bluuebunny/crossref_metadata_2025_split huggingface dataset:
PySpacell: A Python Package for Spatial Analysis of Cell Images
Authors: Rose France , Rappez Luca , Triana Sergio H. , Alexandrov Theodore , Genovesio Auguste 
Published: December 2019

AbstractTechnologies such as microscopy, sequential hybridization, and mass spectrometry enable quantitative single‐cell phenotypic and molecular measurements in situ. Deciphering spatial phenotypic and molecular effects on the single‐cell level is one of the grand challenges and a key to understanding the effects of cell–cell interactions and microenvironment. However, spatial information is usually overlooked by downstream data analyses, which usually consider single‐cell read‐out values as independent measurements for further averaging or clustering, thus disregarding spatial locations. With this work, we attempt to fill this gap. We developed a toolbox that allows one to test for the presence of a spatial effect in microscopy images of adherent cells and estimate the spatial scale of this effect. The proposed Python module can be used for any light microscopy images of cells as well as other types of single‐cell data such as in situ transcriptomics or metabolomics. The input format of our package matches standard output formats from image analysis tools such as CellProfiler, Fiji, or Icy and thus makes our toolbox easy and straightforward to use, yet offering a powerful statistical approach for a wide range of applications. © 2019 International Society for Advancement of Cytometry
In Situ Monitoring of Lipid Phase State Make Target Lipid Mixtures Similar to Intercellular Lipid in the Stratum Corneum
Authors: Fujii Mika Yoshimura , Gato Katsuhiko , Ozawa Yosuke , Hisada Hiroshi , Koide Tatsuo , Inoue Motoki , Fukami Toshiro 
Published: December 2019

AbstractIn this study, lipid structural change is monitored using Raman spectroscopy during heat treatment, along with the impact of lipid states on the structural and physical properties during the preparation process of the dried and hydrated lipid mixture (LM) similar to intercellular lipid in stratum corneum. The microstructures and thermal behavior of these LMs change depending on the melting of lipid ingredients in the preparation process. It is recognized that variable temperature Raman spectroscopy (VT‐Raman) is a useful and attractive tool for the sensitive in situ monitoring of lipid state changes and lipid melting. The LMs can incorporate D2O into their structures regardless of preparation temperature due to increasing lattice distance by hydration. These results suggest that monitoring lipid structural changes during the heating step is important to precisely prepare target LMs.Practical Applications: This study reveals that VT‐Raman is a useful and attractive tool in in situ monitoring of lipid state change and lipid melting. The monitoring of the preparation process by VT‐Raman is necessary to precisely prepare the target LM similar to intercellular lipid of stratum corneum because the microstructures and thermal properties of these LMs change depending on the melting of lipid ingredients during the preparation process.
Sparse linear array in the estimation of AoA and AoD with high resolution and low complexity
Authors: Angeline Beulah V , Venkateswaran N 
Published: December 2019

AbstractHigh resolution with low complexity angle of arrival and departure estimation in real‐time radar and wireless communication has been a topic of intensive research. In this paper, two novel algorithms are proposed, namely, minimum redundancy and minimum redundancy–reduced correlation algorithms, for finding the angles of arrival and departure with high resolution and low complexity. The first of the two proposed algorithms is meant for the reduction in the active number of antennas (minimum redundancy) without generating virtual angles. The second involves a reduction in subspace leakage to enable improvement of the peak power of the estimated true angles. The authors have assumed the users as coherent and the channel following Saleh‐Valenzuela model. This has been done for the validation of the performance of the proposed algorithms. Numerical simulations demonstrate the out performance of the existing sparse array subspace‐based methods in the estimation of angles by the proposed methods.
Survival benefit in patients with peripheral T‐cell lymphomas after treatments with novel therapies and clinical trials
Authors: Ma Helen , Cheng Bin , Falchi Lorenzo , Marchi Enrica , Sawas Ahmed , Bhagat Govind , O'Connor Owen A. 
Published: December 2019

