bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deviating from the Norm: Peculiarities of Aplysia cf. californica Early Cleavage Compared to Traditional Spiralian Models
Authors: Chávez‐Viteri Yolanda E. , Brown Federico D. , Pérez Oscar D. 
Published: December 2016

ABSTRACTSpiralia represents one of the main clades of bilaterally symmetrical metazoans (Bilateria). This group is of particular interest due to the remarkable conservation of its early developmental pattern despite of the high diversity of larval and adult body plans. Variations during embryogenesis are considered powerful tools to determine ancestral and derived characters under a phylogenetic framework. By direct observation of embryos cultured in vitro, we analyzed the early cleavage of the euopisthobranchs Aplysia cf. californica. We used tubulin immunocytochemistry to stain mitotic spindles during early cleavages, and followed each division with the aid of an autofluorescent compound inside yolk platelets, which differed from the characteristic pink‐brownish pigment of the vegetal cytoplasm in zygotes and early embryos. We found that this species exhibits an unequal cleavage characterized by ooplasmic segregation, oblique inclination of mitotic spindles, and differences in size and positioning of the asters in relation to the cellular cortex. Furthermore, we detected asynchrony in cleavage timing between the two large macromeres C and D, which increases the number of cleavage rounds required to reach a particular cell stage in comparison to other spiralians. Here, we report the presence of a transient and previously undescribed U‐shaped embryo in this species. The present detailed description of A. californica early development deviates considerably from stereotypical patterns described in other spiralians. Our observations demonstrate that early spiralian development can be more plastic than previously thought.
Evaluating the Role of a Protected Area on Hedgerow Conservation: The Case of a Spanish Cultural Landscape
Authors: Schmitz María F. , Herrero‐Jáuregui Cristina , Arnaiz‐Schmitz Cecilia , Sánchez Iván A. , Rescia Alejandro J. , Pineda Francisco D. 
Published: December 2016

AbstractHedgerows are key features in agricultural landscapes performing diverse functions that are both economically and ecologically significant. Here, we quantify how the characteristics of a relict hedgerow network of a Spanish cultural landscape (Guadarrama mountains in the north of Madrid region) have changed over a single decade both inside and outside the boundaries of a Protected Area, the aim of which is to conserve cultural uses and biodiversity. A gradient of abandonment of pasture systems was detected, including a decline and loss of woody species from hedgerows associated with grazed areas towards shrub encroachment zones. These tendencies were similar inside and outside the boundaries of the Protected Area. The results highlight the management weaknesses of the Protected Area in order to achieve its objectives. Based on the results, we propose to include a specific conservation status for hedgerow landscapes in the regulatory framework of Spanish protected areas. Copyright © 2016 John Wiley & Sons, Ltd.
The use of a numerical weather prediction model to simulate the release of a dense gas with an application to the Lake Nyos disaster of 1986
Authors: Burton R. R. , Dudhia J. , Gadian A. M. , Mobbs S. D. 
Published: December 2016

ABSTRACTThe spread of a dense gas in the atmosphere is a phenomenon that occurs widely with natural (and anthropogenic) causes and is often associated with high impact and hazardous events. In this study a method of simulating the spread of dense gases in a numerical weather prediction model is presented. This approach has the advantage that dense gases can be simulated in regions of complex terrain using realistic forcings (in terms of both the driving meteorological fields and the representation of surface characteristics). The model formulation is tested against semi‐idealized gravity‐current‐type experiments and similar modelling studies. As an example application, the Lake Nyos disaster of 1986, where a dense CO2 cloud spread through a mountainous region of Cameroon, is simulated. The predicted spread of CO2 agrees (qualitatively) very well with the observations. The method provides a means of determining a potential ‘safe height’ above which simulated concentrations are not hazardous, and thus the height above which refuge should be taken during similar future events. The simulation demonstrates a novel application which can be rapidly applied to other scenarios.
Building a family network from genetic testing
Authors: Leppig Kathleen A. , Thiese Heidi A. , Carrel David , Crosslin David R. , Dorschner Michael O. , Gordon Adam S. , Hartzler Andrea , Ralston James , Scrol Aaron , Larson Eric B. , Jarvik Gail P. 
Published: December 2016

