bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term recurrence rates of whole specimen intraoperative frozen section analysis in basal cell carcinomas of the face with WIFSA
Authors: Scholten Laura A. , Kedilioglu Muhammed A. , Huizinga Pauline M. , Kibbelaar Robby E. , de Jong Kim , Mouës Chantal M. 
Published: February 2019

AbstractBackground and ObjectivesRecent studies show that whole specimen intraoperative frozen section analysis (WIFSA) is a reliable method for margin analysis in basal cell carcinoma (BCC) and has low recurrence rates after five‐years follow‐up. There are no studies with longer follow‐up. Our aim is to present long‐term recurrence rates after WIFSA.Materials and MethodsAll patients with a facial BCC receiving excision with WIFSA between 1992 and 2007 were evaluated. Recurrence rates were examined for primary BCC (pBCC), recurrent BCCs (rBCC), and the different histological subtypes. The accuracy of WIFSA was assessed by comparing with formalin‐fixed paraffin‐embedded section analysis.ResultsA total of 1140 patients with 1265 BCCs underwent excision with WIFSA, with a median and maximum follow‐up of 10 and 25.3 years, respectively. Of all tumors, 90.0% were primary. Excisions were radical after an average of 1.4 excision rounds;5, 10, and 15‐year recurrence rates for pBCCs are 3.3%, 5.1%, and 7.3%, respectively. An aggressive growth pattern and rBCCs are associated with more recurrences. The accuracy of WIFSA is 98.4%.ConclusionsWIFSA provides a highly accurate analysis and has a low recurrence rate for primary BCCs. The increasing recurrence rates over time imply 5 years of follow‐up may be insufficient.
Risk factors for post‐pancreaticoduodenectomy delayed gastric emptying in the absence of pancreatic fistula or intra‐abdominal infection
Authors: Ellis Ryan J. , Gupta Aakash R. , Hewitt D. Brock , Merkow Ryan P. , Cohen Mark E. , Ko Clifford Y. , Bilimoria Karl Y. , Bentrem David J. , Yang Anthony D. 
Published: February 2019

AbstractBackground and ObjectivesDelayed gastric emptying (DGE) occurs commonly following pancreaticoduodenectomy (PD), but the rate of DGE in the absence of other intra‐abdominal complications is poorly understood. The objectives of this study were to define the incidence of DGE and identify risk factors for DGE in patients without pancreatic fistula or other intra‐abdominal infections.MethodsRetrospective cohort study utilizing the American College of Surgeons National Surgical Quality Improvement Program pancreatectomy variables to identify patients with DGE following PD without evidence of fistula or intra‐abdominal infection. Multivariable models were developed to assess preoperative, intraoperative, and technical factors associated with DGE.ResultsThe rate of DGE was 11.7% in 10502 cases without pancreatic fistula or intra‐abdominal infection. Patients were more likely to develop DGE if age ≥75 (odds ratio [OR], 1.22; P = 0.003), male (OR, 1.29;
P < 0.001), underwent pylorus‐sparing PD (OR, 1.27;
P = 0.004), or had a prolonged operative time (OR, 1.38 if greater than seven vs less than 5 hours;
P = 0.005). Factors not associated with DGE included BMI, pathologic indication, and surgical approach.ConclusionThe incidence of DGE after PD is notable even in patients without other abdominal complications. Identification of patients at increased risk for DGE may aid patient counseling as well as decisions regarding surgical technique, enteral feeding access, and enhanced‐recovery pathways.
Rapid change in forms of inorganic nitrogen in soil and moderate weed invasion following translocation of wet meadows to reclaimed post‐industrial land
Authors: Chmolowska Dominika , Nobis Marcin , Nowak Arkadiusz , Maślak Magdalena , Kojs Paweł , Rutkowska Joanna , Zubek Szymon 
Published: February 2019

