bluuebunny/crossref_metadata_2025_split huggingface dataset:
The oldest Gondwanan cephalopod mandibles (Hangenberg Black Shale, Late Devonian) and the mid‐Palaeozoic rise of jaws
Authors: Klug Christian , Frey Linda , Korn Dieter , Jattiot Romain , Rücklin Martin 
Published: July 2016

AbstractIt is widely accepted that the effects of global sea‐level changes at the transition from the Devonian to the Carboniferous are recorded in deposits on the shelf of northern Gondwana. These latest Devonian strata had been thought to be poor in fossils due to the Hangenberg mass extinction. In the Ma'der (eastern Anti‐Atlas), however, the Hangenberg Black Shale claystones (latest Famennian) are rich in exceptionally preserved fossils displaying the remains of non‐mineralized structures. The diversity in animal species of these strata is, however, low. Remarkably, the organic‐rich claystones have yielded abundant remains of Ammonoidea preserved with their jaws, both in situ and isolated. This is important because previously, the jaws of only one of the main Devonian ammonoid clades had been found (Frasnian Gephuroceratina). Here, we describe four types of jaws of which two could be assigned confidently to the Order Clymeniida and to the Suborder Tornoceratina. These findings imply that chitinous normal‐type jaws were likely to have already been present at the origin of the whole clade Ammonoidea, i.e. in the early Emsian (or earlier). Vertebrate jaws evolved prior to the Early Devonian origin of ammonoids. The temporal succession of evolutionary events suggests that it could have been the indirect positive selection pressure towards strong (and thus preservable) jaws since defensive structures of potential prey animals would otherwise have made them inaccessible to jawless predators in the course of the mid‐Palaeozoic marine revolution. In this respect, our findings reflect the macroecological changes that occurred in the Devonian. [Correction added on 28 July 2016 after first online publication: In the Abstract, the sentence “Vertebrate jaws probably … in the Early Devonian” was amended]
Successful Treatment of Pediatric Alopecia Areata of the Scalp Using Topical Bimatoprost
Authors: Li Alvin W. , Antaya Richard J. 
Published: July 2016

AbstractAlopecia areata (AA) is a genetic and immune‐mediated disease that targets anagen hair follicles. Despite limited evidence supporting the efficacy of corticosteroid treatments, they are often prescribed as first‐line therapy because of their favorable safety profile. Prostaglandin analogues are currently being studied as an alternate therapy for scalp AA in adults. Herein we present a case of steroid‐resistant multifocal AA that was successfully treated with topical bimatoprost.
Determinants of neonatal mortality in rural and urban Nigeria: Evidence from a population‐based national survey
Authors: Adewuyi Emmanuel O , Zhao Yun 
Published: July 2016

AbstractBackgroundSignificant reduction in the global burden of neonatal mortality was achieved through the millennium development goals. In Nigeria, however, only a marginal reduction was realized. This study assesses the rural–urban differences in neonatal mortality rate (NMR) and the associated risk factors in Nigeria.MethodsThe dataset from the 2013 Nigeria demographic and health survey (NDHS), disaggregated by rural–urban residence (n = 20 449 and 9935, respectively), was explored using univariate, bivariate, and multivariable analysis. Complex samples analysis was applied to adjust for the unequal selection probabilities due to the multi‐stage cluster sampling method used in the 2013 NDHS. The adjusted relationship between the outcome and predictor variables was assessed on multi‐level logistic regression analysis.ResultsNMR for rural and urban populations was 36 and 28 deaths per 1000 live births, respectively. Risk factors in urban residence were lack of electricity access (adjusted OR [AOR], 1.555; 95%CI: 1.089–2.220), small birth size (as a proxy for low birthweight; AOR, 3.048; 95%CI: 2.047–4.537), and male gender (AOR, 1.666; 95%CI: 1.215–2.284). Risk factors in rural residence were small birth size (a proxy for low birthweight; AOR, 2.118; 95%CI: 1.600–2.804), and birth interval <2 years (AOR, 2.149; 95%CI: 1.760–2.624). Cesarean delivery was a risk factor both in rural (AOR, 5.038; 95%CI: 2.617–9.700) and urban Nigeria (AOR, 2.632; 95%CI: 1.543–4.489).ConclusionsDeterminants of neonatal mortality were different in rural and urban Nigeria, and rural neonates had greater risk of mortality than their urban counterparts.
Type 2 diabetes is associated with a higher incidence of hospitalization for pulmonary embolism in Spain: Analysis of hospital discharge data during 2004–2013
Authors: de Miguel‐Díez Javier , Muñoz‐Rivas Nuria , Jiménez‐García Rodrigo , Hernández‐Barrera Valentín , Carrasco‐Garrido Pilar , Monreal Manuel , Jiménez David , Guijarro Ricardo , López de Andrés Ana 
Published: July 2016

