bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance improvement of weakly supervised fully convolutional networks by skip connections for brain structure segmentation
Authors: Sugino Takaaki , Roth Holger R. , Oda Masahiro , Kin Taichi , Saito Nobuhito , Nakajima Yoshikazu , Mori Kensaku 
Published: August 2021

AbstractPurposeFor the planning and navigation of neurosurgery, we have developed a fully convolutional network (FCN)‐based method for brain structure segmentation on magnetic resonance (MR) images. The capability of an FCN depends on the quality of the training data (i.e., raw data and annotation data) and network architectures. The improvement of annotation quality is a significant concern because it requires much labor for labeling organ regions. To address this problem, we focus on skip connection architectures and reveal which skip connections are effective for training FCNs using sparsely annotated brain images.MethodsWe tested 2D FCN architectures with four different types of skip connections. The first was a U‐Net architecture with horizontal skip connections that transfer feature maps at the same scale from the encoder to the decoder. The second was a U‐Net++ architecture with dense convolution layers and dense horizontal skip connections. The third was a full‐resolution residual network (FRRN) architecture with vertical skip connections that pass feature maps between each downsampled scale path and the full‐resolution scale path. The last one was a hybrid architecture with a combination of horizontal and vertical skip connections. We validated the effect of skip connections on medical image segmentation from sparse annotation based on these four FCN architectures, which were trained under the same conditions.ResultsFor multiclass segmentation of the cerebrum, cerebellum, brainstem, and blood vessels from sparsely annotated MR images, we performed a comparative evaluation of segmentation performance among the above four FCN approaches: U‐Net, U‐Net++, FRRN, and hybrid architectures. The experimental results show that the horizontal skip connections in the U‐Net architectures were effective for the segmentation of larger sized objects, whereas the vertical skip connections in the FRRN architecture improved the segmentation of smaller sized objects. The hybrid architecture with both horizontal and vertical skip connections achieved the best results of the four FCN architectures. We then performed an ablation study to explore which skip connections in the FRRN architecture contributed to the improved segmentation of blood vessels. In the ablation study, we compared the segmentation performance between architectures with a horizontal path (HP), an HP and vertical up paths (HP+VUPs), an HP and vertical down paths (HP+VDPs), and an HP and vertical up and down paths (FRRN). We found that the vertical up paths were effective in improving the segmentation of smaller sized objects.ConclusionsThis paper investigated which skip connection architectures were effective for multiclass brain segmentation from sparse annotation. Consequently, using vertical skip connections with horizontal skip connections allowed FCNs to improve segmentation performance.
Microwave breast tumor localization using wavelet feature extraction and genetic algorithm‐neural network
Authors: Lu Min , Xiao Xia , Liu Guancong , Lu Hong 
Published: August 2021

AbstractPurposeUltra‐Wide Band (UWB) microwave breast cancer detection is a promising new technology for routine physical examination and home monitoring. The existing microwave imaging algorithms for breast tumor detection are complex and the effect is still not ideal, due to the heterogeneity of breast tissue, skin reflection, and fibroglandular tissue reflection in backscatter signals. This study aims to develop a machine learning method to accurately locate breast tumor.MethodsA microwave‐based breast tumor localization method is proposed by time‐frequency feature extraction and neural network technology. First, the received microwave array signals are converted into representative and compact features by 4‐level Discrete Wavelet Transform (DWT) and Principal Component Analysis (PCA). Then, the Genetic Algorithm‐Neural Network (GA‐NN) is developed to tune hyper‐parameters of the neural network adaptively. The neural network embedded in the GA‐NN algorithm is a four‐layer architecture and 10‐fold cross‐validation is performed. Through the trained neural network, the tumor localization performance is evaluated on four datasets that are created by FDTD simulation method from 2‐D MRI‐derived breast models with varying tissue density, shape, and size. Each dataset consists of 1000 backscatter signals with different tumor positions, in which the ratio of training set to test set is 9:1. In order to verify the generalizability and scalability of the proposed method, the tumor localization performance is also tested on a 3‐D breast model.ResultsFor these 2‐D breast models with unknown tumor locations, the evaluation results show that the proposed method has small location errors, which are 0.6076 mm, 3.0813 mm, 2.0798 mm, and 3.2988 mm, respectively, and high accuracy, which is 99%, 80%, 94%, and 85%, respectively. Furthermore, the location error and the prediction accuracy of the 3‐D breast model are 3.3896 mm and 81%.ConclusionsThese evaluation results demonstrate that the proposed machine learning method is effective and accurate for microwave breast tumor localization. The traditional microwave‐based breast cancer detection method is to reconstruct the entire breast image to highlight the tumor. Compared with the traditional method, our proposed method can directly get the breast tumor location by applying neural network to the received microwave array signals, and circumvent any complicated image reconstruction processing.
Radiomics analysis combining unsupervised learning and handcrafted features: A multiple‐disease study
Authors: Wan Yidong , Yang Pengfei , Xu Lei , Yang Jing , Luo Chen , Wang Jing , Chen Feng , Wu Yan , Lu Yun , Ruan Dan , Niu Tianye 
Published: August 2021

