bluuebunny/crossref_metadata_2025 huggingface dataset:
TH‐EF‐BRB‐03: Enhancement of Image Contrast Along the Beam's‐Eye‐View (BEV) Direction Through Development of Imagers Based On Segmented Scintillators and Photon‐Counting Arrays
Authors: Antonuk L , El‐Mohri Y , Zhao Q , Liang A , Koniczek M
Published: June 2015

Purpose:

The contrast provided by conventional portal imagers is constrained by inefficient conversion of the incident radiation, and by the small diagnostic x‐ray component of the treatment beam. Toward improved visualization of the tumor region prior to treatment, as well as improved tumor tracking during treatment, progress is reported on the design of a pair of novel detectors that would address these constraints.

Methods:

A dual‐energy imager based on a segmented scintillator is being designed using a hybrid model to simulate radiation and optical transport. The simulations, which model operation with a megavoltage treatment beam and with a BEV imaging beam with a significant diagnostic component, employ parameters extracted from a previously developed prototype. Separately, the conceptual design of a second imager incorporating a 2D array of photon counting pixels is being explored through extrapolation of the design of the first prototype photon counting arrays fabricated using thin‐film processing, a process scalable to very large area detectors.

Results:

The simulations identified a segmented scintillator imager design that, when operated with a BEV imaging beam, provides spatial resolution and contrast comparable to that of gantry‐mounted kV imagers. When operated with a treatment beam, the design provides significantly improved DQE and contrast compared to conventional portal imagers. Extrapolation of initial photon counting array designs indicates that the circuitry necessary to provide energy‐windowing of the diagnostic portion of a therapy beam can be achieved at the pixel pitch associated with current treatment room imagers.

Conclusion:

These early studies demonstrate potential for improved contrast in projection and volumetric images obtained with the megavoltage beam prior to treatment, while also providing good performance when used with BEV imaging beams. In addition, these studies also support the possibility of improved capability for tumor tracking with such dual‐energy imagers as well as by photon counting array imagers.

NIH grant R01‐EB000558
TH‐EF‐BRB‐08: An Efficient and Continuous Surface Reconstruction Method On Point Cloud Captured by a 3D Surface Imaging System
Authors: Liu W , Cheung Y , Sawant A , Ruan D
Published: June 2015

Purpose:

Surface photogrammetry‐based systems (e.g., VisionRT, C‐Rad) are gaining increasing acceptance for patient localization and motion monitoring in radiotherapy. The purpose of this work is to accurately and efficiently reconstruct a continuous surface from noisy point clouds captured by a VisionRT system with high‐speed‐image‐capture capability. In contrast to the conventional approach of explicit/discrete meshing‐type scheme that is often error‐prone, our method yields a continuous representation of the underlying patient surface, which is particularly advantageous for subsequent surface registration and motion tracking.

Methods:

We developed a level‐set based surface reconstruction method by optimizing a regularized fitting energy from the noisy point cloud from VisionRT. This approach offers additional robustness to noise and missing measurements caused by view occlusion. We applied an efficient narrowband evolving scheme and significantly reduced the time‐complexity by one order of magnitude. Validation was performed on surface data from a lung cancer patient during CT‐simulation by comparing the local geometry of our reconstructed surface against that of the skin surface from CT, within comparable ROIs in the chest area based on mean curvature distributions.

Results:

Our method successfully reconstructed a continuous and smooth surface, with the missing region reasonably filled. We obtained two similar mean curvature distributions from both reconstructed surface and CT surface, with empirical mean and standard deviation of (µ = −2.7E‐3mm−1, σ = 7.0E‐3mm−1) and (µ = −2.5E‐3mm−1, σ = 5.3E‐3 mm−1), respectively. The similarity of those two distributions demonstrated the ability of our method in preserving local geometry of the reconstructed surface.

Conclusion:

We have proposed an efficient and accurate surface reconstruction method on point cloud from VisionRT. The proposed method has generated a continuous representation of the underlying patient surface with good robustness against noise and missing measurement. It serves as an important first step for further development of motion tracking methods during radiotherapy.