ABSTRACTBackground and objectiveWe compared the incidence and outcome of pulmonary embolism (PE) in individuals with and without type 2 diabetes mellitus (T2DM) in Spain during 2004–2013.MethodsThe study was based on National Hospital Discharge Data, and the study population comprised patients hospitalized for PE. Annual incidence rates were classified according to T2DM status. In‐hospital mortality (IHM), length of hospital stay (LOHS), comorbidities and use of diagnosis and therapeutic procedures were analysed.ResultsWe identified 123 872 discharges of patients (56 361 men and 67 511 women) with PE as their primary diagnosis (15.3% with T2DM). Incidence of discharge diagnoses of PE increased significantly in all groups. Crude rates were higher in diabetic patients. A positive association was identified between T2DM and PE: adjusted IRR was 2.00 (95% CI: 1.95–2.05) for men and 2.50 (95% CI: 2.45–2.57) for women. LOHS, readmissions and IHM decreased significantly for both groups. An association between IHM and risk factors (older age, Charlson comorbidity index >3, atrial fibrillation and cancer) was observed. T2DM was associated with higher IHM in men (OR: 1.22, 95% CI: 1.12–1.32) and women (OR: 1.24, 95% CI: 1.15–1.33). The use of computed tomography pulmonary angiography increased significantly overtime.ConclusionWe confirmed that in both men and women, diabetes was an independent risk factor for IHM. The incidence of discharge of patients with PE increased significantly during the study period. Diabetic men and women had a higher risk of hospitalization for PE than non‐diabetic men and women. Diabetic women had higher IHM than diabetic men.
Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes
Authors: Pavlištová Veronika , Dvořáčková Martina , Jež Michal , Mozgová Iva , Mokroš Petr , Fajkus Jiří 
Published: July 2016

SummaryArabidopsis thaliana mutants dysfunctional in the evolutionarily conserved protein complex chromatin assembly factor‐1 (CAF‐1), which deposits the canonical histone H3 variant H3.1 during DNA synthesis‐dependent chromatin assembly, display complex phenotypic changes including meristem and growth alterations, sensitivity to DNA‐damaging agents, and reduced fertility. We reported previously that mutants in the FAS1 subunit of CAF‐1 progressively lose telomere and 45S rDNA repeats. Here we show that multiple aspects of the fas phenotype are recovered immediately on expression of a reintroduced FAS1 allele, and are clearly independent of the recovery of rDNA copy‐numbers and telomeres. In reverted lines, 45S rDNA genes are recovered to diverse levels with a strikingly different representation of their variants, and the typical association of nucleolar organizing region 4 with the nucleolus is perturbed. One of 45S rDNA variants (VAR1), which is silenced in wild‐type (WT) plants without mutation history (Col‐0 WT), dominates the expression pattern, whereas VAR2 is dominant in Col‐0 WT plants. We propose an explanation for the variability of telomere and 45S rDNA repeats associated with CAF‐1 function, suggesting that the differences in nuclear partitioning and expression of the rDNA variants in fas mutants and their revertants provide a useful experimental system to study genetic and epigenetic factors in gene dosage compensation.
N‐linked glycosylation of Kv1.2 voltage‐gated potassium channel facilitates cell surface expression and enhances the stability of internalized channels
Authors: Thayer Desiree A. , Yang Shi‐Bing , Jan Yuh Nung , Jan Lily Y. 
Published: July 2016

