bluuebunny/crossref_metadata_2025_split huggingface dataset:
TH‐EF‐BRA‐04: Direct Organ Dose Measurements in a Human Cadaver Scanned with Pediatric CT Protocols
Authors: Lipnharski I , Lamoureux R , Carranza C , Cormack B , Bidari S , Rill L , Arreola M 
Published: June 2015

Purpose:To measure pediatric organ doses and assess clinical image quality in a cadaver scanned with pediatric protocols on a clinical CT scanner.Methods:Organ doses were measured in the thoracic and abdominal regions of a small sized cadaver by inserting optically stimulated luminescent dosimeters (OSLDs) into various organs. The subject's effective diameter was measured as 22.9 cm in the chest, and 22.3 cm in the abdomen, corresponding to the size of an 11‐year old pediatric patient, based on AAPM Report No. 204. The subject was scanned with a pediatric chest and pediatric abdomen protocol on a Toshiba Aquilion ONE CT scanner. Scans were acquired with filtered back projection (FBP) and iterative reconstruction (IR) to quantify organ dose reduction capabilities of IR in pediatric patients. The subject was scanned with reduced dose protocols by increasing the noise tolerance level (SD) from 12.5 to 17.5 and 25.0. Image quality was assessed by a blinded observer study utilizing pediatric radiologists. Readers graded the images with a three point scale on the basis of diagnostic ability.Results:In comparing IR versus FBP reconstructed images, we measured average organ dose reductions of 25% and 32% for the chest and abdomen scans, respectively. Increasing the SD from 12.5 to 17.5 offered organ dose savings of 51% and 58% for the chest and abdomen scans. Further dose reduction was achieved by increasing the SD to 25, allowing substantial dose savings of 75% and 80% for the chest and abdomen scans. The majority of the images were found to be of acceptable image quality.Conclusion:Organ dose quantification and reduction were investigated in this clinical CT study. Iterative reconstruction algorithms provide significant dose reduction to pediatric patients undergoing CT scans. Further dose reductions can be achieved by increasing noise tolerance levels while still maintaining acceptable image quality.
TH‐EF‐BRA‐08: Extending the Concept of Weighted CT Dose Index to Elliptical Phantoms of Various Aspect Ratios
Authors: Markovich A , Morgan A , Dong F , Primak A , Li X 
Published: June 2015

Purpose:Standard CT dosimetry phantoms are currently perfectly circular cylinders. Lately elliptical cylinders have been proposed as an alternative because they better represent the shapes of the human body and allow the evaluation of tube current modulation systems. The purpose of this study was to extend the concept of CTDIw to elliptical phantoms of various aspect ratios.Methods:Based on published adult and pediatric data, eight body aspect ratios were chosen from the full range between 1 (perfectly circular) and 1.72 (extremely elliptical). For each value, two elliptical cylinders were created digitally to represent adult and pediatric bodies. They had the same cross‐sectional areas as the standard 32‐cm and 16‐cm CTDI phantoms. For each digital phantom, CTDI₁₀₀ at central and peripheral locations were simulated for tube voltages between 70–140 kVp using a Monte Carlo program previously validated for a clinical CT system (SOMATOM Definition Flash, Siemens Healthcare). The simulation also output the average dose over the cross‐sectional area, Dxsec, the quantity CTDIw is intended to represent. Values of Dxsec and CTDI₁₀₀ allowed linear systems of equations to be established, from which central and peripheral weighting coefficients were solved.Results:All elliptical phantoms had the same Dxsec as the standard circular phantoms. Regardless of phantom shape, only two weighting coefficients (w1 and w2) were needed: w1 for central CTDI₁ ₀₀ and w2 for the average of the four peripheral CTDI₁₀₀'s. For perfectly circular phantoms, w1 and w2 were 0.37 and 0.63, respectively, agreeing well with the conventional weighting coefficients of 1/3 and 2/3. Over the full range of aspect ratios, w1 increased linearly from 0.37 to 0.46, whereas w2 decreased linearly from 0.63 to 0.54.Conclusion:CTDI₁₀₀ weighting coefficients are linear functions of phantom aspect ratio, allowing the concept of CTDIw to be easily extended to elliptical phantoms of various shapes.This research is supported in part by a Faculty Startup Fund from Cleveland State University.
TH‐EF‐BRA‐10: Monte Carlo Simulation of CT Dose Index and Equilibrium Dose‐Pitch Product: Effect of Ion Chamber Model On Simulated Dose Response
Authors: Liptak C , Morgan A , Dong F , Primak A , Li X 
Published: June 2015