NIH 5R01CA169102‐02
TH‐EF‐BRA‐01: Patient‐Size Specific Analysis of CT Doses From Lung Cancer Screening
Authors: Fujii K , McMillan K , Bostani M , Cagnon C , McNitt‐Gray M
Published: June 2015

Purpose:

The US Centers for Medicare & Medicaid Services (CMS) recently issued its final decision to approve the use of low dose CT for lung cancer screening and described some dose index requirements. The aim of this study is to evaluate CT dose indices from lung cancer screening taking into account patient size.

Methods:

CT dose index data (CTDIvol, DLP) and patient size (height and weight) to calculate body mass index (BMI) were collected for lung cancer screening exams from Jan 1st to Dec 31th, 2014. All exams used Tube Current Modulation with identical Image Quality Reference parameter (Quality Reference mAs). X‐ray dose management software was used to mine the data. CTDIvol and DLP values were analyzed based on patient's BMI classification. For a subset of patients, the average water equivalent diameter was estimated as well as Size Specific Dose Estimate (SSDE). All results were compared to the Medicare requirements (CTDIvol ≤ 3.0 mGy for a standard sized patient; appropriate reductions for smaller patients and increases for larger patients).

Results:

The dose indices over 351 patients were (mean ± SD): CTDIvol of 2.1 ± 0.7 mGy (min‐max: 1.2 – 6.0 mGy); DLP of 75 ± 24 mGy*cm (min‐max: 38 – 202 mGy*cm). The CTDIvol values by patient size (BMI) were 1.4 ± 0.2 mGy for underweight (BMI<18.5), 1.7 ± 0.3 mGy for normal weight (BMI of 18.5–24.9), 2.2 ± 0.4 mGy for overweight (BMI of 25.0– 29.9), and 2.9 ± 0.8 mGy for obese (BMI≥30.0). Approximately 9% of total patients had CTDIvol > 3.0 mGy; for each of these cases, the BMI was at least 27.0.

Conclusion:

The scan protocol used resulted in CTDIvol values well within the Medicare requirements. Patients with larger BMI receive higher CTDIvol, but values > 3.0 mGy only occurred for overweight and obese patients.
TH‐EF‐BRA‐05: Investigation of Full Dose Reduction Potential of ASiRâ„¢ for Head CT Protocols in a Predominantly Pediatric Population
Authors: Mirro A , Brady S , Kaufman R
Published: June 2015

Purpose:

To ascertain and implement the maximum level of adaptive statistical iterative reconstruction (ASiR) that can be used to establish dose reduced pediatric head CT protocols.

Methods:

Noise power spectrum (NPS), modulation transfer function (MTF), and qualitative visual assessment were used as image quality metrics to calculate image quality based on filtered back projection (FBP) and ASiR reconstruction. The effect on image quality as a function of level of ASiR implementation and tube current reduction was analyzed by comparing image noise magnitude and frequency, and spatial resolution with similar measured image quality for FBP. Relative patient dose reduction was estimated using both CTDIvol and effective dose calculated using pediatric sized physical anthropomorphic phantoms. Dose reduced protocols were investigated for CT head examinations (i.e. brain, orbits, sinus, maxillary and temporal bones) by implementing ASiR and lowering CT tube current.

Results:

An analysis of the effects on noise texture from implementation of statistical iterative reconstruction determined that the level of ASiR that correlated closest with FBP for the GE soft reconstruction kernel (for both 100 and 120 kVp) was determined to be 30%, and for the GE standard reconstruction kernel at 100 kVp was 20% ASiR. However, implementation of 60% ASiR (GE soft reconstruction kernel) and 30% ASiR (GE standard reconstruction kernel) led to an average relative reduction in CTDIvol by 40% (range: 30%‐47%) and effective dose by 36% (range: 12%‐54%) while maintaining the same overall noise magnitude and improving the CNR of the image as compared to FBP. A coarser noise texture was visualized at 60% ASiR.

Conclusion:

The data in this study are provided to allow customized selection of ASiR implementation relating to acceptable tolerance for change in noise texture appearance in reconstructed images, and level of relative dose reduction for a pediatric population undergoing head CT examination.
TH‐EF‐BRA‐06: A Novel Method of ACR Dose Index Registry Report Interpretation: Population Dose Reduction for Thoracic CT Angiography
Authors: Zamora D , Robinson J , Kanal K
Published: June 2015

Purpose:

To identify a method of ACR Dose Index Registry (DIR) report analysis and interpretation that focuses dose reduction efforts on exams that most affect our patient population.