AbstractAnthropogenic expansion and loss of natural environments calls for the more sustainable use of resources, including land. To combine the conservation of highly valuable meadow habitat with reclamation of post‐industrial land, 1.3 ha of turf were translocated from an urban area to basins constructed near an abandoned quarry. In contrast to the usual method of choosing similar habitats as salvage sites, the selected quarry possessed different environmental properties to the meadows, challenging their acclimatisation. To evaluate the project, we monitored three meadows (Molinion caeruleae alliance) for three seasons: immediately before the transfer and for 2 years afterwards. We recorded vegetation composition in tandem with 27 physico‐chemical properties of the soil. In the first year following translocation, enrichment of soil in total calcium, potassium, sodium, and sulphur was noted. The contents of available phosphorus, nitrogen, and magnesium, as well as soil pH, were lower in the second year. The domination of ammonia over nitrate, which is characteristic of wetlands, decreased markedly. Water holding capacity slowly decreased as well, suggesting humus decomposition. The plant communities maintained their high level of diversity, and the dominance of characteristic meadow species continued. However, an increase in the number of weeds was observed, along with the replacement of some meadow plant species by others. We conclude that if a receptor site does not resemble a habitat type of a donor site, the ecosystem becomes more human‐dependent and requires site‐specific aftercare. In this case, the active control of competitive and ruderal species invasion and moisture management is required.
Elemental content and stoichiometry of SAR11 chemoheterotrophic marine bacteria
Authors: White Angelicque E. , Giovannoni Stephen J. , Zhao Yanlin , Vergin Kevin , Carlson Craig A. 
Published: February 2019

AbstractWe measured the carbon, nitrogen, and phosphorus content and production of cultured SAR11 cells in the genus Pelagibacter, from members of the 1a.1 and 1a.3 lineages, which are adapted to productive coastal waters and oligotrophic tropical/subtropical environments, respectively. The average growing SAR11 cell contained ~ 6.5 fg C, from which we calculated a global standing stock of 1.4 × 1013 g C. Calculations that consider uncertainties in cell turnover rates and growth efficiencies indicate this stock could oxidize 6% to 37% of gross ocean primary production. We also found that SAR11 do not incorporate 3H‐thymidine but do incorporate 3H‐leucine. We estimate conversion factors of 0.74–1.51 kg C mol−1 leu, which are comparable to the low end of published leucine conversion factors for marine chemoheterotrophic bacterioplankton production. The molar ratio of elements C : N : P in growing cells was on average 25 : 6 : 1, significantly less than the mean (~ 50 : 10 : 1) for heterotrophic bacteria, indicating these strains are C and N poor relative to P.
A method for correcting breathing‐induced field fluctuations in T2*‐weighted spinal cord imaging using a respiratory trace
Authors: Vannesjo S. Johanna , Clare Stuart , Kasper Lars , Tracey Irene , Miller Karla L. 
Published: February 2019

PurposeSpinal cord MRI at ultrahigh field is hampered by time‐varying magnetic fields associated with the breathing cycle, giving rise to ghosting artifacts in multi‐shot acquisitions. Here, we suggest a correction approach based on linking the signal from a respiratory bellows to field changes inside the spinal cord. The information is used to correct the data at the image reconstruction level.MethodsThe correction was demonstrated in the context of multi‐shot T2*‐weighted imaging of the cervical spinal cord at 7T. A respiratory trace was acquired during a high‐resolution multi‐echo gradient‐echo sequence, used for structural imaging and quantitative T2* mapping, and a multi‐shot EPI time series, as would be suitable for fMRI. The coupling between the trace and the breathing‐induced fields was determined by a short calibration scan in each individual. Images were reconstructed with and without trace‐based correction.ResultsIn the multi‐echo acquisition, breathing‐induced fields caused severe ghosting in images with long TE, which led to a systematic underestimation of T2* in the spinal cord. The trace‐based correction reduced the ghosting and increased the estimated T2* values. Breathing‐related ghosting was also observed in the multi‐shot EPI images. The correction largely removed the ghosting, thereby improving the temporal signal‐to‐noise ratio of the time series.ConclusionsTrace‐based retrospective correction of breathing‐induced field variations can reduce ghosting and improve quantitative metrics in multi‐shot structural and functional T2*‐weighted imaging of the spinal cord. The method is straightforward to implement and does not rely on sequence modifications or additional hardware beyond a respiratory bellows.
Cerebral blood volume mapping using Fourier‐transform–based velocity‐selective saturation pulse trains
Authors: Qin Qin , Qu Yaoming , Li Wenbo , Liu Dapeng , Shin Taehoon , Zhao Yansong , Lin Doris D. , van Zijl Peter C.M. , Wen Zhibo 
Published: February 2019