Key points
Kv1.2 and related voltage‐gated potassium channels have a highly conserved N‐linked glycosylation site in the first extracellular loop, with complex glycosylation in COS‐7 cells similar to endogenous Kv1.2 glycosylation in hippocampal neurons.
COS‐7 cells expressing Kv1.2 show a crucial role of this N‐linked glycosylation in the forward trafficking of Kv1.2 to the cell membrane.
Although both wild‐type and non‐glycosylated mutant Kv1.2 channels that have reached the cell membrane are internalized at a comparable rate, mutant channels are degraded at a faster rate.
Treatment of wild‐type Kv1.2 channels on the cell surface with glycosidase to remove sialic acids also results in the faster degradation of internalized channels.
Glycosylation of Kv1.2 is important with respect to facilitating trafficking to the cell membrane and enhancing the stability of channels that have reached the cell membrane.
AbstractStudies in cultured hippocampal neurons and the COS‐7 cell line demonstrate important roles for N‐linked glycosylation of Kv1.2 channels in forward trafficking and protein degradation. Kv1.2 channels can contain complex N‐linked glycans, which facilitate cell surface expression of the channels. Additionally, the protein stability of cell surface‐expressed Kv1.2 channels is affected by glycosylation via differences in the degradation of internalized channels. The present study reveals the importance of N‐linked complex glycosylation in boosting Kv1.2 channel density. Notably, sialic acids at the terminal sugar branches play an important role in dampening the degradation of Kv1.2 internalized from the cell membrane to promote its stability.
SU‐C‐204‐06: Monte Carlo Dose Calculation for Kilovoltage X‐Ray‐Psoralen Activated Cancer Therapy (X‐PACT): Preliminary Results
Authors: Mein S , Gunasingha R , Nolan M , Oldham M , Adamson J 
Published: July 2016

Purpose:X‐PACT is an experimental cancer therapy where kV x‐rays are used to photo‐activate anti‐cancer therapeutics through phosphor intermediaries (phosphors that absorb x‐rays and re‐radiate as UV light). Clinical trials in pet dogs are currently underway (NC State College of Veterinary Medicine) and an essential component is the ability to model the kV dose in these dogs. Here we report the commissioning and characterization of a Monte Carlo (MC) treatment planning simulation tool to calculate X‐PACT radiation doses in canine trials.Methods:FLUKA multi‐particle MC simulation package was used to simulate a standard X‐PACT radiation treatment beam of 80kVp with the Varian OBI x‐ray source geometry. The beam quality was verified by comparing measured and simulated attenuation of the beam by various thicknesses of aluminum (2–4.6 mm) under narrow beam conditions (HVL). The beam parameters at commissioning were then corroborated using MC, characterized and verified with empirically collected commissioning data, including: percent depth dose curves (PDD), back‐scatter factors (BSF), collimator scatter factor(s), and heel effect, etc. All simulations were conducted for N=30M histories at M=100 iterations.Results:HVL and PDD simulation data agreed with an average percent error of 2.42%±0.33 and 6.03%±1.58, respectively. The mean square error (MSE) values for HVL and PDD (0.07% and 0.50%) were low, as expected; however, longer simulations are required to validate convergence to the expected values. Qualitatively, pre‐ and post‐filtration source spectra matched well with 80kVp references generated via SPEKTR software. Further validation of commissioning data simulation is underway in preparation for first‐time 3D dose calculations with canine CBCT data.Conclusion:We have prepared a Monte Carlo simulation capable of accurate dose calculation for use with ongoing X‐PACT canine clinical trials. Preliminary results show good agreement with measured data and hold promise for accurate quantification of dose for this novel psoralen X‐ray therapy.Funding Support, Disclosures, & Conflict of Interest: The Monte Carlo simulation work was not funded; Drs. Adamson & Oldham have received funding from Immunolight LLC for X‐PACT research.
SU‐C‐201‐05: Silicon Array Dosimeter in Situ with Electronic Portal Image Device for Simultaneous Transit Dose and Image Verification in Radiotherapy
Authors: Deshpande S , Alhujaili S , Vial P , Holloway L , Petasecca M , Rozenfeld A , Metcalfe P 
Published: July 2016