Methods:

In place of a direct interpretation of the DIR report, a proposed additional metric — the Total Exposure Variance (TEV) — was calculated for each of the most frequently performed institutional exams. TEV was defined as the product of exam frequency (N) and the difference between institutional and national median dose (CTDIvol or SSDE). TEV indicated total excess institution population dose beyond the equivalent national benchmark. TEV analysis focused investigation of two exams from the 2012 DIR report: 1) CT pulmonary angiography (CTPA), which had SSDE between the median and third quartile; and, 2) CT thoracic angiography (CTTA), optimized for the aorta, which had SSDE in the top quartile.

Results:

CT scan parameter changes were implemented lowering the quality reference mAs by 20% and limiting the automatic kV selection range to 100–120. DIR data from July–December 2012 were compared to same time period for 2013. CTPA showed a decrease of median CTDIvol and SSDE of 14% and 16%, respectively, representing a realized decrease in TEV of 1776 mGy‐persons. Data for CTTA showed a decrease of median CTDIvol and SSDE of 38% and 44%, respectively, representing a realized decrease in TEV of 1050 mGy‐persons. In both cases, the incremental and population dose metrics moved down toward national benchmarks.

Conclusion:

TEV analysis used DIR data to shift the paradigm toward reducing population dose instead of frequency‐independent interpretation of the report. The TEV metric highlighted exams that would have otherwise been overlooked with direct DIR report interpretation. Recent modifications to the DIR report contents may avail additional approaches to dose reduction.
TH‐EF‐BRA‐07: A Reference Organ Dose Database for Body CT Examination Based On AAPM 246
Authors: Tian X , Segars P , Andersson J , Pavlicek W , Samei E
Published: June 2015

Purpose:

This study aims to establish a reference organ dose database for clinical body CT based on detailed modeling of patient anatomy and irradiation condition.

Methods:

Clinical CT images of 40 adult patients (age range: 18–78 y.o., 22 male, 18 female) were included. Each patient received a chest and abdominopelvic CT examination at our institution. Whole‐body computer models were created from clinical CT data, which included most of the radiosensitive organs defined by ICRP Publication 103. A previously‐validated Monte Carlo program was used to simulate organ dose for each patient model. The scanner spectrum, geometry and material information of the bowtie filter, and the tube current modulation (TCM) profiles were explicitly modeled. Three examination conditions were modeled: (1) fixed tube current (2) TCM exams with modest modulation strength (alpha = 0.5), and (3) TCM exams with strong modulation strength (alpha = 1).The calculated organ dose values were provided as a reference database for dosimetry benchmarking for chest and abdominopelvic examinations.

Results:

Given the examination CTDIvol to be 7 mGy, organ dose for chest examination were in the range of 1.42 mGy to 14.4 mGy. For abdominopelvic examination, organ dose were in the range of 1.71 mGy to 10.5 mGy. Organ dose shows a gradual decrease with the increase of tube current modulation level. For chest scan, the average organ dose decreased 42.8% for the heart, and 25.0% for the lungs for strong modulation scans compared to no modulation. For abdominopelvic scan, the average organ dose decreased 33.8% for the stomach and 31.6% for the liver when implemented with strong TCM modulation compared to no modulation.

Conclusion:

A database of organ dose estimation is provided with information available for detailed modeling of the patient anatomy and scanner irradiation condition. Such database may be used as a reference standard in quantification and reporting of organ doses.

Research fundings from GE, Siemens, and Carestream
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 and

Methods:

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

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

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

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

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

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

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

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.
Subdural empyema and unilateral pansinusitis due to a tooth infection
Authors: Derin Serhan , Sahan Murat , Hazer Derya Burcu , Sahan Leyla
Published: June 2015

Paranasal sinus infections are very common. Dental infections, tumours and anatomical malformations can cause unilateral sinusitis. Most cases can be treated without complications. However, rare life-threatening intracranial complications can occur. Generally, an intracranial complication progresses rapidly and can cause meningismus, focal neurological disorders, loss of consciousness and seizures. In such cases, an emergency craniotomy and concurrent sinus surgery are required. This article presents a 16-year-old patient with pansinusitis and subdural empyema that developed after a dental abscess.
Reactivation of chronic hepatitis B during treatment with tenofovir disoproxil fumarate: drug interactions or low adherence?
Authors: Caroleo Benedetto , Staltari Orietta , Gallelli Luca , Perticone Francesco
Published: June 2015

