bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of automated amygdala MRI segmentation approaches in Huntington's disease in the IMAGE‐HD cohort
Authors: Alexander Bonnie , Georgiou‐Karistianis Nellie , Beare Richard , Ahveninen Lotta M. , Lorenzetti Valentina , Stout Julie C. , Glikmann‐Johnston Yifat 
Published: February 2020

AbstractSmaller manually‐segmented amygdala volumes have been associated with poorer motor and cognitive function in Huntington's disease (HD). Manual segmentation is the gold standard in terms of accuracy; however, automated methods may be necessary in large samples. Automated segmentation accuracy has not been determined for the amygdala in HD. We aimed to determine which of three automated approaches would most accurately segment amygdalae in HD: FreeSurfer, FIRST, and ANTS nonlinear registration followed by FIRST segmentation. T1‐weighted images for the IMAGE‐HD cohort including 35 presymptomatic HD (pre‐HD), 36 symptomatic HD (symp‐HD), and 34 healthy controls were segmented using FreeSurfer and FIRST. For the third approach, images were nonlinearly registered to an MNI template using ANTS, then segmented using FIRST. All automated methods overestimated amygdala volumes compared with manual segmentation. Dice overlap scores, indicating segmentation accuracy, were not significantly different between automated approaches. Manually segmented volumes were most statistically differentiable between groups, followed by those segmented by FreeSurfer, then ANTS/FIRST. FIRST‐segmented volumes did not differ between groups. All automated methods produced a bias where volume overestimation was more severe for smaller amygdalae. This bias was subtle for FreeSurfer, but marked for FIRST, and moderate for ANTS/FIRST. Further, FreeSurfer introduced a hemispheric bias not evident with manual segmentation, producing larger right amygdalae by 8%. To assist choice of segmentation approach, we provide sample size estimation graphs based on sample size and other factors. If automated segmentation is employed in samples of the current size, FreeSurfer may effectively distinguish amygdala volume between controls and HD.
Unravelling evapotranspiration controls and components in tropical Andean tussock grasslands
Authors: Ochoa‐Sánchez Ana E. , Crespo Patricio , Carrillo‐Rojas Galo , Marín Franklin , Célleri Rolando 
Published: February 2020

AbstractThe study of the environmental factors that control evapotranspiration and the components of evapotranspiration leads to a better understanding of the actual evapotranspiration (ET) process that links the functioning of the soil, water and atmosphere. It also improves local, regional and global ET modelling. Globally, few studies so far focussed on the controls and components of ET in alpine grasslands, especially in mountainous sites such as the tussock grasslands located in the páramo biome (above 3300 m a.s.l.). The páramo occupies 35 000 km2 and provides water resources for many cities in the Andes. In this article, we unveiled the controls on ET and provided the first insights on the contribution of transpiration to ET. We found that the wet páramo is an energy‐limited region and net radiation (Rn) is primarily controlling ET. ET was on average 1.7 mm/day. The monthly average evaporative fraction (ET/Rn) was 0.47 and it remained similar for wet and dry periods. The secondary controls on ET were wind speed, aerodynamic resistance and surface resistance that appeared more important for dry periods, where significantly higher ET rates were found (20% increase). During dry events, transpiration was on average 1.5 mm/day (range 0.7–2.7 mm/day), similar to other tussock grasslands in New Zealand (range 0.6–3.3 mm/day). Evidence showed interception contributes more to ET than transpiration. This study sets a precedent towards a better understanding of the evapotranspiration process and will ultimately lead to a better land‐atmosphere fluxes modelling in the tropics.
Effect of anisotropy on solute transport in degraded fen peat soils
Authors: Wang Miaorun , Liu Haojie , Zak Dominik , Lennartz Bernd 
Published: February 2020

AbstractPeat soils are heterogeneous, anisotropic porous media. Compared to mineral soils, there is still limited understanding of physical and solute transport properties of fen peat soils. In this study, we aimed to explore the effect of soil anisotropy on solute transport in degraded fen peat. Undisturbed soil cores, taken in vertical and horizontal direction, were collected from one drained and one restored fen peatland both in a comparable state of soil degradation. Saturated hydraulic conductivity (K
s) and chemical properties of peat were determined for all soil cores. Miscible displacement experiments were conducted under saturated steady state conditions using potassium bromide as a conservative tracer. The results showed that (1) the K
s in vertical direction (K
sv) was significantly higher than that in horizontal direction (Ksh), indicating that K
s of degraded fen peat behaves anisotropically; (2) pronounced preferential flow occurred in vertical direction with a higher immobile water fraction and a higher pore water velocity; (3) the 5% arrival time (a proxy for the strength of preferential flow) was affected by soil anisotropy as well as study site. A strong correlation was found between 5% arrival time and dispersivity, K
s and mobile water fraction; (4) phosphate release was observed from drained peat only. The impact of soil heterogeneity on phosphate leaching was more pronounced than soil anisotropy. The soil core with the strongest preferential flow released the highest amount of phosphate. We conclude that soil anisotropy is crucial in peatland hydrology but additional research is required to fully understand anisotropy effects on solute transport.
Deep learning and optimization algorithms for automatic breast cancer detection
Authors: Sha Zijun , Hu Lin , Rouyendegh Babak Daneshvar 
Published: February 2020