Purpose:In Monte Carlo simulations of patient dose from a CT scan, accurate knowledge about the x‐ray energy spectra is essential. Simulated CT dose index (CTDI₁₀₀) free‐in‐air is often used together with measured values to calibrate the intensity of the spectra. To simulate CTDI₁₀₀, a computational model of the ion chamber is required. Various chamber modeling methods have been reported. The purpose of this study was to investigate systematically how chamber modeling affects simulated dose response. Both the pencil chamber and the thimble chamber recently recommended by AAPM TG111 were studied.Methods:A Monte Carlo program previously validated for a clinical CT system (SOMATOM Definition Flash, Siemens Healthcare) was used. To examine the effect of chamber modeling, a highly detailed model of an actual CTDI₁₀₀ pencil chamber (model 10×5−3CT, Radcal Corporation) was first defined. Five additional models with reduced detail were then created. They differed from the first model in terms of their dimensions, component parts, material composition, and the use of quadric or voxel geometry. Two models of a TG111 thimble chamber were also created, representing a highly detailed and a rather crude rendition of an actual thimble chamber (model 10×0.6−3CT, Radcal Corporation). Single axial scans for CTDI₁₀₀ chamber models and helical scans for TG111 chamber models were simulated free‐in‐air at 70 and 120 kVp. Simulated dose responses were then compared amongst different chamber models.Results:For the six models of the CTDI₁₀₀ pencil chamber, the coefficient of variation of the simulated CTDI₁₀₀ was 0.9% at 70 kVp and 1.0% at 120 kVp. For the two models of the TG111 thimble chamber, the difference in the simulated equilibrium‐dose‐pitch product was 1.9% at 70 kVp and 2.1% at 120 kVp.Conclusion:In Monte Carlo simulations of CT ion chambers, detailed modeling of chamber geometry and material composition is not necessary.This research is supported in part by a Faculty Startup Fund from Cleveland State University.
TH‐EF‐BRA‐11: Investigation of Effects of Adipose Tissue Shielding On Organ Doses and Equation Modeling in Post‐Mortem Subjects for CT
Authors: Lamoureux R , Lipnharski I , Carranza C , Mench A , Sinclair L , Cormack B , Bidari S , Rill L , Arreola M 
Published: June 2015

Purpose:To determine the quantitative effect of adipose tissue shielding on organ dose measurements in computed tomography (CT) and model the effects with organ dose equations.Methods:The post‐mortem dose measurement methodology established in house was utilized to perform organ dose measurements on subjects of varying body habitus for a clinically standardized chest/abdomen/pelvis (CAP) protocol and chest protocol on a 320‐slice CT scanner. The outer effective diameter was calculated obtaining the anterior/posterior and lateral dimensions of the entire anatomy imaged at the middle of the scan range, while the inner effective diameter used the AP and Lat dimensions of the anatomy excluding adipose tissue. These parameters determined effective diameter using Effective Diameter= SQRT(AP *Lat). The subjects were matched by their inner effective diameter and the effective shielding radius was calculated by subtracting the inner effective diameter from the outer effective diameter and dividing by two. The relationship to organ specific CTDI‐to‐organ dose conversion factors was analyzed using linear regression analysis.Results:Of 7 subjects scanned with both the CAP and chest protocols, three were found to have the same inner effective diameters. The calculated CTDI‐to‐organ‐dose conversion factors relationship with the effective internal shielding radius was analyzed using a linear regression analysis. The R2 value for organs within the inner effective diameter space to include lungs, liver, stomach, small intestine, colon, uterus, and ovary ranged from 0.74 to 0.99, with an average of 0.91 for the CAP equations. While the R2 values for the chest scans for lungs, liver, and stomach ranged from 0.98 to 0.9991 with an average of 0.99, showing a good linear fit.Conclusion:The effective internal shielding radius shows a strong correlation when matching similar inner effective diameters to the CTDI‐to‐organ‐dose conversion factors.
Transposable Phage Mu
Authors: Harshey Rasika M. 
Published: June 2015

ABSTRACT
Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.
Programmed Genome Rearrangements in
Tetrahymena
Authors: Yao Meng-Chao , Chao Ju-Lan , Cheng Chao-Yin 
Published: June 2015