We describe a case of a 61-year-old man with chronic hepatitis B, hepatitis B e antibody (HBeAb) positive, treated with tenofovir disoproxil fumarate (TDF), who developed virological and biochemical viremic reactivation with an increase in transaminase plasma levels. The patient's history revealed that he had discontinued TDF about 5 days before admission and, from December 2013, had been taking venlafaxine, paroxetine and zolpidem for some episodes of depression. Clinical evaluation and laboratory findings excluded the presence of systemic diseases that might have been able to explain the drug inefficacy, while pharmacological evaluation suggested a possible drug-drug interaction. In order to assess the possible occurrence of resistance, mutational analysis of hepatitis B virus (HBV) was performed and excluded the presence of resistance for TDF. TDF was prescribed, and venlafaxine, paroxetine and zolpidem were discontinued. The follow-up at 3, 6 and 12 months documented a good response to TDF with a time-related decrease of HBV-DNA and alanine aminotransferase.
Bilateral big-bubble deep anterior lamellar keratoplasty for vascularised corneal opacity in a patient with xeroderma pigmentosum
Authors: Reddy Jagadesh C , Korwar Veeresh , Vaddavalli Pravin Krishna
Published: June 2015

A 16-year-old male patient diagnosed with xeroderma pigmentosum developed bilateral vascularised corneal opacities after treatment for ocular surface squamous neoplasia. The patient underwent an uneventful big-bubble deep anterior lamellar keratoplasty in both eyes. The grafts remained clear and the corrected distance visual acuity was 20/30 in both the eyes at the final follow-up visit.
Intrapleural cisplatin for management of malignant pleural effusion in a patient with plasma cell leucaemia
Authors: Agarwal Abhishek , Klair Jagpal , Patolia Setu , Meena Nikhil K
Published: June 2015

Plasma cell leucaemia (PCL) is a rare aggressive form of multiple myeloma. It occasionally involves the pleura, causing malignant pleural effusion (MPE). MPE presents a management dilemma for physicians, given the different treatment options available with varying efficacy and side effects. We report a case of a 64-year-old man with MPE due to PCL, successfully managed with intrapleural cisplatin and a tunnelled pleural catheter. We believe this to be the first report of management of PCL-associated MPE with intrapleural cisplatin.
A slow progressor HIV-infected boy developing quadriplegia with evidence of Epstein-Barr virus associated smooth muscle tumour of the cervical spinal cord
Authors: Wilaisakditipakorn Tanaporn , Vilaisaktipakorn Pitchamol , Bunupuradah Torsak , Puthanakit Thanyawee
Published: June 2015

The authors report a case of slowly progressive HIV in an 11-year-old boy whose initial presenting AIDS-defining symptom was progressive quadriplegia with complete cord compression and pathological confirmation of Epstein-Barr virus associated smooth muscle tumour. Despite tumour removal, quadriplegia persisted as did ventilator dependence.
Benign mixed tumour of the breast and breast skin, two cases with diagnostic difficulties
Authors: Kelten Canan , Boyaci Ceren , Can Trabulus Didem , Sirin Seher
Published: June 2015

We present two cases of pleomorphic adenoma, one that developed in the breast parenchyma and the other in the breast skin, with their histopathological differential diagnosis.
Juvenile salmonid growth, survival, and production in a large river floodplain modified by beavers (Castor canadensis)
Authors: Malison Rachel L. , Eby Lisa A. , Stanford Jack A.
Published: June 2015