PurposeVelocity‐selective saturation (VSS) pulse trains provide a viable alternative to the spatially selective methods for measuring cerebral blood volume (CBV) by reducing the sensitivity to arterial transit time. This study is to compare the Fourier‐transform–based velocity‐selective saturation (FT‐VSS) pulse trains with the conventional flow‐dephasing VSS techniques for CBV quantification.MethodsThe proposed FT‐VSS label and control modules were compared with VSS pulse trains utilizing double refocused hyperbolic tangent (DRHT) and 8‐segment B1‐insensitive rotation (BIR‐8). This was done using both numerical simulations and phantom studies to evaluate their sensitivities to gradient imperfections such as eddy currents. DRHT, BIR‐8, and FT‐VSS prepared CBV mapping was further compared for velocity‐encoding gradients along 3 orthogonal directions in healthy subjects at 3T.ResultsThe phantom studies exhibited more consistent immunity to gradient imperfections for the utilized FT‐VSS pulse trains. Compared to DRHT and BIR‐8, FT‐VSS delivered more robust CBV results across the 3 VS encoding directions with significantly reduced artifacts along the superior‐inferior direction and improved temporal signal‐to‐noise ratio (SNR) values. Average CBV values obtained from FT‐VSS based sequences were 5.3 mL/100 g for gray matter and 2.3 mL/100 g for white matter, comparable to literature expectations.ConclusionAbsolute CBV quantification utilizing advanced FT‐VSS pulse trains had several advantages over the existing approaches using flow‐dephasing VSS modules. A greater immunity to gradient imperfections and the concurrent tissue background suppression of FT‐VSS pulse trains enabled more robust CBV measurements and higher SNR than the conventional VSS pulse trains.
Absolute quantitative MR perfusion and comparison against stable‐isotope microspheres
Authors: Jeong Yong I. , Christoforidis Gregory A. , Saadat Niloufar , Kawaji Keigo , Cantrell Charles G. , Roth Steven , Niekrasz Marek , Carroll Timothy J. 
Published: February 2019

PurposeThis work sought to compare a quantitative T1 bookend dynamic susceptibility contrast MRI based perfusion protocol for absolute cerebral blood flow (qCBF) against CBF measured by the stable‐isotope neutron capture microsphere method, a recognized reference standard for measuring tissue blood flow, at normocapnia, hypercapnia, and in acute stroke.MethodsCBF was measured in anesthetized female canines by MRI and microspheres over 2 consecutive days for each case. On day 1, 5 canines were measured before and during a physiological challenge induced by carbogen inhalation; on day 2, 4 canines were measured following permanent occlusion of the middle cerebral artery. CBF and cerebrovascular reactivity measured by MRI and microsphere deposition were compared.ResultsMRI correlated strongly with microspheres at the hemispheric level for CBF during normo‐ and hypercapnic states (r2 = 0.96), for individual cerebrovascular reactivity (r2 = 0.84), and for postocclusion CBF (r2 = 0.82). Correction for the delay and dispersion of the contrast bolus resulted in a significant improvement in the correlation between MRI and microsphere deposition in the ischemic state (r2 = 0.96). In all comparisons, moderate correlations were found at the regional level.ConclusionIn an experimental canine model with and without permanent occlusion of the middle cerebral artery, MRI‐based qCBF yielded moderate to strong correlations for absolute quantitative CBF and cerebrovascular reactivity measurements during normocapnia and hypercapnia. Correction for delay and dispersion greatly improved the quantitation during occlusion of the middle cerebral artery, underscoring the importance for this correction under focal ischemic condition.
Accuracy and precision of electrical permittivity mapping at 3T: the impact of three mapping techniques
Authors: Gavazzi Soraya , van den Berg Cornelis A.T. , Sbrizzi Alessandro , Kok H. Petra , Stalpers Lukas J. A. , Lagendijk Jan J.W. , Crezee Hans , van Lier Astrid L. H. M. W. 
Published: February 2019