AbstractBackgroundGenetic testing has multigenerational and familial repercussions. However, the “trickle‐down effect” of providing genetic counseling and testing to family members at risk after an initial identification of a pathogenic variant in a medically actionable gene has been poorly understood.MethodsThree probands were identified during the pharmacogenetics research phase of eMERGEII (electronic MEdical Record and Genomics, phase II) to have variants in genes associated with autosomal dominant adult‐onset disorders determined to be actionable by the American College of Medical Genetics (ACMG). Two of the three probands had variants that were classified as pathogenic and the third proband had a variant ultimately classified of uncertain significance, but of concern due to the proband's own phenotype. All probands had additional family members at risk for inheriting the variant. Two of the three probands had family members who received their medical care from the same health care system, Group Health Cooperative (GHC). It was recommended that the proband contact their family members at risk to be referred to genetic counseling for consideration of genetic testing.ResultsThe two probands with pathogenic variants contacted some of their family members at risk. Individuals contacted included children and adult grandchildren, particularly if they received their medical care at GHC. To the best of our knowledge, siblings and more distant relatives at risk were not informed by the proband of their genetic risk.ConclusionsEstablishing a family network is essential to disseminate knowledge of genetic risk. These three initial cases describe our experience of contacting eMERGE participants with identified variants, providing the probands with appropriate genetic counseling and care coordination, and recommendations for contacting family members at risk. Greater challenges were observed for coordinating genetics care for family members and extending the family network to include other relatives at risk.
Beam distortion due to gold fiducial markers during salvage high‐intensity focused ultrasound in the prostate
Authors: Georgiou P. S. , Jaros J. , Payne H. , Allen C. , Shah T. T. , Ahmed H. U. , Gibson E. , Barratt D. , Treeby B. E. 
Published: December 2016

PurposeHigh intensity focused ultrasound (HIFU) provides a non‐invasive salvage treatment option for patients with recurrence after external beam radiation therapy (EBRT). As part of EBRT the prostate is frequently implanted with permanent fiducial markers. To date, the impact of these markers on subsequent HIFU treatment is unknown. The objective of this work was to systematically investigate, using computational simulations, how these fiducial markers affect the delivery of HIFU treatment.MethodsA series of simulations was performed modelling the propagation of ultrasound pressure waves in the prostate with a single spherical or cylindrical gold marker at different positions and orientations. For each marker configuration, a set of metrics (spatial‐peak temporal‐average intensity, focus shift, focal volume) was evaluated to quantify the distortion introduced at the focus. An analytical model was also developed describing the marker effect on the intensity at the focus. The model was used to examine the marker's impact in a clinical setting through case studies.ResultsThe simulations show that the presence of the marker in the pre‐focal region causes reflections which induce a decrease in the focal intensity and focal volume, and a shift of the maximum pressure point away from the transducer's focus. These effects depend on the shape and orientation of the marker and become more pronounced as its distance from the transducer's focus decreases, with the distortion introduced by the marker greatly increasing when placed within 5 mm of the focus. The analytical model approximates the marker's effect and can be used as an alternative method to the computationally intensive and time consuming simulations for quickly estimating the intensity at the focus. A retrospective review of a small patient cohort selected for focal HIFU after failed EBRT indicates that the presence of the marker may affect HIFU treatment delivery.ConclusionsThe distortion introduced by the marker to the HIFU beam when positioned close to the focus may result in an undertreated region beyond the marker due to less energy arriving at the focus, and an overtreated region due to reflections. Further work is necessary to investigate whether the results presented here justify the revision of the patient selection criteria or the markers’ placement protocol.
CT breast dose reduction with the use of breast positioning and organ‐based tube current modulation
Authors: Fu Wanyi , Tian Xiaoyu , Sturgeon Gregory M. , Agasthya Greeshma , Segars William Paul , Goodsitt Mitchell M. , Kazerooni Ella A. , Samei Ehsan 
Published: December 2016

