bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of 36 Cases of Blaschkoid Dyspigmentation: Reading Between the Lines of Blaschko
Authors: Cohen Jared , Shahrokh Katayoon , Cohen Bernard 
Published: July 2014

AbstractGenetic mosaicism indicated by lines of Blaschko pigmentary changes has been described under a number of different and confusing terms, including hypomelanosis of Ito, linear and whorled nevoid hypermelanosis, nevus depigmentosus, and cutis tricolor. Moreover, extracutaneous findings, particularly serious neurologic defects, have been reported in a large number of these cases. We reviewed the cutaneous and extracutaneous findings in 36 patients referred to the Harriet Lane Pediatric Dermatology Clinic, Johns Hopkins University, from June 12, 2008, to May 24, 2009, for evaluation of macular lesions along the lines of Blaschko. Patients with dyspigmentation along the lines of Blaschko and no history of preceding inflammatory skin lesions were identified for inclusion in a database at their initial visit. Information on age at presentation; sex; age when first diagnosed; type, pattern, and location of the pigmentary anomaly; and extracutaneous abnormalities noted on a review‐of‐systems questionnaire and physical examination was recorded for each child. Patients were asked to follow up within 6 to 12 months of the initial visit. Patients included 13 boys and 23 girls ages 3 months to 15 years with lesions noted from birth to 12 years. Lesions were hypopigmented in 21 patients and hyperpigmented in 15. No patients presented with hypopigmented and hyperpigmented lesions. Extracutaneous findings were noted in five children (13.9%). Historically, cases of Blaschkoid hypopigmentation and hyperpigmentation have been associated with a high percentage of extracutaneous manifestations, particularly neurologic and neurodevelopmental defects. In our study, only five patients (13.9%) were noted to have extracutaneous abnormalities, and these findings may have been coincidental. We propose the term ‘Blaschkoid dyspigmentation’ to describe the cutaneous findings. Although serious extracutaneous findings may occur in children with Blaschkoid dyspigmentation and results of careful physical examination and review of systems should direct an evaluation, serious extracutaneous findings occur in a minority of patients.
Meaning, Use and Ostensive Definition in Wittgenstein's Philosophical Investigations
Authors: Cheung Leo K. C. 
Published: July 2014

AbstractIn this paper, I argue that the restricted claim in §43a of the Philosophical Investigations is that, for a large class of cases of word meanings, the meaning of a word is its use in the language. Although Wittgenstein does not provide any example of words having uses but no meaning as exceptions to the claim, he does hint at exceptions, which are names being defined, or explained, ostensively by pointing to their bearers, in §43b. Names in ostensive definitions, or explanations, are meaningful, but not being used, and are therefore exceptions to the claim that meaning is use.
Effects of Montane Heathland Restoration on Leafhopper Assemblages (Insecta: Auchenorrhyncha)
Authors: Borchard Fabian , Fartmann Thomas 
Published: July 2014

AbstractAt the beginning of the 20th century, many montane heathlands were abandoned and became subject to natural succession or afforestation by humans. Thus, the formerly large montane heathlands slowly degraded into small and isolated patches. In this study, we evaluate the influence of restoration measures on leafhopper (Auchenorrhyncha) assemblages of montane heathland ecosystems in Central Europe. Our analyses comprised three different site types that were adjacent to each other: (1) montane heathlands, (2) restoration sites, and (3) control sites. Leafhoppers showed a clear response to montane heathland restoration. Thus, after 4–5 years since implementation of restoration measurements restoration sites were characterized by the highest species richness. However, detailed analyses of leafhopper diversity, species composition, and environmental parameters on the three site types revealed that restoration sites were rather similar to control sites and significantly differing from montane heathlands. We conclude that leafhoppers are excellent bioindicators for restoration measurements because they reflected environmental differences between the three site types. Restoration measurements might only be a useful instrument to promote typical montane heathland leafhopper communities in the long run. Colonization by leafhoppers is, however, dependent on many different factors such as leafhopper mobility, vegetation structure, microclimate, and the establishment of ericaceous dwarf shrubs. Practitioners should establish a management regime (grazing and sod‐cutting) that creates a mosaic of different habitat structures and increases typical heathland vegetation, thus, favoring the colonization of typical heathland leafhoppers.
Antagonistic roles of abscisic acid and cytokinin during response to nitrogen depletion in oleaginous microalga Nannochloropsis oceanica expand the evolutionary breadth of phytohormone function
Authors: Lu Yandu , Tarkowská Danuše , Turečková Veronika , Luo Tingwei , Xin Yi , Li Jing , Wang Qintao , Jiao Nianzhi , Strnad Miroslav , Xu Jian 
Published: July 2014