Beavers (Castor canadensis) may strongly influence juvenile salmon production by damming spring brooks that are primary rearing habitats on expansive floodplains of large Pacific Rim salmon rivers. We studied three floodplain rearing habitats in the Kwethluk River, Alaska: free-flowing (beaver-free, n = 3) and beaver-influenced (below beaver dams, n = 4) spring brooks and early-successional beaver ponds (n = 4). We analyzed juvenile coho (Oncorhynchus kisutch) and Chinook (Oncorhynchus tshawytschwa) salmon movement, survival, densities, and growth using a multistate robust capture–mark–recapture design. Survival (46% to 80%) and densities (0.9 fish·m−2) were highest in beaver-free spring brooks. Ponds had lower salmon densities, producing less biomass per unit area than beaver-influenced or beaver-free spring brooks (1.87 ± 0.57 g·m−2vs. 2.98 ± 1.22 and 3.23 ± 0.73 g·m−2). However, ponds covered 2× greater area than either type of spring brook and therefore produced more salmon biomass at the floodplain scale than either type of spring brook (175 kg vs. 149 kg in beaver-influenced spring brooks and 140 kg in beaver-free spring brooks). We conclude that beaver damming of floodplain spring brooks produces bigger juveniles and more total biomass, but spring brooks produce significantly more, albeit smaller, coho and Chinook juveniles. Thus, the presence of beavers on the floodplain increases habitat variation, which provides a larger range of growth opportunities for juvenile salmon.
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.
Distributed Queuing in Dynamic Networks
Authors: Sharma Gokarna , Busch Costas
Published: June 2015

We consider the problem of forming a distributed queue in the synchronous dynamic network model of Kuhn, Lynch, and Oshman (STOC 2010) in which the network topology changes from round to round but the network stays connected. Queue requests may arrive over rounds at network nodes and the goal is to eventually enqueue them in a distributed queue. We show that in 1-interval connected graphs, where the communication links change arbitrarily between every round, it is possible to solve the distributed queueing problem in [Formula: see text] rounds using [Formula: see text] size messages, where [Formula: see text] is the number of nodes in the network and [Formula: see text] is the number of queue requests. Further, we show that for more stable graphs, e.g. [Formula: see text]-interval connected graphs where the communication links change in every [Formula: see text] rounds, the distributed queuing problem can be solved in [Formula: see text] rounds using the same [Formula: see text] size messages, where [Formula: see text] is the concurrency level parameter that captures the minimum number of active queue requests in the system at any round. These results hold in any arbitrary arrival of queue requests and ensure correctness of the queue formed. To our best knowledge, these are the first solutions to the distributed queuing problem in highly dynamic networks.
Beneficial Effects ofPolygonum multiflorumon Hippocampal Neuronal Cells and Mouse Focal Cerebral Ischemia
Authors: Ahn Sung Min , Kim Yu Ri , Kim Ha Neui , Shin Hwa Kyoung , Choi Byung Tae
Published: June 2015

Beneficial effects of the water extract of Polygonum multiflorum (WEPM) and their mechanisms were investigated in HT22 hippocampal cells and hippocampus of middle cerebral artery occlusion (MCAO) mice. In HT22 cells against glutamate-induced oxidative stress, pretreatment with WEPM resulted in significantly reduced apoptotic neuronal death. Pretreatment with WEPM resulted in the suppression of ROS accumulation in connection with cellular Ca2+level after exposure to glutamate. Treatment with glutamate alone led to suppressed protein level of mature brain-derived neurotrophic factor (BDNF) and phosphorylated cAMP response element binding protein (CREB); however, pretreatment with either WEPM or anti-oxidant N-acetyl-ʟ-cysteine (NAC) resulted in the significant enhancement of levels of these proteins. In addition, levels of mature BDNF expression and CREB phosphorylation were increased by combined treatment with WEPM, NAC, and intracellular Ca2+inhibitor BAPTA compared to other treatment groups. In MCAO mice, we confirmed the critical role of mature BDNF expression and CREB phosphorylation by WEPM in the neurons of the hippocampus. Our results suggest that WEPM mainly exerted beneficial effects on hippocampal neurons through the suppression of ROS accumulation and up-regulation of mature BDNF expression and CREB phosphorylation.
Protocatechuic Acid from Alpinia oxyphylla Induces Schwann Cell Migration via ERK1/2, JNK and p38 Activation
Authors: Ju Da-Tong , Kuo Wei-Wen , Ho Tsung-Jung , Paul Catherine Reena , Kuo Chia-Hua , Viswanadha Vijaya Padma , Lin Chien-Chung , Chen Yueh-Sheng , Chang Yung-Ming , Huang Chih-Yang
Published: June 2015