AbstractThe peripheral T‐cell lymphomas (PTCL) are rare and heterogeneous diseases characterized by an unfavorable prognosis. Chemotherapy is standard upfront treatment in most patients, but responses are short‐lived with few FDA‐approved “novel” agents available. We sought to define the impact of these novel agents as single agents or in clinical trials on the outcomes of patients with PTCL. From January 1994 to May 2019, adult patients with PTCL who were managed at our institution were included in this analysis. In addition to patients with incomplete data, those diagnosed with large granular lymphocytic leukemia and cutaneous T‐cell lymphoma (CTCL) except for transformed mycosis fungoides were excluded. Statistical analyses were performed using SAS version 9.4. There were 219 patients included in the analysis. The median age at diagnosis was 56 years (range, 18‐90 years). First line therapies mostly consisted of combination chemotherapy (75%). There was a statistical difference among patients who received chemotherapy, novel agents alone and in chemotherapy‐free combinations, other, and no treatment (P < .0001). In patients who were treated with second line chemotherapy, novel agents alone and in combination without chemotherapy, or other, there was a still a survival benefit favoring novel agents (P = .0417). In the third line, there was no statistical difference among the three groups (P = .569). All patients who received novel therapies and underwent autologous stem cell transplant (autoSCT) achieved a complete response (CR) and had a better survival compared with patients who underwent chemotherapy who had a 70% CR rate prior to autoSCT (P = .046). Exposure to FDA‐approved novel agents, immunoepigenetic trials, and clinical trials in general was associated with an overall survival (OS) benefit (P = .003, P = .04, and P = .006, respectively). These data suggest that patients who receive novel agents have superior outcomes compared with patients without exposure to novel therapies who receive chemotherapy‐predicated treatments.
Does adoption of an evidence‐based practice lead to job turnover? Results from a randomized trial
Authors: Whitaker Daniel J. , Lyons Matthew , Weeks Erin A. , Hayat Matthew J. , Self‐Brown Shannon , Zahidi Rabab 
Published: December 2019

AbstractIt is important to understand the impact of implementation of evidence‐based practices (EBPs) on the workforce. EBP implementation can increase job demands, stress, and burnout, and may thereby exacerbate turnover. This study examined the effects of implementation of an EBP on turnover among staff at nine child welfare agencies. A total of 102 providers were randomized to either adopt an EBP, SafeCare©, or continue providing services as usual. Participants completed a baseline survey assessing demographics, attitudes toward EBPs, and organizational functioning, and provider turnover was recorded for up to 18 months following implementation. The overall turnover rate was 35%, but did not differ by EBP assignment (odds ratio [OR] = 1.27; 95% confidence interval [0.66, 2.45]). Variables associated with turnover included age (OR = 0.92), years since degree completion (OR = 0.94), prior exposure to EBP (OR = 3.91), believing that adopting an EBP was burdensome (OR = 0.52), and motivation for change (OR = 0.89). EBP assignment moderated two aspects of negative attitudes toward EBP (divergence and monitoring) to predict turnover; those attitudes were only positively related to turnover for individuals assigned to the EBP (OR = 1.46, 1.16). Implications of the findings for implementation are discussed.
Validation of Automated Perfusion‐Weighted Phase‐Resolved Functional Lung (PREFUL)‐MRI in Patients With Pulmonary Diseases
Authors: Behrendt Lea , Voskrebenzev Andreas , Klimeš Filip , Gutberlet Marcel , Winther Hinrich B. , Kaireit Till F. , Alsady Tawfik Moher , Pöhler Gesa H. , Derlin Thorsten , Wacker Frank , Vogel‐Claussen Jens 
Published: December 2019