SummaryThe origin of phytohormones is poorly understood, and their physiological roles in microalgae remain elusive. Genome comparison of photosynthetic autotrophic eukaryotes has revealed that the biosynthetic pathways of abscisic acid (ABA) and cytokinins (CKs) emerged in unicellular algae. While ABA and CK degradation mechanisms emerged broadly in algal lineages, complete vascular plant‐type conjugation pathways emerged prior to the rise of Streptophyta. In microalgae, a complete set of proteins from the canonical ABA and CK sensing and signaling pathways is not essential, but individual components are present, suggesting stepwise recruitment of phytohormone signaling components. In the oleaginous eustigmatophyte Nannochloropsis oceanica IMET1, UHPLC‐MS/MS detected a wide array of plant hormones, despite a phytohormone profile that is very distinct from that of flowering plants. Time‐series transcriptional analysis during nitrogen depletion revealed activation of the ABA biosynthetic pathway and antagonistic transcription of CK biosynthetic genes. Correspondingly, the ABA level increases while the dominant bioactive CK forms decrease. Moreover, exogenous CKs stimulate cell‐cycle progression while exogenous ABA acts as both an algal growth repressor and a positive regulator in response to stresses. The presence of such functional flowering plant‐like phytohormone signaling systems in Nannochloropsis sp. suggests a much earlier origin of phytohormone biosynthesis and degradation than previously believed, and supports the presence in microalgae of as yet unknown conjugation and sensing/signaling systems that may be exploited for microalgal feedstock development.
Evidence‐Based Stillbirth Prevention Strategies: Combining Empirical and Theoretical Paradigms to Inform Health Planning and Decision‐Making
Authors: King Mary Lou , Aden Amna , Tapa Stephany , Jumah Reem , Khan Salma 
Published: July 2014

ABSTRACTIntroductionA global health project undertaken in Qatar on the Arabian Peninsula immersed undergraduate nursing students in hands‐on learning to address the question: What strategies are effective in preventing stillbirth? Worldwide stillbirth estimates of 2.6 million per year and the high rate in the Eastern Mediterranean Region of 27 per 1,000 total live births provided the stimulus for this inquiry.MethodsWe used a dual empirical and theoretical approach that combined the principles of evidence‐based practice and population health planning. Students were assisted to translate pre‐appraised literature based on the 6S hierarchical pyramid of evidence. The PRECEDE‐PROCEED (P‐P) model served as an organizing template to assemble data extracted from the appraisal of 21 systematic literature reviews ± meta‐analyses, 2 synopses of synthesized reports, and 9 individual studies summarizing stillbirth prevention strategies in low, middle, and high income countries. Consistent with elements of the P‐P model, stillbirth prevention strategies were classified as social, epidemiological, educational, ecological, administrative, or policy.ResultsTen recommendations with clear evidence of effectiveness in preventing stillbirth in low, middle, or high income countries were identified. Several other promising interventions were identified with weak, uncertain, or inconclusive evidence. These require further rigorous testing.Linking Evidence to ActionTwo complementary paradigms—evidence‐based practice and an ecological population health program planning model—helped baccalaureate nursing students transfer research evidence into useable knowledge for practice. They learned the importance of comprehensive assessments and evidence‐informed interventions. The multidimensional elements of the P‐P model sensitized students to the complex interrelated factors influencing stillbirth and its prevention.
Control Port Influence on Swirl, Operating, and Flow Characteristics
of a Mini-Vortex Amplifier on Glove Box Service
Authors: Francis J. , Parker D. , Whitty J. , Zhang G. 
Published: July 2014