PurposeTo investigate the sequence‐specific impact of amplitude mapping on the accuracy and precision of permittivity reconstruction at 3T in the pelvic region.Methods maps obtained with actual flip angle imaging (AFI), Bloch–Siegert (BS), and dual refocusing echo acquisition mode (DREAM) sequences, set to a clinically feasible scan time of 5 minutes, were compared in terms of accuracy and precision with electromagnetic and Bloch simulations and MR measurements. Permittivity maps were reconstructed based on these maps with Helmholtz‐based electrical properties tomography. Accuracy and precision in permittivity were assessed. A 2‐compartment phantom with properties and size similar to the human pelvis was used for both simulations and measurements. Measurements were also performed on a female volunteer’s pelvis.ResultsAccuracy was evaluated with noiseless simulations on the phantom. The maximum bias relative to the true distribution was 1% for AFI and BS and 6% to 15% for DREAM. This caused an average permittivity bias relative to the true permittivity of 7% to 20% for AFI and BS and 12% to 35% for DREAM. Precision was assessed in MR experiments. The lowest standard deviation in permittivity, found in the phantom for BS, measured 22.4 relative units and corresponded to a standard deviation in of 0.2% of the average value. As regards precision, in vivo and phantom measurements were comparable.ConclusionsOur simulation framework quantitatively predicts the different impact of mapping techniques on permittivity reconstruction and shows high sensitivity of permittivity reconstructions to sequence‐specific bias and noise perturbation in the map. These findings are supported by the experimental results.
Development and clinical implementation of SeedNet: A sliding‐window convolutional neural network for radioactive seed identification in MRI‐assisted radiosurgery (MARS)
Authors: Sanders Jeremiah W. , Frank Steven J. , Kudchadker Rajat J. , Bruno Teresa L. , Ma Jingfei 
Published: February 2019

PurposeTo develop and evaluate a sliding‐window convolutional neural network (CNN) for radioactive seed identification in MRI of the prostate after permanent implant brachytherapy.MethodsSixty‐eight patients underwent prostate cancer low‐dose‐rate (LDR) brachytherapy using radioactive seeds stranded with positive contrast MR‐signal seed markers and were scanned using a balanced steady‐state free precession pulse sequence with and without an endorectal coil (ERC). A sliding‐window CNN algorithm (SeedNet) was developed to scan the prostate images using 3D sub‐windows and to identify the implanted radioactive seeds. The algorithm was trained on sub‐windows extracted from 18 patient images. Seed detection performance was evaluated by computing precision, recall, F1‐score, false discovery rate, and false–negative rate. Seed localization performance was evaluated by computing the RMS error (RMSE) between the manually identified and algorithm‐inferred seed locations. SeedNet was implemented into a clinical software package and evaluated on sub‐windows extracted from 40 test patients.ResultsSeedNet achieved 97.6 ± 2.2% recall and 97.2 ± 1.9% precision for radioactive seed detection and 0.19 ± 0.04 mm RMSE for seed localization in the images acquired with an ERC. Without the ERC, the recall remained high, but the false–positive rate increased; the RMSE of the seed locations increased marginally. The clinical integration of SeedNet slightly increased the run‐time, but the overall run‐time was still low.ConclusionSeedNet can be used to perform automated radioactive seed identification in prostate MRI after LDR brachytherapy. Image quality improvement through pulse sequence optimization is expected to improve SeedNet’s performance when imaging without an ERC.
A black‐blood ultra‐short echo time (UTE) sequence for 3D isotropic resolution imaging of the lungs
Authors: Delacoste Jean , Feliciano Helene , Yerly Jérôme , Dunet Vincent , Beigelman‐Aubry Catherine , Ginami Giulia , van Heeswijk Ruud B. , Piccini Davide , Stuber Matthias , Sauty Alain 
Published: February 2019

PurposeUltra‐short echo time MRI is a promising alternative to chest CT for cystic fibrosis patients. Black‐blood imaging in particular could help discern small‐sized anomalies, such as mucoid plugging, which may otherwise be confused with neighboring blood vessels, particularly when contrast agent is not used. We, therefore, implemented and tested an ultra‐short echo time sequence with black‐blood preparation. Additionally, this sequence may also be used to generate bright‐blood angiograms.MethodsUsing this sequence, data was acquired during free breathing in 10 healthy volunteers to obtain respiratory‐motion‐resolved 3D volumes covering the entire thorax with an isotropic resolution of (1 mm)3. The magnitude of signal suppression relative to a bright‐blood reference acquisition was quantified and compared with that obtained with a turbo‐spin echo (TSE) acquisition. Bright‐blood angiograms were also generated by subtraction. Finally, an initial feasibility assessment was performed in 2 cystic fibrosis patients, and images were visually compared with contrast‐enhanced images and with CT data.ResultsBlack‐blood preparation significantly decreased the average normalized signal intensity in the vessel lumen (−66%; P < 0.001). Similarly, blood signal was significantly lowered (−60%; P = 0.001) compared with the TSE acquisition. In patients, mucoid plugging could be emphasized in the black‐blood datasets. An intercostal artery could also be visualized in the subtraction angiograms.ConclusionBlack‐blood free‐breathing ultra‐short echo time imaging was successfully implemented and motion‐resolved full volumetric coverage of the lungs with high spatial resolution was achieved, while obtaining an angiogram without contrast agent injection. Encouraging initial results in patients prompt further investigations in a larger cohort.
Dynamic 31P spectroscopic imaging of skeletal muscles combining flyback echo‐planar spectroscopic imaging and compressed sensing
Authors: Santos‐Díaz Alejandro , Harasym Diana , Noseworthy Michael D. 
Published: February 2019