Alpinia oxyphylla MIQ (Alpinate Oxyphyllae Fructus, AOF) is an important traditional Chinese medicinal herb whose fruits is widely used to prepare tonics and is used as an aphrodisiac, anti salivary, anti diuretic and nerve-protective agent. Protocatechuic acid (PCA), a simple phenolic compound was isolated from the kernels of AOF. This study investigated the role of PCA in promoting neural regeneration and the underlying molecular mechanisms. Nerve regeneration is a complex physiological response that takes place after injury. Schwann cells play a crucial role in the endogenous repair of peripheral nerves due to their ability to proliferate and migrate. The role of PCA in Schwann cell migration was determined by assessing the induced migration potential of RSC96 Schwann cells. PCA induced changes in the expression of proteins of three MAPK pathways, as determined using Western blot analysis. In order to determine the roles of MAPK (ERK1/2, JNK, and p38) pathways in PCA-induced matrix-degrading proteolytic enzyme (PAs and MMP2/9) production, the expression of several MAPK-associated proteins was analyzed after siRNA-mediated inhibition assays. Treatment with PCA-induced ERK1/2, JNK, and p38 phosphorylation that activated the downstream expression of PAs and MMPs. PCA-stimulated ERK1/2, JNK and p38 phosphorylation was attenuated by individual pretreatment with siRNAs or MAPK inhibitors (U0126, SP600125, and SB203580), resulting in the inhibition of migration and the uPA-related signal pathway. Taken together, our data suggest that PCA extract regulate the MAPK (ERK1/2, JNK, and p38)/PA (uPA, tPA)/MMP (MMP2, MMP9) mediated regeneration and migration signaling pathways in Schwann cells. Therefore, PCA plays a major role in Schwann cell migration and the regeneration of damaged peripheral nerve.
Butein Shows Cytotoxic Effects and Induces Apoptosis in Human Ovarian Cancer Cells
Authors: Yang Pei-Yu , Hu Dan-Ning , Lin I-Ching , Liu Fu-Shing
Published: June 2015

Butein is a polyphenol, one of the compounds of chalcones, which are flavonoids that are widely biosynthesized in plants, and exhibits different pharmacological activities. Plants containing butein have been used in Chinese traditional medicine. Recently, it has been reported that butein suppresses proliferation and triggers apoptosis in various human cancer cells in vitro and in vivo. The aim of this study was to investigate its pro-apoptotic effect and mechanisms in two cultured human ovarian cancer cells (ES-2 and TOV-21G). The effects of butein on cell viability were assessed by a MTT assay at 3, 10, 30, and 100 μ/M. The apoptotic pathway related factors, including the mitochondrial transmembrane potential (MTP), cytochrome c, caspase cascade, and Bcl-2 family proteins, were examined. MTT assay revealed that butein was cytotoxic to both ovarian cancer cells in a dose- and time-dependent manner. JC-1 flow cytometry, cytochrome c, and caspase activity assays revealed that butein damaged the MTP, increased the level of cytosol cytochrome c and the activities of caspase-3, -8, and -9 in the two ovarian cancer cells. Western blot analysis revealed that butein down-regulated the anti-apoptotic proteins Bcl-2 and Bcl-xL and increased the pro-apoptotic proteins Bax and Bad. These findings suggest that butein-induced apoptosis in ovarian cancer cells via the activation of both extrinsic and intrinsic pathways. In addition, butein also down-regulated the expressions of the inhibitor of apoptosis (IAP) proteins, XIAP, survivin, CIAP-1, and CIAP-2. This indicates that the inhibition of IAP proteins was also involved in butein-induced apoptosis. The results of our study suggest that butein may be a promising anticancer agent in treating ovarian cancer.
Search for anomalous quartic WWZγ couplings at the future linear e+e− collider
Authors: Köksal M. , Senol A.
Published: June 2015

In this paper, the potentials of two different processes [Formula: see text] and [Formula: see text] at the Compact Linear Collider (CLIC) are examined to probe the anomalous quartic [Formula: see text] gauge couplings. For [Formula: see text], 1.5 and 3[Formula: see text]TeV energies at the CLIC, 95% confidence level limits on the anomalous coupling parameters defining the dimension-six operators are found via the effective Lagrangian approach in a model independent way. The best limits on the anomalous couplings [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] which can be achieved with the integrated luminosity of [Formula: see text] at the CLIC with [Formula: see text] are [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text], respectively.
Higgs couplings in noncommutative Standard Model
Authors: Batebi S. , Haghighat M. , Tizchang S. , Akafzade H.
Published: June 2015

