to produce a repertoire of vectors with different tissue tropisms, immunogenic profiles and transduction efficiencies. The story of AAV is one of continued progress and surprising discoveries in a viral system that, at first glance, is deceptively simple. This apparent simplicity has enabled the advancement of AAV into the clinic, where despite some challenges it has provided hope for patients and a promising new tool for physicians. Although a great deal of work remains to be done, both in studying the basic biology of AAV and in optimizing its clinical application, AAV vectors are currently the safest and most efficient platform for gene transfer in mammalian cells.
A Framework for Efficient Execution of Data Parallel Irregular Applications on Heterogeneous Systems
Authors: Ribeiro Roberto , Barbosa João , Santos Luís Paulo 
Published: June 2015

Exploiting the computing power of the diversity of resources available on heterogeneous systems is mandatory but a very challenging task. The diversity of architectures, execution models and programming tools, together with disjoint address spaces and different computing capabilities, raise a number of challenges that severely impact on application performance and programming productivity. This problem is further compounded in the presence of data parallel irregular applications. This paper presents a framework that addresses development and execution of data parallel irregular applications in heterogeneous systems. A unified task-based programming and execution model is proposed, together with inter and intra-device scheduling, which, coupled with a data management system, aim to achieve performance scalability across multiple devices, while maintaining high programming productivity. Intra-device scheduling on wide SIMD/SIMT architectures resorts to consumer-producer kernels, which, by allowing dynamic generation and rescheduling of new work units, enable balancing irregular workloads and increase resource utilization. Results show that regular and irregular applications scale well with the number of devices, while requiring minimal programming effort. Consumer-producer kernels are able to sustain significant performance gains as long as the workload per basic work unit is enough to compensate overheads associated with intra-device scheduling. This not being the case, consumer kernels can still be used for the irregular application. Comparisons with an alternative framework, StarPU, which targets regular workloads, consistently demonstrate significant speedups. This is, to the best of our knowledge, the first published integrated approach that successfully handles irregular workloads over heterogeneous systems.
Responses of Tropical Deep Convection to the QBO: Cloud-Resolving Simulations
Authors: Nie Ji , Sobel Adam H. 
Published: June 2015

Abstract
Observational studies suggest that the stratospheric quasi-biennial oscillation (QBO) can modulate tropical deep convection. The authors use a cloud-resolving model with a limited domain, representing a convective column in the tropics, to study the mechanisms of this modulation. The large-scale circulation is parameterized using the weak temperature gradient (WTG) approximation, under which the parameterized large-scale vertical motion acts to relax the horizontal-mean temperature toward a specified reference profile. Temperature variations typically seen in easterly and westerly phases are imposed in the upper troposphere and lower stratosphere of this reference profile. The responses of convection are studied over different sea surface temperatures, holding the reference temperature profile fixed. This can be thought of as studying the response of convection to the QBO over different “relative SSTs” and also corresponds to different equilibrium precipitation rates in the control simulation. The equilibrium precipitation rate shows slight increases in response to a QBO easterly phase temperature perturbation over small SST anomalies and strong decreases over large SST anomalies, and vice versa for the QBO westerly phase perturbation. A column moist static energy budget analysis reveals that the QBO modulates the convective precipitation through two pathways: it changes the high-cloud properties and thus the column radiative cooling, and it alters the shape of the large-scale vertical motion and thus the efficiency of energy transport by the large-scale flow. The nonmonotonicity of the precipitation response with respect to relative SST results from the competition of these two effects.
Temporal Dynamics of Anxiety Phenotypes in a Dental Pulp Injury Model
Authors: Shang Lin , Xu Tian-Le , Li Fei , Su Jiansheng , Li Wei-Guang 
Published: June 2015