AbstractPurposeTo study and investigate the synergistic benefit of incorporating both conventional handcrafted and learning‐based features in disease identification across a wide range of clinical setups.Methods and materialsIn this retrospective study, we collected 170, 150, 209, and 137 patients with four different disease types associated with identification objectives : Lymph node metastasis status of gastric cancer (GC), 5‐year survival status of patients with high‐grade osteosarcoma (HOS), early recurrence status of intrahepatic cholangiocarcinoma (ICC), and pathological grades of pancreatic neuroendocrine tumors (pNETs). Computed tomography (CT) and magnetic resonance imaging (MRI) were used to derive image features for GC/HOS/pNETs and ICC, respectively. In each study, 67 universal handcrafted features and study‐specific features based on the sparse autoencoder (SAE) method were extracted and fed into the subsequent feature selection and learning model to predict the corresponding disease identification. Models using handcrafted alone, SAE alone, and hybrid features were optimized and their performance was compared. Prominent features were analyzed both qualitatively and quantitatively to generate study‐specific and cross‐study insight. In addition to direct performance gain assessment, correlation analysis was performed to assess the complementarity between handcrafted features and SAE features.ResultsOn the independent hold‐off test, the handcrafted, SAE, and hybrid features based prediction yielded area under the curve of 0.761 versus 0.769 versus 0.829 for GC, 0.629 versus 0.740 versus 0.709 for HOS, 0.717 versus 0.718 versus 0.758 for ICC, and 0.739 versus 0.715 versus 0.771 for pNETs studies, respectively. In three out of the four studies, prediction using the hybrid features yields the best performance, demonstrating the general benefit in using hybrid features. Prediction with SAE features alone had the best performance in the HOS study, which may be explained by the complexity of HOS prognosis and the possibility of a slight overfit due to higher correlation between handcrafted and SAE features.ConclusionThis study demonstrated the general benefit of combing handcrafted and learning‐based features in radiomics modeling. It also clearly illustrates the task‐specific and data‐specific dependency on the performance gain and suggests that while the common methodology of feature combination may be applied across various studies and tasks, study‐specific feature selection and model optimization are still necessary to achieve high accuracy and robustness.
Occurrence of symptoms in different stages of Duchenne muscular dystrophy and their impact on social participation
Authors: Houwen‐van Opstal Saskia L. S. , Heutinck Lotte , Jansen Merel , Krom Yvonne D. , Cup Edith H. C. , Hendriksen Jos G. M. , Willemsen Michel A. A. P. , Verschuuren Jan J. G. M. , Niks Erik H. , de Groot Imelda J. M. 
Published: August 2021

AbstractIntroduction/AimsAs life expectancy improves for patients with Duchenne muscular dystrophy (DMD), new symptoms are likely to arise. This aims of this study are: (1) to explore the prevalence of a broad variety of symptoms in the various stages of DMD (with and without steroid use); (2) to explore the prevalence of common secondary diagnoses; and (3) to evaluate the social participation level of patients with DMD older than 16 y of age; and to explore correlations between social participation and symptoms.MethodsA cross‐sectional self‐report questionnaire, including questions on functional level and health status, as well as a standardized participation scale was distributed among Dutch patients with DMD.ResultsEighty‐four male patients with a mean age of 22.0 (SD = 10.0) y were enrolled. The most prevalent and limiting symptoms were difficulty coughing (58%), coldness of hands (57%), contractures (51%), stiffness (49%), fatigue (40%), myalgia (38%), and low speech volume (33%). Prevalent secondary diagnoses included cardiac disease (14%), neurobehavioral diagnosis (13%), low blood pressure (13%), and arthrosis (5%). Social participation correlated negatively with coldness of hands (r = − .29; P < .03), decreased intelligibility (r = − .40; P < .003), and chewing problems (r = − .33; P < .02).DiscussionThe prevalence of a broad spectrum of symptoms and secondary diagnoses is high in patients with DMD, and some of these symptoms are correlated with social participation. Growing awareness of new symptoms and secondary diagnoses among patients, caregivers, and professionals can enhance their recognition, possibly facilitating prevention and early treatment.
Dysfunctional voiding behavior and impaired muscle contractility in a rat model of detrusor underactivity
Authors: Gonzalez Eric J. , Odom Michael R. , Hannan Johanna L. , Grill Warren M. 
Published: August 2021