BackgroundPerfusion‐weighted (Qw) noncontrast‐enhanced proton lung MRI is a promising technique for assessment of pulmonary perfusion, but still requires validation.PurposeTo improve perfusion‐weighted phase‐resolved functional lung (PREFUL)‐MRI, to validate PREFUL with perfusion single photon emission computed tomography (SPECT) as a gold standard, and to compare PREFUL with dynamic contrast‐enhanced (DCE)‐MRI as a reference.Study TypeRetrospective.PopulationTwenty patients with chronic obstructive pulmonary disease (COPD), 14 patients with cystic fibrosis (CF), and 21 patients with chronic thromboembolic pulmonary hypertension (CTEPH) were included.Field Strength/SequenceFor PREFUL‐MRI, a spoiled gradient echo sequence and for DCE‐MRI a 3D time‐resolved angiography with stochastic trajectories sequence were used at 1.5T.AssessmentPREFUL‐MRI coronal slices were acquired in free‐breathing. DCE‐MRI was performed in breath‐hold with injection of 0.03 mmol/kg bodyweight of gadoteric acid at a rate of 4 cc/s. Perfusion SPECT images were obtained for six CTEPH patients. Images were coregistered. An algorithm to define the appropriate PREFUL perfusion phase was developed using perfusion SPECT data. Perfusion defect percentages (QDP) and Qw‐values were calculated for all methods. For PREFUL quantitative perfusion values (PREFULQ) and for DCE pulmonary blood flow (PBF) was calculated.Statistical TestsObtained parameters were assessed using Pearson correlation and Bland–Altman analysis.ResultsQw‐SPECT correlated with Qw‐DCE (r = 0.50, P < 0.01) and Qw‐PREFUL (r = 0.47, P < 0.01). Spatial overlap of QDP maps showed an agreement ≥67.7% comparing SPECT and DCE, ≥64.1% for SPECT and PREFUL, and ≥60.2% comparing DCE and PREFUL. Significant correlations of Qw‐PREFUL and Qw‐DCE were found (COPD: r = 0.79, P < 0.01; CF: r = 0.77, P < 0.01; CTEPH: r = 0.73, P < 0.01). PREFULQ/PBF correlations were similar/lower (CF, CTEPH: P > 0.12; COPD: P < 0.01) compared to Qw‐PREFUL/DCE correlations. PREFULQ‐values were higher/similar compared to PBF‐values (COPD, CF: P < 0.01; CTEPH: P = 0.026).Data ConclusionThe automated PREFUL algorithm may allow for noncontrast‐enhanced pulmonary perfusion assessment in COPD, CF, and CTEPH patients comparable to DCE‐MRI.Level of Evidence 3Technical Efficacy Stage 2J. Magn. Reson. Imaging 2020;52:103–114.
Bridging the gap: Using 3D printed polycaprolactone implants to reconstruct circumferential tracheal defects in rabbits
Authors: Chan David S. , Gabra Nathalie , Baig Ayesha , Manoukian John J. , Daniel Sam J. 
Published: December 2019

Objective1) To assess the feasibility of reconstructing 2‐cm‐long circumferential tracheal defects with a 3D printed polycaprolactone (PCL) implant in rabbits. 2) To evaluate endoscopic, histologic, and functional characteristics of a PCL tracheal implant over time.MethodsTen New Zealand rabbits were included in this study. A 2‐cm‐long 3D printed PCL tracheal implant was created. All rabbits underwent surgical excision of a 2‐cm‐long cm segment of cervical trachea, which was reconstructed with the implant. Rabbits were sacrificed at the following time points: 0, 4, 5, 6, and 7 weeks postoperatively. At these time points, a rigid bronchoscopy was performed, and blinded evaluators calculated the percentage of airway stenosis. The tracheas were then harvested and prepared for histologic analysis.ResultsAll rabbits survived to their date of sacrifice except for one. Rabbits were euthanized between 0 to 54 days postoperatively with a median of 30 days. All rabbits developed significant granulation tissue with an average percentage stenosis of 92.3% ± 6.1%. On histology, granulation was present with extensive neovascularization and mixed inflammatory cells. There was re‐epithelialization present on the luminal surface of the PCL implant near the anastomoses but absent at the center of the implant.ConclusionThis study demonstrates that our 2‐cm‐long 3D printed PCL tracheal implant can be used to reconstruct a tracheal defect of equivalent size in a New Zealand rabbit model in the short term. However, significant granulation tissue formation limits long‐term survival. Further research is warranted to limit the granulation tissue overgrowth.Level of EvidenceNALaryngoscope, 2019
Legacy nitrate in the deep loess deposits after conversion of arable farmland to non‐fertilized land uses for degraded land restoration
Authors: Ji Wangjia , Huang Yanan , Li Bingbing , Hopkins David W , Liu Wenzhao , Li Zhi 
Published: December 2019