Background Accumulating clinical and preclinical evidence indicates that chronic pain is often comorbid with persistent low mood and anxiety. However, the mechanisms underlying pain-induced anxiety, such as its causality, temporal progression, and relevant neural networks are poorly understood, impeding the development of efficacious therapeutic approaches. Results Here, we have identified the sequential emergence of anxiety phenotypes in mice subjected to dental pulp injury (DPI), a prototypical model of orofacial pain that correlates with human toothache. Compared with sham controls, mice subjected to DPI by mechanically exposing the pulp to the oral environment exhibited significant signs of anxiogenic effects, specifically, altered behaviors on the elevated plus maze (EPM), novelty-suppressed feeding (NSF) tests at 1 but not 3 days after the surgery. Notably, at 7 and 14 days, the DPI mice again avoided the open arm, center area, and novelty environment in the EPM, open field, and NSF tests, respectively. In particular, DPI-induced social phobia and increased repetitive grooming did not occur until 14 days after surgery, suggesting that DPI-induced social anxiety requires a long time. Moreover, oral administration of an anti-inflammatory drug, ibuprofen, or an analgesic agent, ProTx-II, which is a selective inhibitor of NaV1.7 sodium channels, both significantly alleviated DPI-induced avoidance in mice. Finally, to investigate the underlying central mechanisms, we pharmacologically blocked a popular form of synaptic plasticity with a GluA2-derived peptide, long-term depression, as that treatment significantly prevented the development of anxiety phenotype upon DPI. Conclusions Together, these results suggest a temporally progressive causal relationship between orofacial pain and anxiety, calling for more in-depth mechanistic studies on concomitant pain and anxiety disorders.
Physician burnout: can we make a difference together?
Authors: Siedsma Matthew , Emlet Lillian 
Published: June 2015

Expanded abstract
Citation
West CP, Dyrbye LN, Rabatin JT, Call TG, Davidson JH, Multari A, Romanski SA, Hellyer JMH, Sloan JA, Shanafelt TF. Intervention to promote physician well-being, job satisfaction, and professionalism: a randomized clinical trial. JAMA Intern Med. 2014;174:527–33.

Background
Despite the documented prevalence and clinical ramifications of physician distress, few rigorous studies have tested interventions to address the problem.

Methods
Objective: To test the hypothesis that an intervention involving a facilitated physician small-group curriculum would result in improvement in well-being.
Design: A randomized clinical trial of practicing physicians. Additional data were collected on nontrial participants responding to annual surveys timed to coincide with the trial surveys.
Setting: Department of Medicine at the Mayo Clinic in Rochester, Minnesota between September 2010 and June 2012.
Participants: The study involved 74 practicing physicians in the Department of Medicine and 350 nontrial participants responding to annual surveys.
Interventions: The intervention involved 19 biweekly facilitated physician discussion groups incorporating elements of mindfulness, reflection, shared experience, and small-group learning for 9 months. Protected time (1 hour of paid time every other week) for participants was provided by the institution.
Outcomes: Meaning in work, empowerment and engagement in work, burnout, symptoms of depression, quality of life, and job satisfaction were assessed using validated metrics.

Results
Empowerment and engagement at work increased by 5.3 points in the intervention arm vs. a 0.5-point decline in the control arm by 3 months after the study (P = .04), an improvement sustained at 12 months (+5.5 vs. +1.3 points; P = .03). Rates of high depersonalization at 3 months had decreased by 15.5 % in the intervention arm vs. a 0.8 % increase in the control arm (P = .004). This difference was also sustained at 12 months (9.6 % vs. 1.5 % decrease; P = .02). No statistically significant differences in stress, symptoms of depression, overall quality of life, or job satisfaction were seen. In additional comparisons including the nontrial physician cohort, the proportion of participants strongly agreeing that their work was meaningful increased 6.3 % in the study intervention arm but decreased 6.3 % in the study control arm and 13.4 % in the nonstudy cohort (P = .04). Rates of depersonalization, emotional exhaustion, and overall burnout decreased substantially in the trial intervention arm, decreased slightly in the trial control arm, and increased in the nontrial cohort (P = .03, P = .007, and P = .002 for each outcome, respectively).

Conclusions
An intervention for physicians based on a facilitated small-group curriculum improved meaning and engagement in work and reduced depersonalization, with sustained results 12 months after the study.