Abstract
Vortex amplifiers (VA) use fluidic phenomena to modify flow through a containment breach, when used to protect glove box workers from exposure to the contents. The influence of control port geometry on swirl, operating characteristics, global flow, and momentum characteristics is studied experimentally. Shape and size of the control flow channels and the pressure applied at the tangential ports are critical in determining the trajectory of the jet issuing from the tangential ports and deflection of radial flow and vortex strength. Dominance of control-to-exit area ratio is confirmed. A clear improvement in performance is noted for a practical geometry derived from shaped passages of the device. Flow and momentum characteristics provide additional design data. The relationship of swirl number to output flow is demonstrated. Global flow and momentum characteristics provide insight into design and operation that is useful when avoiding back diffusion.
SU‐E‐T‐488: An Iso‐Dose Curve Based Interactive IMRT Optimization System for Physician‐Driven Plan Tuning
Authors: Shi F , Tian Z , Zarepisheh M , Cervino L , Jia X , Jiang S 
Published: July 2014

Purpose:In treatment plan optimization for Intensity Modulated Radiation Therapy (IMRT), after a plan is initially developed by a dosimetrist, the attending physician evaluates its quality and often would like to improve it. As opposed to having the dosimetrist implement the improvements, it is desirable to have the physician directly and efficiently modify the plan for a more streamlined and effective workflow. In this project, we developed an interactive optimization system for physicians to conveniently and efficiently fine‐tune iso‐dose curves.Methods:An interactive interface is developed under C++/Qt. The physician first examines iso‐dose lines. S/he then picks an iso‐dose curve to be improved and drags it to a more desired configuration using a computer mouse or touchpad. Once the mouse is released, a voxel‐based optimization engine is launched. The weighting factors corresponding to voxels between the iso‐dose lines before and after the dragging are modified. The underlying algorithm then takes these factors as input to re‐optimize the plan in near real‐time on a GPU platform, yielding a new plan best matching the physician's desire. The re‐optimized DVHs and iso‐dose curves are then updated for the next iteration of modifications. This process is repeated until a physician satisfactory plan is achieved.Results:We have tested this system for a series of IMRT plans. Results indicate that our system provides the physicians an intuitive and efficient tool to edit the iso‐dose curves according to their preference. The input information is used to guide plan re‐optimization, which is achieved in near real‐time using our GPU‐based optimization engine. Typically, a satisfactory plan can be developed by a physician in a few minutes using this tool.Conclusion:With our system, physicians are able to manipulate iso‐dose curves according to their preferences. Preliminary results demonstrate the feasibility and effectiveness of this tool.
SU‐E‐T‐504: Usefulness of CT‐MR Fusion in Radiotherapy Planning for Prostate Cancer Patient with Bilateral Hip Replacements
Authors: He R. , Kumar P. , Hu Y. , Suggs J. , Yang C. , Giri Shankar 
Published: July 2014

Purpose:Target localization of prostate for Intensity Modulated Radiation Therapy (IMRT) in patients with bilateral hip replacements is difficult due to artifacts in Computed Tomography (CT) images generated from the prostheses high Z materials. In this study, Magnetic Resonance (MR) images fused with CT images are tested as a solution.Methods:CT images of 2.5 mm slice thickness were acquired on a GE Lightspeed scanner with a flat‐topped couch for a prostate cancer patient with bilateral hip replacements. T2 weighted images of 5 mm separation were acquired on a MR Scanner. After the MR‐CT registration on a radiotherapy treatment planning system (Eclipse, Varian), the target volumes were defined by the radiation oncologists on MR images and then transferred to CT images for planning and dose calculation. The CT Hounsfield Units (HU) was reassigned to zero (as water) for artifacts. The Varian flat panel treatment couch was modeled for dose calculation accuracy with heterogeneity correction. A Volume Matrix Arc Therapy (VMAT) and a seven‐field IMRT plans were generated, each avoiding any beam transversing the prostheses; the two plans were compared. The superior VMAT plan was used for treating the patient. In‐vivo dosimetry was performed using MOSFET (Best Canada) placed in a surgical tube inserted into the patient rectum during therapy. The measured dose was compared with planned dose for MOSFET location.Results:The registration of MR‐CT images and the agreement of target volumes were confirmed by three physicians. VMAT plan was deemed superior to IMRT based on dose to critical nearby structures and overall conformality of target dosing. In‐vivo measured dose compared with calculated dose was ‐4.5% which was likely due to attenuation of the surgical tube surrounding MOSFET.Conclusion:When artifacts are present on planning CT due to bilateral hip prostheses, MR‐CT image fusion is a feasible solution for target delineation.
SU‐E‐T‐507: Interfractional Variation of Fiducial Marker Position During HDR Brachytherapy with Cervical Interstitial Needle Template
Authors: Shen S , Kim R , Benhabib S , Araujo J , Burnett L , Duan J , Popple R , Wu X , Cardan R , Brezovich I 
Published: July 2014