We consider the Higgs and Yukawa parts of the Noncommutative Standard Model (NCSM). We explore the NC-action to give all Feynman rules for couplings of the Higgs boson to electroweak gauge fields and fermions.
The nucleation of false vacuum bubbles with compact geometries
Authors: Lee Bum-Hoon , Lee Chul H. , Lee Wonwoo , Oh Changheon
Published: June 2015

We investigate and classify the possible types of false vacuum bubbles in Einstein gravity. The false vacuum bubbles can occur only if gravity is taken into account. We show that there exist solutions only with compact geometries. The analytic computations for the radius and nucleation rate of a vacuum bubble are evaluated using the thin-wall approximation. We discuss possible cosmological implications of our new solutions.
Search via quantum walks with intermediate measurements
Authors: Buksman Efrain , de Oliveira André L. Fonseca , de Lacalle Jesús García López
Published: June 2015

A modification of Tulsi's quantum search algorithm with intermediate measurements of the control qubit is presented. In order to analyze the effect of measurements in quantum searches, a different choice of the angular parameter is used. The study is performed for several values of time lapses between measurements, finding close relationships between probabilities and correlations (mutual information and cumulative correlation measure). The order of this modified algorithm is estimated, showing that for some time lapses the performance is improved, and becomes of order O(N) (classical brute-force search) when measurements are taken in every step. The results provide a possible way to analyze improvements to other quantum algorithms using one, or more, control qubits.
Emergent gauge fields and their nonperturbative effects in correlated electrons
Authors: Kim Ki-Seok , Tanaka Akihiro
Published: June 2015

The history of modern condensed matter physics may be regarded as the competition and reconciliation between Stoner’s and Anderson’s physical pictures, where the former is based on momentum–space descriptions focusing on long wave-length fluctuations while the latter is based on real-space physics emphasizing emergent localized excitations. In particular, these two view points compete with each other in various nonperturbative phenomena, which range from the problem of high [Formula: see text] superconductivity, quantum spin liquids in organic materials and frustrated spin systems, heavy-fermion quantum criticality, metal-insulator transitions in correlated electron systems such as doped silicons and two-dimensional electron systems, the fractional quantum Hall effect, to the recently discussed Fe-based superconductors. An approach to reconcile these competing frameworks is to introduce topologically nontrivial excitations into the Stoner’s description, which appear to be localized in either space or time and sometimes both, where scattering between itinerant electrons and topological excitations such as skyrmions, vortices, various forms of instantons, emergent magnetic monopoles, and etc. may catch nonperturbative local physics beyond the Stoner’s paradigm. In this review paper, we discuss nonperturbative effects of topological excitations on dynamics of correlated electrons. First, we focus on the problem of scattering between itinerant fermions and topological excitations in antiferromagnetic doped Mott insulators, expected to be relevant for the pseudogap phase of high [Formula: see text] cuprates. We propose that nonperturbative effects of topological excitations can be incorporated within the perturbative framework, where an enhanced global symmetry with a topological term plays an essential role. In the second part, we go on to discuss the subject of symmetry protected topological states in a largely similar light. While we do not introduce itinerant fermions here, the nonperturbative dynamics of topological excitations is again seen to be crucial in classifying topologically nontrivial gapped systems. We point to some hidden links between several effective field theories with topological terms, starting with one-dimensional physics, and subsequently finding natural generalizations to higher dimensions.
The essence of gravitational waves and energy
Authors: Cooperstock F. I.
Published: June 2015

In this paper, we discuss the essential element of gravity as spacetime curvature and a gravitational wave as the propagation of spacetime curvature. Electromagnetic waves are necessarily localized carriers of spacetime curvature and hence are also gravitational waves. Thus, electromagnetic waves have dual character and detection of gravitational waves is the routine of our everyday experience. Regarding the transferring energy from a gravitational wave to an apparatus, both Rosen and Bondi waves lack the essential characteristic of inducing a gradient of acceleration between detector elements. We discuss our simple invariant energy expression for general relativity and its extension. If the cosmological term is present in the field equations, its universal presence characteristic implies that gravitational waves would necessarily have an energy aspect in their propagation in every case.