Purpose:To investigate an Electronic Portal Imaging Device (EPID) coupled to a 2D array dosimeter to provide simultaneous imaging and dose verification.Methods:The novel dual detector configuration comprised of a 2D diode array dosimeter, referred to as a Magic Plate (MP) placed directly on a standard EPID. Dose response of the MP was evaluated by measuring the detector's response with respect to off‐axis position and field size with 30 cm of solid water (SW) acting as a transit object in the beam. Measurements were performed with 3, 5, 10 and 15 mm SW build‐up and compared to 2D ionisation chamber array (ICA) measurements and the PinnacleTM treatment planning system (TPS) at a source to detector distance of 150 cm with a 6 MV beam. Clinical dosimetric performance was evaluated by measuring a number of intensity‐modulated radiation therapy (IMRT) beams in transit geometry. Imaging performance of the EPID was quantified by measuring the contrast‐to‐noise ratio (CNR) and spatial resolution. Images of a Rando phantom were used for qualitative assessment.Results:Measured MP off‐axis and field size response agreed within 2% of TPS and ICA responses when measured using 15 mm SW build‐up. Clinical IMRT beams had gamma pass rates of ≥95% at 3%/3mm criteria. Measured CNR and spatial resolution (f50) were 264.96, 210.6, and 0.41, 0.40 with build‐up of 5 and 15 mm respectively for the dual detector configuration. CNR and spatial resolution of 643.9 and 0.41 were measured for standard EPID. CNR was quantitatively worse in the dual detector configuration. Differences in imaging performance were not visible in a qualitative assessment using a Rando phantom.Conclusion:Combining a prototype MP 2D dosimeter with a conventional EPID did not significantly detract from the performance of either device and has the potential for simultaneous on‐line patient transit dosimetry and image assessment in radiation therapy.Cancer Institute NSW Australia(Research Equipment Grant 10/REG/1‐20) and Cancer Council NSW (Grant ID RG 1‐06)
SU‐C‐207A‐03: Development of Proton CT Imaging System Using Thick Scintillator and CCD Camera
Authors: Tanaka S , Nishio T , Matsushita K , Tsuneda M , Kabuki S , Uesaka M 
Published: July 2016

Purpose:In the treatment planning of proton therapy, Water Equivalent Length (WEL), which is the parameter for the calculation of dose and the range of proton, is derived by X‐ray CT (xCT) image and xCT‐WEL conversion. However, about a few percent error in the accuracy of proton range calculation through this conversion has been reported. The purpose of this study is to construct a proton CT (pCT) imaging system for an evaluation of the error.Methods:The pCT imaging system was constructed with a thick scintillator and a cooled CCD camera, which acquires the two‐dimensional image of integrated value of the scintillation light toward the beam direction. The pCT image is reconstructed by FBP method using a correction between the light intensity and residual range of proton beam. An experiment for the demonstration of this system was performed with 70‐MeV proton beam provided by NIRS cyclotron. The pCT image of several objects reconstructed from the experimental data was evaluated quantitatively.Results:Three‐dimensional pCT images of several objects were reconstructed experimentally. A finestructure of approximately 1 mm was clearly observed. The position resolution of pCT image was almost the same as that of xCT image. And the error of proton CT pixel value was up to 4%. The deterioration of image quality was caused mainly by the effect of multiple Coulomb scattering.Conclusion:We designed and constructed the pCT imaging system using a thick scintillator and a CCD camera. And the system was evaluated with the experiment by use of 70‐MeV proton beam. Three‐dimensional pCT images of several objects were acquired by the system.This work was supported by JST SENTAN Grant Number 13A1101 and JSPS KAKENHI Grant Number 15H04912.
SU‐C‐206‐04: Region‐Specific Total‐Variation Regularization for X‐Ray CT Reconstruction
Authors: Xu Q , Han H , Xing L 
Published: July 2016

Purpose:Total‐variation (TV) regularization methods are very effective to handle the non‐sufficient data reconstruction, such as few‐view problem, low‐dose data, etc. Usually one single regularization parameter is employed to balance the data fidelity and the TV minimization penalty in all regions of the object. However, noise and structural details vary from region to region. Here we proposed a method to select the regularization parameter adaptively by the region specific noise.Methods:The image was reconstructed by minimizing the data fidelity term and the TV term alternatively. After the image was updated by the data fidelity step, its noise distribution was estimated out by calculating the variance of neighboring pixels. Then a fuzzy clustering method was applied on it to proportionally assign the membership of each pixel into several clustering groups which correspond to regions with different noise levels, respectively. A heuristic function was developed to describe the relationship between the noise and the regularization parameter. The TV was performed under different parameters which were determined by the noise levels. The final image of TV minimization step was generated by fusing these results according to the weighting coefficients determined by the fuzzy membership. After that a new iteration was repeated until the stopping criterion was satisfied. A view down sampled human thorax dataset was used to evaluate the proposed method.Results:Since the noise distribution was not uniform, the conventional TV method with one single parameter cannot make a good balance between the noise and structural details in all regions simultaneously while the proposed region‐specific method can achieve a better result. The structure similarity index (SSIM) increased 2.1% and the root mean squared error (RMSE) decreased 9% in the vertebra region with comparable results in other regions.Conclusion:The proposed region specific regularization can improve the current TV‐based reconstruction.
SU‐C‐207B‐05: Tissue Segmentation of Computed Tomography Images Using a Random Forest Algorithm: A Feasibility Study
Authors: Polan D , Brady S , Kaufman R 
Published: July 2016