Purpose:HDR brachytherapy using interstitial needle template for cervical cancer is commonly delivered in 4‐5 fractions. Routine verification of needle positions before each fraction is often based on radiographic imaging of implanted fiducial markers. The current study evaluated interfractional displacement of implanted fiducial markers using CT images.Methods:9 sequential patients with cervical interstitial needle implants were evaluated. The superior and inferior borders of the target volumes were defined by fiducial markers in planning CT. The implant position was verified with kV orthogonal images before each fraction. A second CT was acquired prior 3rd fraction (one or 2 days post planning CT). Distances from inferior and superior fiducial markers to pubic symphysis plane (perpendicular to vaginal obtulator)were measured. Distance from needle tip of a reference needle (next to the inferior marker) to the pubic symphysis plane was also determined. The difference in fiducial marker distance or needle tip distance between planning CT and CT prior 3rd fraction were measured to assess markers migration and needle displacement.Results:The mean inferior marker displacement was 4.5 mm and ranged 0.9 to 11.3 mm. The mean superior marker displacement was 2.7 mm and ranged 0 to 10.4 mm. There was a good association between inferior and superior marker displacement (r=0.95). Mean averaged inferior and superior marker displacement was 3.3 mm and ranged from 0.1 to 10.9 mm, with a standard deviation of 3.2 mm. The mean needle displacement was 5.6 mm and ranged 0.2 to 15.6 mm. Needle displacements were reduced (p<0.05) after adjusting according to needle‐to‐fiducials distance.Conclusion:There were small fiducial marker displacements between HDR fractions. Our study suggests a target margin of 9.7 mm to cover interfractional marker displacements (in 95% cases) for pretreatment verification based on radiographic imaging.
SU‐E‐T‐512: Electromagnetic Simulations of the Dielectric Wall Accelerator
Authors: Uselmann A , Mackie T 
Published: July 2014

Purpose:To characterize and parametrically study the key components of a dielectric wall accelerator through electromagnetic modeling and particle tracking.Methods:Electromagnetic and particle tracking simulations were performed using a commercial code (CST Microwave Studio, CST Inc.) utilizing the finite integration technique. A dielectric wall accelerator consists of a series of stacked transmission lines sequentially fired in synchrony with an ion pulse. Numerous properties of the stacked transmission lines, including geometric, material, and electronic properties, were analyzed and varied in order to assess their impact on the transverse and axial electric fields. Additionally, stacks of transmission lines were simulated in order to quantify the parasitic effect observed in closely packed lines. Particle tracking simulations using the particle‐in‐cell method were performed on the various stacks to determine the impact of the above properties on the resultant phase space of the ions.Results:Examination of the simulation results show that novel geometries can shape the accelerating pulse in order to reduce the energy spread and increase the average energy of accelerated ions. Parasitic effects were quantified for various geometries and found to vary with distance from the end of the transmission line and along the beam axis. An optimal arrival time of an ion pulse relative to the triggering of the transmission lines for a given geometry was determined through parametric study. Benchmark simulations of single transmission lines agree well with published experimental results.Conclusion:This work characterized the behavior of the transmission lines used in a dielectric wall accelerator and used this information to improve them in novel ways. Utilizing novel geometries, we were able to improve the accelerating gradient and phase space of the accelerated particle bunch. Through simulation, we were able to discover and optimize design issues with the device at low cost. Funding: Morgridge Institute for Research, Madison WI; Conflict of Interest: Dr. Mackie is an investor and board member at CPAC, a company developing compact accelerator designs similar to those discussed in this work, but designs discussed are not directed by CPAC.Funding: Morgridge Institute for Research, Madison WI; Conflict of Interest: Dr. Mackie is an investor and board member at CPAC, a company developing compact accelerator designs similar to those discussed in this work, but designs discussed are not directed by CPAC.
Automatic Requirement Classification: Tackling Inconsistencies Between Requirements and Regulations
Authors: Ott Daniel , Houdek Frank 
Published: July 2014