ABSTRACT

Ciliates are champions in programmed genome rearrangements. They carry out extensive restructuring during differentiation to drastically alter the complexity, relative copy number, and arrangement of sequences in the somatic genome. This chapter focuses on the model ciliate
Tetrahymena
, perhaps the simplest and best-understood ciliate studied. It summarizes past studies on various genome rearrangement processes and describes in detail the remarkable progress made in the past decade on the understanding of DNA deletion and other processes. The process occurs at thousands of specific sites to remove defined DNA segments that comprise roughly one-third of the genome including all transposons. Interestingly, this DNA rearranging process is a special form of RNA interference. It involves the production of double-stranded RNA and small RNA that guides the formation of heterochromatin. A domesticated piggyBac transposase is believed to cut off the marked chromatin, and the retained sequences are joined together through nonhomologous end-joining processes. Many of the proteins and DNA players involved have been analyzed and are described. This link provides possible explanations for the evolution, mechanism, and functional roles of the process. The article also discusses the interactions between parental and progeny somatic nuclei that affect the selection of sequences for deletion, and how the specific deletion boundaries are determined after heterochromatin marking.
An Overview of Tyrosine Site-specific Recombination: From an Flp Perspective
Authors: Jayaram Makkuni , Ma Chien-Hui , Kachroo Aashiq H , Rowley Paul A , Guga Piotr , Fan Hsui-Fang , Voziyanov Yuri 
Published: June 2015

ABSTRACT
Tyrosine site-specific recombinases (YRs) are widely distributed among prokaryotes and their viruses, and were thought to be confined to the budding yeast lineage among eukaryotes. However, YR-harboring retrotransposons (the DIRS and PAT families) and DNA transposons (Cryptons) have been identified in a variety of eukaryotes. The YRs utilize a common chemical mechanism, analogous to that of type IB topoisomerases, to bring about a plethora of genetic rearrangements with important physiological consequences in their respective biological contexts. A subset of the tyrosine recombinases has provided model systems for analyzing the chemical mechanisms and conformational features of the recombination reaction using chemical, biochemical, topological, structural, and single molecule-biophysical approaches. YRs with simple reaction requirements have been utilized to bring about programmed DNA rearrangements for addressing fundamental questions in developmental biology. They have also been employed to trace the topological features of DNA within high-order DNA interactions established by protein machines. The directed evolution of altered specificity YRs, combined with their spatially and temporally regulated expression, heralds their emergence as vital tools in genome engineering projects with wide-ranging biotechnological and medical applications.
Copy-out–Paste-in Transposition of IS
911
: A Major Transposition Pathway
Authors: Chandler Michael , Fayet Olivier , Rousseau Philippe , Ton Hoang Bao , Duval-Valentin Guy 
Published: June 2015

ABSTRACT

IS
911
has provided a powerful model for studying the transposition of members of a large class of transposable element: the IS
3
family of bacterial Insertion Sequences (IS). These transpose by a Copy-out–Paste-in mechanism in which a double-strand IS circle transposition intermediate is generated from the donor site by replication and proceeds to integrate into a suitable double strand DNA target. This is perhaps one of the most common transposition mechanisms known to date. Copy-out–Paste-in transposition has been adopted by members of at least eight large IS families. This chapter details the different steps of the Copy-out–Paste-in mechanism involved in IS
911
transposition. At a more biological level it also describes various aspects of regulation of the transposition process. These include transposase production by programmed translational frameshifting, transposase expression from the circular intermediate using a specialized promoter assembled at the circle junction and binding of the nascent transposase while it remains attached to the ribosome during translation (co-translational binding). This co-translational binding of the transposase to neighboring IS ends provides an explanation for the longstanding observation that transposases show a
cis
-preference for their activities.
The Long Terminal Repeat Retrotransposons Tf1 and Tf2 of
Schizosaccharomyces pombe
Authors: Esnault Caroline , Levin Henry L. 
Published: June 2015

ABSTRACT

The long terminal repeat (LTR) retrotransposons Tf1 and Tf2 of
Schizosaccharomyces pombe
are active mobile elements of the Ty3/gypsy family. The mobilization of these retrotransposons depends on particle formation, reverse transcription and integration, processes typical of other LTR retrotransposons. However, Tf1 and Tf2 are distinct from other LTR elements in that they assemble virus-like particles from a single primary translation product, initiate reverse transcription with an unusual self-priming mechanism, and, in the case of Tf1, integrate with a pattern that favors specific promoters of RNA pol II-transcribed genes. To avoid the chromosome instability and genome damage that results from increased copy number,
S. pombe
applies a variety of defense mechanisms that restrict Tf1 and Tf2 activity. The mRNA of the Tf elements is eliminated by an exosome-based pathway when cells are in favorable conditions whereas nutrient deprivation triggers an RNA interference-dependent pathway that results in the heterochromatization of the elements. Interestingly, Tf1 integrates into the promoters of stress-induced genes and these insertions are capable of increasing the expression of adjacent genes. These properties of Tf1 transposition raise the possibility that Tf1 benefits cells with specific insertions by providing resistance to environmental stress.
The Tn
3
-family of Replicative Transposons
Authors: Nicolas Emilien , Lambin Michael , Dandoy Damien , Galloy Christine , Nguyen Nathan , Oger Cédric A. , Hallet Bernard 
Published: June 2015