PurposeDynamic phosphorus MR spectroscopic imaging (31P‐MRSI) experiments require temporal resolution on the order of seconds to concurrently assess different muscle groups. A highly accelerated pulse sequence combining flyback echo‐planar spectroscopic imaging (EPSI) and compressed sensing was developed and tested in a phantom and healthy humans during an exercise‐recovery challenge of the lower leg muscles, using a clinical 3T MRI.MethodsA flyback EPSI readout designed to achieve 2.25 × 2.25 cm2 resolution over a 18 × 18 cm2 field of view (i.e., 8 × 8 matrix) was combined with compressed sensing through the inclusion of pseudorandom gradient blips to sub‐sample the ky‐kt dimensions by a factor of 2.7×, achieving a temporal resolution of 9 s. The sequence was first tested in a phantom to assess performance compared to fully sampled EPSI (fidEPSI) and phase encoded chemical shift imaging (fidCSI). Then, tests were performed in 11 healthy volunteers during an exercise‐recovery challenge of the lower leg muscles. Voxels containing tissue from different muscle groups were evaluated measuring percentage phosphocreatine (%PCr) depletion, time constant of PCr recovery (τPCr) and intracellular pH at rest and following exercise.ResultsThe sequence was capable to track the dynamic PCr response of multiple muscles simultaneously. No statistical differences were found in the metabolite ratio, pH or linewidth when compared with fidEPSI and fidCSI in the phantom study. Dynamic experiments showed differences in PCr depletion when comparing soleus with gastrocnemius muscles. Intracellular pH, τPCr and %PCr decrease were consistent with reported values.ConclusionHighly accelerated 31P‐MRSI combining flyback EPSI and compressed sensing is capable of assessing concurrent energy metabolism in multiple muscle groups using a clinical 3T MR system.
Effect of a Long Bout Versus Short Bouts of Walking on Weight Loss During a Weight‐Loss Diet: A Randomized Trial
Authors: Madjd Ameneh , Taylor Moira A. , Delavari Alireza , Malekzadeh Reza , Macdonald Ian A. , Farshchi Hamid R. 
Published: February 2019

ObjectiveThis study aimed to evaluate the effect of different daily physical activity (PA) frequencies, while maintaining the same daily volume of PA, on weight loss, carbohydrate metabolism, and lipid metabolism in women with overweight or obesity throughout a 24‐week intervention.MethodsDuring their weight‐loss plan, 65 women (BMI = 27‐35 kg/m2; age = 18‐40 years) who had a sedentary lifestyle were randomly allocated to the following groups: diet plus a long bout of moderate physical activity (LBP) (one 50‐minute bout of moderate‐intensity PA) 6 d/wk or diet plus short bouts of moderate physical activity (SBP) (two 25‐minute bouts of moderate‐intensity PA) 6 d/wk. Anthropometric and blood measurements were taken at baseline and at 24 weeks.ResultsCompared with the LBP group, the SBP group had a greater decrease in weight (SBP: −8.08 ± 2.20 kg; LBP: −6.39 ± 2.28 kg; P = 0.019), BMI (SBP: −3.11 ± 0.87 kg/m2; LBP: −2.47 ± 0.86 kg/m2; P = 0.027), and waist circumference (SBP: −8.78 ± 2.62 cm; LBP: −5.76 ± 2.03 cm; P = 0.026). No significant differences were seen in carbohydrate and lipid metabolism characteristics after 24 weeks.ConclusionsPA undertaken in two shorter bouts per day could be more effective for weight loss than PA undertaken in a daily long bout in adult women in a 24‐week weight‐loss program.