AbstractThe legacy nitrate–nitrogen (NO3−−N) in the soils is a long‐term threat to groundwater in regions with thick unsaturated zones, and it is thus important to investigate the amounts and sources of NO3−−N for effective environmental management. Given the substantial conversions of arable farmlands to non‐fertilizer land uses for the restoration of degraded land, the legacy effects of NO3−−N in thick loessial unsaturated zones in China remain uncertain. We collected soil samples from loess profiles >13‐m deep under arable farmland and grassland, apricot, pine, peashrub, willow, and poplar converted from arable farmland over 15–35 years. We determined their nitrate content and isotope compositions to quantify the accumulation and sources of the former and its potential threat to groundwater. The seven NO3−−N profiles exhibited a parabolic shape with peak depths at 2.6–9.2 m. Greater peak depths corresponded to greater NO3−−N values, and the peak nitrate level varied from 0 to 10 m. The total NO3−−N accumulation ranged 3,181–9,018 kg N ha−1, and the non‐fertilizer profiles accounted for 35–73% of the arable farmland. The nitrate sources varied with depths. According to the isotope mass balance, the nitrate above, near, and below the peak depths mainly originated from atmospheric NO3− (25–34%), synthetic N fertilizer (49–68%), and soil organic N and manure (50–73%). The estimated residence time of nitrate in the soil ranged from 270 to 620 years. As such, the nitrate legacy effects should be given considerable attention for the protection of the soil and groundwater environment.
Metabolic Network Abnormalities in Drug‐Naïve Parkinson's Disease
Authors: Schindlbeck Katharina A. , Lucas‐Jiménez Olaia , Tang Chris C. , Morbelli Silvia , Arnaldi Dario , Pardini Matteo , Pagani Marco , Ibarretxe‐Bilbao Naroa , Ojeda Natalia , Nobili Flavio , Eidelberg David 
Published: December 2019

AbstractBackgroundAn ideal imaging biomarker for a neurodegenerative disorder should be able to measure abnormalities in the earliest stages of the disease.ObjectiveWe investigated metabolic network changes in two independent cohorts of drug‐naïve Parkinson's disease (PD) patients who have not been exposed to dopaminergic medication.MethodsWe scanned 85 de novo, drug‐naïve PD patients and 85 age‐matched healthy control subjects from Italy (n = 96) and the United States (n = 74) with [18F]‐fluorodeoxyglucose PET. All patients had clinical follow‐ups to verify the diagnosis of idiopathic PD. Spatial covariance analysis was used to identify and validate de novo PD‐related metabolic patterns in the Italian and U.S. cohorts. We compared the de novo PD‐related metabolic patterns to the original PD‐related pattern that was identified in more advanced patients who had been on chronic dopaminergic treatment.ResultsDe novo PD‐related metabolic patterns were identified in each of the two independent cohorts of drug‐naïve PD patients, and each differentiated PD patients from healthy control subjects. Expression values for these disease patterns were elevated in drug‐naïve PD patients relative to healthy controls in the identification as well as in each of the validation subgroups. The two de novo PD‐related metabolic patterns were topographically very similar to each other and to the original PD‐related pattern.ConclusionsReproducible PD‐related patterns are expressed in de novo, drug‐naïve PD patients. In PD, disease‐related metabolic patterns have stereotyped topographies that develop independently of chronic levodopa treatment. © 2019 International Parkinson and Movement Disorder Society
Transformer matched gilbert mixer with active balun for D band transmitter
Authors: Yu Jiayang , Chen Jixin , Li Huanbo , Zhou Peigen , Hou Debin , Hong Wei , Yan Pinpin 
Published: December 2019

AbstractA Gilbert mixer for the application of a D band transmitter is presented. In the work, the differential pair below the mixing quad is replaced by an active balun. A source resistor is introduced to improve balance performance of the active balun. Owing to the resistor, the LO‐to RF isolation of the mixer is also improved. At the output end, a transformer‐based balun is used to transform differential signal to single‐end signal and realize wideband output match. The circuit is designed on a 130 nm SiGe BiCMOS technology with fT/fmax of 300/500 GHz. The compact mixer covers 5 GHz intermediate frequency (IF) tuning range (1 to 6 GHz) with LO frequency fixed at 150 GHz. The measured RF 3‐dB bandwidth varying from 128 to 160 GHz with maximum −6 dB conversion gain, when the LO frequency is tuned. And the output referred 1‐dB compression point (OP1dB) is nearly −15 dBm. The mixer except test circuit consumes 14 mW DC power.
Low‐cost and miniaturized metamaterial absorber using 3D printed swastika symbol
Authors: Kim Minseok , Jeong Heijun , Lim Daecheon , Ghosh Saptarshi , Lim Sungjoon 
Published: December 2019