AbstractAimsDetrusor underactivity (DU) is an understudied health concern with inadequate clinical management. The pathophysiology of DU is unclear, and current therapies fail to improve symptoms. The current studies characterized voiding function and contractility of bladder and urethral tissues in a novel rat model of DU.MethodsFemale obese prone (OP) and obese resistant (OR) rats were fed a 60 kcal% fat diet at 8 weeks old. A subset of rats (n = 4/strain) underwent uroflowmetry biweekly for 18 weeks in metabolic cages. At 40–56 weeks old, rats (n = 9–10/strain) underwent instrumented cystometry under urethane anesthesia. Following cystometry, bladder and urethral tissues (n = 8–9/strain) were harvested for in vitro assessments of contractility in response to carbachol, electric field stimulation, atropine, alpha, beta‐methylene ATP, and caffeine.ResultsOP rats exhibited increased urinary frequency (p = 0.0031), decreased voided volume (p = 0.0093), and urine flow rate (p = 0.0064) compared to OR rats during uroflowmetry. Bethanechol (10 mg/kg) did not alter uroflowmetry parameters. During cystometry, OP rats exhibited decreased bladder emptying efficiency (p < 0.0001), decreased pressure to generate a void (p < 0.0001), and increased EUS activity during filling (p = 0.0011). Bladder contractility was decreased in OP rats when exposed to carbachol (p < 0.0003) and ATP (p = 0.0004), whereas middle urethral contractility was increased when exposed to carbachol (p = 0.0014), EFS (p = 0.0289), and caffeine (p = 0.0031).ConclusionImpaired cholinergic and purinergic signaling in the bladder may contribute to poor voiding function in OP rats. In addition, increased urethral activity may engage a guarding reflex to augment continence and exacerbate incomplete emptying.
Pigs in the Neolithic of the Eastern Fertile Crescent: New evidence from Pre‐Pottery Neolithic Bestansur and Shimshara, Iraqi Kurdistan (7800–7100 BC)
Authors: de Groene Donna , Bendrey Robin , Matthews Roger 
Published: August 2021

AbstractPigs are one of the earliest domesticated livestock species, first domesticated at least 10,000 years ago. The domestication of wild boar, including associated morphological changes, is a long process over several millennia. Across Southwest Asia, management, domestication, and the adaption of the different livestock species was a highly localized process, influenced by both cultural and environmental factors.This paper explores the size, age, and diet of the suids of the Pre‐Pottery Neolithic sites of Bestansur and Shimshara in order to further our understanding of the origins of suid management in the Neolithic Eastern Fertile Crescent. Our data suggest that the relationship between wild boar and humans was more complex than a strict hunter–prey relationship. This study demonstrates that the Neolithic in the Zagros was not uniform in the adaption and exploitation of different animals.
Practicable self‐healing polyurethane binder for energetic composites combining thermo‐reversible DA action and shape‐memory effect
Authors: Li Yubin , Yang Zhijian , Zhao Xu , Zhang Jianhu , Ding Ling , Pan Liping , Lin Congmei , Zheng Xue 
Published: August 2021

AbstractA novel thermally mendable polyurethane binder for energetic composites was designed and prepared via the Diels‐Alder (DA) cycloaddition reaction between a furan functionalized polycaprolactone (PCL) prepolymer and a bismaleimide compound. The structures and properties of synthesized PCL‐DA‐PU were fully characterized via Proton Nuclear Magnetic Resonance (1H‐NMR) and Fourier Transform Infrared spectroscopy (FT‐IR), Gel Permeation Chromatography (GPC), Thermogravimetric Analysis (TGA), and Differential Scanning Calorimetry (DSC) measurements. As‐prepared material showed good self‐healing ability of scratches by virtue of combining the shape recovery effect of PCL segments favoring scratch closure with the re‐crosslinking of the cleaved DA bonds, which was evidenced by optical microscopy and tensile analysis. A scratch healing efficiency determined by tensile tests of about 89% was achieved. Moreover, with the contribution of DA bonds in PCL‐DA‐PU binder, the microcracks and other damages in the TATB based energetic composites were almost mended and the mechanical strength can recovery above 78%.
The effect of two different UV absorbers combined with antioxidants on UV resistance of HDPE
Authors: Jiang Tiankai , Mao Zepeng , Qi Yanli , Wu Yuchen , Zhang Jun 
Published: August 2021