Current Requirement Engineering research must face the need to deal with the increasing scale of today's requirement specifications. One important and recent research direction is handling the consistency assurance between large scale specifications and many additional regulations (e.g. national and international norms and standards), which the specifications must consider or satisfy. For example, the specification volume for a single electronic control unit (ECU) in the automotive domain sums up to 3000 to 5000 pages distributed over 30 to 300 individual documents (specification and regulations). In this work, we present an approach to automatically classify the requirements in a set of specification documents and regulations to content topics in order to improve review activities in identifying cross-document inconsistencies. An essential success criteria for this approach from an industrial perspective is a sufficient classification quality with minimal manual effort. In this paper, we show the results of an evaluation in the domain of automotive specifications at Mercedes-Benz passenger cars. The results show that one manually classified specification is sufficient to derive automatic classifications for other documents within this domain with satisfactory recall and precision. So, the approach of using content topics is not only effective but also efficient in large scale industrial environments.
Multiplex PCR assay for identification of commonly used disarmed Agrobacterium tumefaciens strains
Authors: Deeba Farah , Hyder Muhammad Zeeshan , Shah Shahzad Hussain , Naqvi Syed Muhammad Saqlan 
Published: July 2014

Abstract
The success of Agrobacterium mediated plant transformation depends to a certain extent on appropriate selection of the A. tumefaciens strain for a particular plant species. Many stages in a plant transformation procedure are prone to bacterial contamination with similar antibiotic resistance that may compromise the identity of the A. tumefaciens strain used, in turn adversely affecting success of a transformation experiment. Different primer sets were designed to exploit genetic differences among different strains of A. tumefaciens which are commonly used for plant genetic transformation, to identity confirmation as well as to distinguish them from one another. The primer sets Ach5FtsZ-F/R specific for Ach5 and C58GlyA-F/R specific for C58 were designed on chromosomal DNA while primer sets pTiBo542-F/R and nptI-F/R specific for plasmid pTiBo542 are capable to identify and distinguish these strains from one another. These primer sets when used simultaneously in multiplex PCR, produce a pattern which uniquely identifies all these strains and distinguishes them except for GV3101 and C58C1, which can further be distinguished from each other by rifampicin screening. The multiplex PCR assay and primers being reported here serve as a valuable tool in determining the identity of A. tumefaciens strains at any stage of plant transformation procedure.
Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network
Authors: Li Peng , Gong Ping , Li Haoni , Perkins Edward J , Wang Nan , Zhang Chaoyang 
Published: July 2014

AbstractThe Dialogue for Reverse Engineering Assessments and Methods (DREAM) project was initiated in 2006 as a community-wide effort for the development of network inference challenges for rigorous assessment of reverse engineering methods for biological networks. We participated in thein siliconetwork inference challenge of DREAM3 in 2008. Here we report the details of our approach and its performance on the synthetic challenge datasets. In our methodology, we first developed a model called relative change ratio (RCR), which took advantage of the heterozygous knockdown data and null-mutant knockout data provided by the challenge, in order to identify the potential regulators for the genes. With this information, a time-delayed dynamic Bayesian network (TDBN) approach was then used to infer gene regulatory networks from time series trajectory datasets. Our approach considerably reduced the searching space of TDBN; hence, it gained a much higher efficiency and accuracy. The networks predicted using our approach were evaluated comparatively along with 29 other submissions by two metrics (area under the ROC curve and area under the precision-recall curve). The overall performance of our approach ranked the second among all participating teams.