PurposeThis study aimed to investigate the breast dose reduction potential of a breast‐positioning (BP) technique for thoracic CT examinations with organ‐based tube current modulation (OTCM).MethodsThis study included 13 female anthropomorphic computational phantoms (XCAT, age range: 27–65 y.o., weight range: 52–105.8 kg). Each phantom was modified to simulate three breast sizes in standard supine geometry. The modeled breasts were then morphed to emulate BP that constrained the majority of the breast tissue inside the 120° anterior tube current (mA) reduction zone. The OTCM mA value was modeled using a ray‐tracing program, which reduced the mA to 20% in the anterior region with a corresponding increase to the posterior region. The organ doses were estimated by a validated Monte Carlo program for a typical clinical CT system (SOMATOM Definition Flash, Siemens Healthcare). The simulated organ doses and organ doses normalized by CTDIvol were used to compare three CT protocols: attenuation‐based tube current modulation (ATCM), OTCM, and OTCM with BP (OTCMBP).ResultsOn average, compared to ATCM, OTCM reduced breast dose by 19.3 ± 4.5%, whereas OTCMBP reduced breast dose by 38.6 ± 8.1% (an additional 23.8 ± 9.4%). The dose saving of OTCMBP was more significant for larger breasts (on average 33, 38, and 44% reduction for 0.5, 1, and 2 kg breasts, respectively). Compared to ATCM, OTCMBP also reduced thymus and heart dose by 15.1 ± 7.4% and 15.9 ± 6.2% respectively.ConclusionsIn thoracic CT examinations, OTCM with a breast‐positioning technique can markedly reduce unnecessary exposure to radiosensitive organs in anterior chest wall, specifically breast tissue. The breast dose reduction is more notable for women with larger breasts.
A novel pre‐processing technique for improving image quality in digital breast tomosynthesis
Authors: Kim Hyeongseok , Lee Taewon , Hong Joonpyo , Sabir Sohail , Lee Jung‐Ryun , Choi Young Wook , Kim Hak Hee , Chae Eun Young , Cho Seungryong 
Published: December 2016

PurposeNonlinear pre‐reconstruction processing of the projection data in computed tomography (CT) where accurate recovery of the CT numbers is important for diagnosis is usually discouraged, for such a processing would violate the physics of image formation in CT. However, one can devise a pre‐processing step to enhance detectability of lesions in digital breast tomosynthesis (DBT) where accurate recovery of the CT numbers is fundamentally impossible due to the incompleteness of the scanned data. Since the detection of lesions such as micro‐calcifications and mass in breasts is the purpose of using DBT, it is justified that a technique producing higher detectability of lesions is a virtue.MethodsA histogram modification technique was developed in the projection data domain. Histogram of raw projection data was first divided into two parts: One for the breast projection data and the other for background. Background pixel values were set to a single value that represents the boundary between breast and background. After that, both histogram parts were shifted by an appropriate amount of offset and the histogram‐modified projection data were log‐transformed. Filtered‐backprojection (FBP) algorithm was used for image reconstruction of DBT. To evaluate performance of the proposed method, we computed the detectability index for the reconstructed images from clinically acquired data.ResultsTypical breast border enhancement artifacts were greatly suppressed and the detectability of calcifications and masses was increased by use of the proposed method. Compared to a global threshold‐based post‐reconstruction processing technique, the proposed method produced images of higher contrast without invoking additional image artifacts.ConclusionsIn this work, we report a novel pre‐processing technique that improves detectability of lesions in DBT and has potential advantages over the global threshold‐based post‐reconstruction processing technique. The proposed method not only increased the lesion detectability but also reduced typical image artifacts pronounced in conventional FBP‐based DBT.
Exploring researchers' participation in online research identity management systems
Authors: Wu Shuheng , Stvilia Besiki , Lee Dong Joon 
Published: December 2016

ABSTRACTPrior studies have identified a need for engaging researchers in providing and curating their identity data. This poster reports preliminary findings of a qualitative study exploring how researchers use and engage in online research identity management (RIM) systems. The findings identify nine activity or task related motivations of using RIM systems. This study also identified three levels of participation in RIM systems: Readers, Personal Record Managers, and Community Members. Most participants of this study fell into the category of Personal Record Managers, who may maintain their own profiles in a RIM system. This suggests that a majority of researchers may be willing to maintain their research identity profiles. Institutional repository managers may consider recruiting researchers as not only research information and data providers, but also curators of their own research identity data.
Human capital matters: Market valuation of firm investments in training and the role of complementary assets
Authors: Riley Shawn M. , Michael Steven C. , Mahoney Joseph T. 
Published: December 2016

Research summary:This article empirically examines the economic value to firms of investing in the training of their employees and firm‐level factors that influence how much the firms benefit. Event study methodology is used to obtain a measure of the economic impact of information regarding a firm's human capital management investments and policies. Subsequent regression analyses are then used to test hypotheses regarding possible complementary relationships between firm‐level factors and human capital investments. Results provide robust support for the proposition that effective investments in human capital and training matter, and that these human capital investments are more impactful when combined with complementary assets of R&D, physical capital, and advertising investments.Managerial summary:Do firm investments in training and the development of employee human capital matter with regard to financial performance? We find that, yes, these investments do matter. Our results show that managers who view employee human capital as an asset to be invested in and developed can expect to outperform those who view it as a cost to be minimized. In addition, we find that these human capital investments will be of even greater economic value to firms when they have made complementary investments in R&D, physical capital, and advertising. Copyright © 2016 John Wiley & Sons, Ltd.
Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns
Authors: Dunaway Keith , Goorha Sarita , Matelski Lauren , Urraca Nora , Lein Pamela J. , Korf Ian , Reiter Lawrence T. , LaSalle Janine M. 
Published: December 2016