AbstractIn order to improve the aging resistance of HDPE, antioxidants (Irganox1010 and Irgafos168) are combined with UV absorber (UV‐326 or UV‐531). Analyses of ultraviolet–visible (UV–vis) and Fourier transform infrared spectroscopy show that UV‐326 has a better capacity of UV absorbance, but easier to migrate to the HDPE surface due to the bigger difference of solubility parameter with HDPE than UV‐531. The mechanical property indicates a better synergistic effect between UV‐531 and antioxidants. With the single addition of antioxidant, the mechanical property sharply decreased to low level during irradiation for 200 h. With single addition of UV absorber, the elongation at break of the sample can still be maintained at about 700% until irradiation for 600 h. When two different UV absorbers are used in combination with antioxidants, HDPE with UV‐326 maintains high mechanical property when irradiated for 1200 h, while the samples containing UV‐531 still maintain good mechanical property when irradiated for 1600 h.
SARS‐CoV‐2 persistence in immunocompromised children
Authors: Dolan Susan A. , Mulcahy Levy Jean , Moss Angela , Pearce Kelly , Butler Molly , Jung Sarah , Dominguez Samuel R. , Mwangi Eric , Maloney Kelly , Rao Suchitra 
Published: August 2021

AbstractObjectivesWe evaluated the length of time immunocompromised children (ICC) remain positive for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), identified factors associated with viral persistence, and determined cycle threshold (CT) values of children with viral persistence as a surrogate of viral load.MethodsWe conducted a retrospective cohort study of ICC at a pediatric hospital from March 2020 to March 2021. Immunocompromised status was defined as primary, secondary, or acquired due to medical comorbidities/immunosuppressive treatment. The primary outcome was time to first of two consecutive negative SARS‐CoV‐2 polymerase chain reaction (PCR) tests at least 24 hours apart. Testing of sequential clinical specimens from the same subject was conducted using the Centers for Disease Control (CDC) 2019‐nCoV real‐time reverse transcriptase (RT)‐PCR Diagnostic Panel assay. Descriptive statistics, Kaplan–Meier curve median event times and log‐rank tests were used to compare outcomes between groups.ResultsNinety‐one children met inclusion criteria. Median age was 15.5 years (interquartile range [IQR] 8–18), 64% were male, 58% were White, and 43% were Hispanic/Latinx. Most (67%) were tested in outpatient settings and 58% were asymptomatic. The median time to two negative tests was 42 days (IQR 25.0–55.0), with no differences in median time by illness presentation or level of immunosuppression. Seven children had more than one sample available for repeat testing, and five of seven (71%) children had initial CT values of <30 (moderate to high viral load); four children had CT values of <30, 3–4 weeks later, suggesting persistent moderate to high viral loads.ConclusionsMost ICC with SARS‐CoV‐2 infection had mild disease, with prolonged viral persistence >6 weeks and moderate to high viral load.
In vivo evaluation of the lysine‐specific demethylase (KDM1A/LSD1) inhibitor SP‐2577 (Seclidemstat) against pediatric sarcoma preclinical models: A report from the Pediatric Preclinical Testing Consortium (PPTC)
Authors: Kurmasheva Raushan T. , Erickson Stephen W. , Han Ruolan , Teicher Beverly A. , Smith Malcolm A. , Roth Michael , Gorlick Richard , Houghton Peter J. 
Published: August 2021