AbstractIn this paper, a low‐cost metamaterial (MM) absorber is proposed using 3‐dimensional (3D) printing technology. The unit cell of the proposed MM absorber is motivated from a swastika symbol to minimize the footprint size. For further miniaturization, the unit cell is 3D printed by stacking two blocks. The conductive top patterns are realized by painting with a silver ink. The proposed MM absorber consists of 2 × 4 unit cell array which is loaded in the rectangular waveguide. Its absorptivity is simulated and measured to demonstrate the performance. The simulated and measured absorptivity at 1.91 GHz are 99% and 92%, respectively.
Is high sensitivity always desirable for a grating‐based differential phase contrast imaging system?
Authors: Ji Xu , Zhang Ran , Li Ke , Chen Guang‐Hong 
Published: December 2019

PurposeIn grating‐based x‐ray differential phase contrast (DPC) imaging, the measured signal amplitude of the phase shift induced by an image object is proportional to the so‐called system sensitivity. Therefore, to achieve a better signal‐to‐noise (SNR) for improved imaging performance, it is generally believed that one should increase the system sensitivity by reducing the period of the analyzer grating or increasing the distance between the phase grating and analyzer grating. The purpose of this work is to theoretically and experimentally demonstrate that there is an optimal system sensitivity to attain the highest SNR for a given task provided that the standard phase‐stepping acquisition and phase retrieval methods are used. When system sensitivity goes beyond this optimal value, SNR decreases and the imaging performance deteriorates.MethodsDue to the fundamental fact that the measured phase signal is a cyclic variable, the phase wrapping effect is inevitable in DPC imaging when the system sensitivity increases. The phase wrapping effect appears in both signal and noise measurements. The effect in the signal measurement is manifested in the so‐called signal statistical bias and such effect often impacts the accuracy of the measurement. The phase wrapping effect also appears in the noise variance measurement and impacts the precision of the measurement. A thorough theoretical analysis was performed in this work to demonstrate the quantitative impacts of phase wrapping on both signal bias and noise variance and thus on the actual system SNR. The joint effect of phase wrapping in both the signal bias and noise variance yields an optimal system sensitivity to achieve the highest SNR. Both extensive numerical simulation studies and experimental studies were performed to validate the theoretical analysis.ResultsBoth theoretical analysis and experimental studies show that the SNR of the DPC signal is not always proportional to the sensitivity due to the cyclic nature of the signal and the phase wrapping effect. For a given refraction angle and exposure level, there exists an optimal sensitivity factor that maximizes the SNR, beyond which, increasing the sensitivity will decrease the SNR.ConclusionsIncrease of system sensitivity does not always improve x‐ray DPC imaging performance provided that the standard phase‐stepping acquisition and phase retrieval methods are used.
d‐glucose weighted chemical exchange saturation transfer (glucoCEST)‐based dynamic glucose enhanced (DGE) MRI at 3T: early experience in healthy volunteers and brain tumor patients
Authors: Xu Xiang , Sehgal Akansha Ashvani , Yadav Nirbhay N. , Laterra John , Blair Lindsay , Blakeley Jaishri , Seidemo Anina , Coughlin Jennifer M. , Pomper Martin G. , Knutsson Linda , van Zijl Peter C. M. 
Published: December 2019

PurposeDynamic glucose enhanced (DGE) MRI has shown potential for imaging glucose delivery and blood–brain barrier permeability at fields of 7T and higher. Here, we evaluated issues involved with translatingd‐glucose weighted chemical exchange saturation transfer (glucoCEST) experiments to the clinical field strength of 3T.MethodsExchange rates of the different hydroxyl proton pools and the field‐dependentT2relaxivity of water ind‐glucose solution were used to simulate the water saturation spectra (Z‐spectra) and DGE signal differences as a function of static field strengthB0, radiofrequency field strengthB1, and saturation timetsat. Multislice DGE experiments were performed at 3T on 5 healthy volunteers and 3 glioma patients.ResultsSimulations showed that DGE signal decreases withB0, because of decreased contributions of glucoCEST and transverse relaxivity, as well as coalescence of the hydroxyl and water proton signals in the Z‐spectrum. At 3T, because of this coalescence and increased interference of direct water saturation and magnetization transfer contrast, the DGE effect can be assessed over a broad range of saturation frequencies. Multislice DGE experiments were performed in vivo using aB1of 1.6 µT and atsatof 1 second, leading to a small glucoCEST DGE effect at an offset frequency of 2 ppm from the water resonance. Motion correction was essential to detect DGE effects reliably.ConclusionMultislice glucoCEST‐based DGE experiments can be performed at 3T with sufficient temporal resolution. However, the effects are small and prone to motion influence. Therefore, motion correction should be used when performing DGE experiments at clinical field strengths.