ABSTRACT

Transposons of the Tn
3
family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn
3
-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn
3
-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.
THE INFLUENCE OF THE GREEN INNOVATION IN THE SEARCH OF COMPETITIVE ADVANTAGE OF ENTERPRISES OF THE ELECTRICAL AND ELECTRONIC BRAZILIAN SECTORS
Authors: ARENHARDT DANIEL LUIS , BATTISTELLA LUCIANA FLORES , GROHMANN MARCIA ZAMPIERI 
Published: June 2015

This study aimed to verify how the adoption of green innovations influences in the obtention of competitive advantage of companies in the electrical and electronic Brazilian sectors. Quantitative in nature, the study adopted the conceptual model proposed by [Chen et al. (2006). The influence of green innovation performance on corporate advantage in Taiwan. Journal of Business Ethics, 67(4), 331–339]. Using as target population companies linked to the Brazilian Association of Electrical and Electronics Industry (ABINEE), the sample consisted of 113 organisations representing 20.62% of this population. The results showed that the level of adoption of innovative green practices among the participating companies is high and that the relationship between products innovation and green processes and the achievement of competitive advantage is significant, but at a moderate level.
Time-Warp
Authors: Diegues Nuno , Romano Paolo 
Published: June 2015

The multicore revolution that took place one decade ago has turned parallel programming into a major concern for the mainstream software development industry. In this context, Transactional Memory (TM) has emerged as a simpler and attractive alternative to that of lock-based synchronization, whose complexity and error-proneness are widely recognized.
The notion of permissiveness in TM translates to only aborting a transaction when it cannot be accepted in any history that guarantees a target correctness criterion. This theoretically powerful property is often neglected by state-of-the-art TMs because it imposes considerable algorithmic costs. Instead, these TMs opt to maximize their implementation’s efficiency by aborting transactions under overly conservative conditions. As a result, they risk rejecting a significant number of safe executions.

In this article, we seek to identify a sweet spot between permissiveness and efficiency by introducing the Time-Warp Multiversion (TWM) algorithm. TWM is based on the key idea of allowing an update transaction that has performed stale reads (i.e., missed the writes of concurrently committed transactions) to be serialized by “committing it in the past,” which we call a
time-warp
commit. At its core, TWM uses a novel, lightweight validation mechanism with little computational overhead. TWM also guarantees that read-only transactions can never be aborted. Further, TWM guarantees
Virtual World Consistency
, a safety property that is deemed as particularly relevant in the context of TM.

We demonstrate the practicality of this approach through an extensive experimental study: we compare TWM with five other TMs, representative of typical alternative design choices, and on a wide variety of benchmarks. This study shows an average performance improvement across all considered workloads and TMs of 65% in high concurrency scenarios, with gains extending up to 9 × with the most favorable benchmarks. These results are a consequence of TWM’s ability to achieve drastic reduction of aborts in scenarios of nonminimal contention, while introducing little overhead (approximately 10%) in worst-case, synthetically designed scenarios (i.e., no contention or contention patterns that cannot be optimized using TWM).
MSE Minus CAPE is the True Conserved Variable for an Adiabatically Lifted Parcel
Authors: Romps David M. 
Published: June 2015

Abstract
For an adiabatic parcel convecting up or down through the atmosphere, it is often assumed that its moist static energy (MSE) is conserved. Here, it is shown that the true conserved variable for this process is MSE minus convective available potential energy (CAPE) calculated as the integral of buoyancy from the parcel’s height to its level of neutral buoyancy and that this variable is conserved even when accounting for full moist thermodynamics and nonhydrostatic pressure forces. In the calculation of a dry convecting parcel, conservation of MSE minus CAPE gives the same answer as conservation of entropy and potential temperature, while the use of MSE alone can generate large errors. For a moist parcel, entropy and equivalent potential temperature give the same answer as MSE minus CAPE only if the parcel ascends in thermodynamic equilibrium. If the parcel ascends with a nonisothermal mixed-phase stage, these methods can give significantly different answers for the parcel buoyancy because MSE minus CAPE is conserved, while entropy and equivalent potential temperature are not.