AbstractSP‐2577(Seclidemstat), an inhibitor of lysine‐specific demthylase KDM1A (LSD1) that is overexpressed in pediatric sarcomas, was evaluated against pediatric sarcoma xenografts. SP‐2577 (100 mg/kg/day × 28 days) statistically significantly (p < .05) inhibited growth of three of eight Ewing sarcoma (EwS), four of five rhabdomyosarcoma (RMS), and four of six osteosarcoma (OS) xenografts. The increase in EFS T/C was modest (<1.5) for all models except RMS Rh10 (EFS T/C = 2.8). There were no tumor regressions or consistent changes in dimethyl histone H3(K4), HOXM1, DAX1, c‐MYC and N‐MYC, or tumor histology/differentiation. SP‐2577 has limited activity against these pediatric sarcoma models at the dose and schedule evaluated.
Proton pump inhibitors long term use‐trends and patterns over 15 years of a large health maintenance organization
Authors: Rosenberg Vered , Tzadok Roie , Chodick Gabriel , Kariv Revital 
Published: August 2021

AbstractBackgroundProton pump inhibitors (PPI) are used for a variety of indications. Despite reported associations with undesirable effects, their long‐term use is on the rise, while appropriate indications, dose, and treatment duration may deviate from guideline recommendations.ObjectivesPrimary to examine the annual patterns of PPI use. Secondary‐ to assess indications for initiating PPI treatment, long‐term use, and factors associated with long‐term use in a large Israeli health maintenance organization.MethodsA historical cohort study of 528 420 eligible PPI users during 2000–2015, analyzed PPI use using defined daily doses and the proportion of patients covered method. Data on indications for treatment initiation, clinical and socio‐demographic parameters were captured as well. A multivariable logistic‐regression model was used to identify factors associated with long‐term use of PPI.ResultsThe annual incidence rates of patients initiating PPI treatment were relatively constant, ranging between 2.4% and 3.1% of the adult population, with a monotonic increase in annual consumption and prevalence (reaching 12.7% in 2015). Reflux, functional symptoms, and Helicobacter pylori eradication were the most common indications for initiating PPI therapy. However, 27% of patients had no recorded indication for treatment. Fifteen percent of patients used PPI for over 6 months, especially in older age groups.ConclusionsUtilization of PPI increases steadily, mainly due to chronic use. Prolonged consumption is associated with specific clinical indications and older age. Health organizations should encourage awareness of appropriate use among physicians, specifically in the elderly, patients with reflux, and those with functional disorders.
Study on highly thermostable low‐k polymer films based on fluorene‐containing polyetherimides
Authors: Olariu Marius Andrei , Hamciuc Corneliu , Asandulesa Mihai , Hamciuc Elena , Epure Elena‐Luiza , Tsakiris Violeta , Lisa Gabriela 
Published: August 2021

AbstractHighly thermostable low‐k polymer films with potential applications as dielectric materials in microelectronic industry were synthesized starting from 9,9‐bis[4‐(3,4‐dicarboxyphenoxy)phenyl]fluorene dianhydride and various diamines. A polyetherimide/silica nanocomposite film was obtained using methyltriethoxysilane as precursor of inorganic phase. The chemical structure was confirmed by FTIR and 1H NMR spectroscopy. Water vapor's sorption capacity, thermal stability, glass transition temperature, thermal diffusivity, specific heat, thermal conductivity, and dielectric characteristics of the films were determined. All the films exhibited excellent thermal stability, with an initial decomposition temperature in the range of 500–530°C. They showed low dielectric constant of 1.98–2.86 and low dielectric loss of 0.0037–0.011, at a frequency of 1 Hz and room temperature. The subglass γ‐ and β‐relaxations, primary α‐relaxation, and conductivity relaxation processes were discussed according to the chemical structure of the samples. Quantitative structure–property relationship (QSPR) study was conducted, and linear regression models were formulated to describe the causal relationships between different parameters and polyetherimide properties.
RapiGest precipitation depends on peptide concentration
Authors: Mosen Peter R. , Hardt Robert , Winter Dominic 
Published: August 2021

AbstractThe mass spectrometry‐compatible surfactant RapiGest promotes the enzymatic digestion of proteins by facilitating their unfolding while retaining enzymatic activity. RapiGest consists of a hydrophilic head and a hydrophobic tail, which can be separated by acid hydrolysis. This allows for removal of RapiGest prior to mass spectrometric analysis via precipitation and solid phase extraction. During in‐solution digestion experiments with RapiGest, we noticed a high variability in the formation of precipitates after acid hydrolysis, implying that RapiGest precipitation is sample‐dependent. We show that RapiGest hydrolyses efficiently under acidic conditions and that differences in precipitation are solely due to protein/peptide concentration. Furthermore, we demonstrate that RapiGest precipitation can be triggered by the addition of intact proteins, providing a strategy for its efficient removal from highly diluted samples. Data are available via ProteomeXchange with identifier PXD025982.