Abstract
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs are a useful model for epigenomic and functional studies of human neurodevelopmental disorders.
Hope and anxiety in physics class: Exploring their motivational antecedents and influence on metacognition and performance
Authors: González Antonio , Fernández María‐Victoria Carrera , Paoloni Paola‐Verónica 
Published: December 2016

AbstractRecent research on achievement in science asserts that motivation, emotion, and metacognition are important driving forces for learning. This study sought to examine the relationships between two physics class emotions (hope and anxiety), their motivational predictors (instrumentality and self‐efficacy), and their effects on metacognitive problem solving strategies (planning, monitoring, and evaluation) and performance. Data were collected from 520 grade 11 Spanish students (54.7% girls). Structural equation models (SEM), followed by a bootstrap procedure, were used to examine direct and mediated relationships. The results supported the model, suggesting that instrumentality and self‐efficacy negatively predicted anxiety, and enhanced hope, planning, monitoring, evaluation, and performance; metacognitive strategies and performance were negatively predicted by anxiety, and were positively predicted by hope; metacognitive strategies positively predicted performance. Furthermore, the hypothesized mediated relations were also statistically significant. The interpretation of these findings, their implications for physics teaching and learning, and future lines of research are discussed. © 2016 Wiley Periodicals, Inc. J Res Sci Teach 54:558–585, 2017
Extraction of Phospholipids from Egg Yolk Flakes Using Aqueous Alcohols
Authors: Wang Hui , Yao Linxing , Lee Show‐Ling , Wang Tong 
Published: December 2016

AbstractTwo alcohols, ethanol and butanol, with different water contents were evaluated for phospholipids (PL) sequential extraction from drum dried egg yolk flakes. It showed that butanol was more effective in extracting total yolk lipids compared to ethanol, but the PL in the extract had the same concentration as in the original yolk total lipid. The use of aqueous ethanol of 95 and 75% resulted in lipid extracts with higher PL concentration during the initial stages of the sequential extraction. When ethanol was further diluted to a concentration of 55%, the solvent lost its PL extraction ability, and the total lipid recovery also decreased dramatically. When both the PL purity and recovery were considered, 75% ethanol was the most effective aqueous alcohol for PL extraction and enrichment from the yolk flakes. In the first stage of extraction using such a solvent, 67% of the total PL in the original yolk was recovered in a lipid fraction with a PL purity of 75%. This study identified the optimal ethanol concentration for PL extraction from dried egg yolk. With this information, the best solid:solvent ratio can be designed to extract and enrich the polar lipids from lipid‐bearing materials with known moisture content using a renewable or “green” solvent, ethanol.
Targeted genome editing, an alternative tool for trait improvement in horticultural crops
Authors: Subburaj Saminathan , Tu Luhua , Jin Yong-Tae , Bae Sangsu , Seo Pil Joon , Jung Yu Jin , Lee Geung-Joo 
Published: December 2016

Abstract
Improving crops through plant breeding, an important approach for sustainable agriculture, has been utilized to increase the yield and quality of foods and other biomaterials for human use. Crops, including cereals, vegetables, ornamental flowers, fruits, and trees, have long been cultivated to produce high-quality products for human consumption. Conventional breeding technologies, such as natural cross-hybridization, mutation induction through physical or chemical mutagenesis, and modern transgenic tools are often used to enhance crop production. However, these breeding methods are sometimes laborious and complicated, especially when attempting to improve desired traits without inducing pleiotropic effects. Recently, targeted genome editing (TGE) technology using engineered nucleases, including meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR) nucleases, has been used to improve the traits of economically important plants. TGE has emerged as a novel plant-breeding tool that represents an alternative approach to classical breeding, but with higher mutagenic efficiency. Here, we briefly describe the basic principles of TGE and the types of engineered nucleases utilized, along with their advantages and disadvantages. We also discuss their potential use to improve the traits of horticultural crops through genome engineering.