Purpose:Develop an automated Random Forest algorithm for tissue segmentation of CT examinations.Methods:Seven materials were classified for segmentation: background, lung/internal gas, fat, muscle, solid organ parenchyma, blood/contrast, and bone using Matlab and the Trainable Weka Segmentation (TWS) plugin of FIJI. The following classifier feature filters of TWS were investigated: minimum, maximum, mean, and variance each evaluated over a pixel radius of 2n, (n = 0–4). Also noise reduction and edge preserving filters, Gaussian, bilateral, Kuwahara, and anisotropic diffusion, were evaluated. The algorithm used 200 trees with 2 features per node. A training data set was established using an anonymized patient's (male, 20 yr, 72 kg) chest‐abdomen‐pelvis CT examination. To establish segmentation ground truth, the training data were manually segmented using Eclipse planning software, and an intra‐observer reproducibility test was conducted. Six additional patient data sets were segmented based on classifier data generated from the training data. Accuracy of segmentation was determined by calculating the Dice similarity coefficient (DSC) between manual and auto segmented images.Results:The optimized autosegmentation algorithm resulted in 16 features calculated using maximum, mean, variance, and Gaussian blur filters with kernel radii of 1, 2, and 4 pixels, in addition to the original CT number, and Kuwahara filter (linear kernel of 19 pixels). Ground truth had a DSC of 0.94 (range: 0.90–0.99) for adult and 0.92 (range: 0.85–0.99) for pediatric data sets across all seven segmentation classes. The automated algorithm produced segmentation with an average DSC of 0.85 ± 0.04 (range: 0.81–1.00) for the adult patients, and 0.86 ± 0.03 (range: 0.80–0.99) for the pediatric patients.Conclusion:The TWS Random Forest auto‐segmentation algorithm was optimized for CT environment, and able to segment seven material classes over a range of body habitus and CT protocol parameters with an average DSC of 0.86 ± 0.04 (range: 0.80–0.99).
SU‐D‐204‐01: A Methodology Based On Machine Learning and Quantum Clustering to Predict Lung SBRT Dosimetric Endpoints From Patient Specific Anatomic Features
Authors: Lafata K , Ren L , Wu Q , Kelsey C , Hong J , Cai J , Yin F 
Published: July 2016

Purpose:To develop a data‐mining methodology based on quantum clustering and machine learning to predict expected dosimetric endpoints for lung SBRT applications based on patient‐specific anatomic features.Methods:Ninety‐three patients who received lung SBRT at our clinic from 2011–2013 were retrospectively identified. Planning information was acquired for each patient, from which various features were extracted using in‐house semi‐automatic software. Anatomic features included tumor‐to‐OAR distances, tumor location, total‐lung‐volume, GTV and ITV. Dosimetric endpoints were adopted from RTOG‐0195 recommendations, and consisted of various OAR‐specific partial‐volume doses and maximum point‐doses. First, PCA analysis and unsupervised quantum‐clustering was used to explore the feature‐space to identify potentially strong classifiers. Secondly, a multi‐class logistic regression algorithm was developed and trained to predict dose‐volume endpoints based on patient‐specific anatomic features. Classes were defined by discretizing the dose‐volume data, and the feature‐space was zero‐mean normalized. Fitting parameters were determined by minimizing a regularized cost function, and optimization was performed via gradient descent. As a pilot study, the model was tested on two esophageal dosimetric planning endpoints (maximum point‐dose, dose‐to‐5cc), and its generalizability was evaluated with leave‐one‐out cross‐validation.Results:Quantum‐Clustering demonstrated a strong separation of feature‐space at 15Gy across the first‐and‐second Principle Components of the data when the dosimetric endpoints were retrospectively identified. Maximum point dose prediction to the esophagus demonstrated a cross‐validation accuracy of 87%, and the maximum dose to 5cc demonstrated a respective value of 79%. The largest optimized weighting factor was placed on GTV‐to‐esophagus distance (a factor of 10 greater than the second largest weighting factor), indicating an intuitively strong correlation between this feature and both endpoints.Conclusion:This pilot study shows that it is feasible to predict dose‐volume endpoints based on patient‐specific anatomic features. The developed methodology can potentially help to identify patients at risk for higher OAR doses, thus improving the efficiency of treatment planning.R01‐184173