AbstractBreast cancer is caused by the abnormal and rapid growth of breast cells. An early diagnosis can ensure an easier and effective treatment. A mass in the breast is a significant early sign of breast cancer, even though differentiating the cancerous mass's tissue from normal tissue for diagnosis is a difficult task for radiologists. The development of computer‐aided detection systems in recent years has led to nondestructive and efficient cancer diagnostic techniques. This paper proposes a comprehensive method to locate the cancerous region in the mammogram image. This method employs image noise reduction, optimal image segmentation based on the convolutional neural network, a grasshopper optimization algorithm, and optimized feature extraction and feature selection based on the grasshopper optimization algorithm, thereby improving precision and decreasing the computational cost. This method was applied to the Mammographic Image Analysis Society Digital Mammogram Database and Digital Database for Screening Mammography breast cancer databases and the simulation results were compared with 10 different state‐of‐the‐art methods to analyze the proposed system's efficiency. Final results showed that the proposed method had 96% Sensitivity, 93% Specificity, 85% PPV, 97% NPV, 92% accuracy, and better efficiency than other traditional methods in terms of Sensitivity, Specificity, PPV, NPV, and Accuracy.
Improved chicken swarm optimization to classify dementia MRI images using a novel controlled randomness optimization algorithm
Authors: Bharanidharan N. , Rajaguru Harikumar 
Published: February 2020

AbstractThe objective of this research paper is to categorize the magnetic resonance imaging (MRI) images as demented (DEM) or nondemented (ND) using improved chicken swarm optimization technique (ICSO). In literature, CSO technique is widely used to solve numerical optimization and feature selection problem. Using this optimization technique for medical image classification problem will be a pioneering idea. If this technique is directly used to classify the medical images, it provides poor results. Hence, appropriate enhancements are made on the original algorithm using a novel controlled randomness optimization algorithm and control parameter tuning. Cross‐over and Rooster selection methods are also implemented in cascaded manner for further performance improvization. All the experiments are made for two cases: with and without statistical features. The brain MRI images of 65 ND and 52 DEM subjects obtained from the Open Access Series of Imaging Studies website are used in this analysis. The ICSO without statistical features provides the highest accuracy of 86.32%, whereas the original chicken swarm optimization technique provides the accuracy of 52.13% and 52.99% with and without statistical features, respectively.
Electrically conductive materials for in vitro cardiac microtissue engineering
Authors: Baei Payam , Hosseini Mahya , Baharvand Hossein , Pahlavan Sara 
Published: February 2020

AbstractCardiac tissue engineering, a fairly new concept in cardiovascular research, could substantially improve our success in both in vitro modeling of cardiac microtissue and in vivo cardiac regenerative medicine. To a large extent, this success was attributed to mechanical as well as electrical properties of cardiac‐designated biomaterials which inherit the fundamental characteristics of a native myocardial extracellular matrix. Large efforts have been made toward designation and construction of these scaffolds which paved the way for more natural‐like biomaterials. As an important characteristic, electrical conductivity has grabbed special attention, thus opening up a whole new area of research to achieve the best biomaterial. Electroconductive scaffolds have benefitted from both incorporation of conductive particles in polymeric matrix and fabrication of organic conductive polymers which supported cardiac tissue engineering. However, conductive scaffolds have not yet achieved full success and more work is required to obtain the optimal conductivity with highest similarity to the native heart for in vitro cardiac microtissue engineering.
Definitions and determinants of audit quality
Authors: Dresdner Hana , Fischer Dov 
Published: February 2020

AbstractBased on a review of the academic literature, we define audit quality from the perspectives of auditors and investors. We then discuss historical events that have impacted audit quality, including the effects of Sarbanes–Oxley; Public Company Accounting Oversight Board's restriction on auditor‐provided tax services; mandatory audit partner rotation; and the merger of Price Waterhouse and Coopers & Lybrand.
Pelvic morphology medial to the femoral head center predicts anterior coverage and range of motion after curved periacetabular osteotomy
Authors: Kamenaga Tomoyuki , Hayashi Shinya , Hashimoto Shingo , Fukuda Koji , Takayama Koji , Tsubosaka Masanori , Takashima Yoshinori , Niikura Takahiro , Kuroda Ryosuke , Matsumoto Tomoyuki 
Published: February 2020

AbstractThis study observed anterior coverage extent after lateral rotation of the acetabulum, without anterior or posterior rotation, during curved periacetabular osteotomy by three‐dimensional simulation, and determined if preoperative pelvic morphology affects postoperative anterior coverage and range of motion. Thirty patients scheduled for consecutive primary curved periacetabular osteotomy for developmental hip dysplasia at our hospital between 2016 and 2017 were included. Virtual acetabular osteotomies were performed to achieve a postoperative lateral center‐edge angle of 30°. We measured anterior center‐edge angles before curved periacetabular osteotomy through the medial one‐third and one‐quarter of the femoral head as an index reflecting the pelvic morphology medial to the femoral head center. The range of motion simulation was performed after virtual curved periacetabular osteotomy. Single linear regression analysis was performed to examine correlations between preoperative pelvic morphology parameters and anterior center‐edge angles after virtual osteotomy. Furthermore, linear regression analysis was used to assess correlations between center‐edge angles and simulated range of motions (P < .05). Anterior center‐edge angle after virtual osteotomy was more strongly correlated with the anterior center‐edge angle through the medial one‐third (r = .92, P < .0001) and one‐quarter (r = .84, P < .0001) of the femoral head. Flexion angle and internal rotation at 90° flexion showed significant correlations with anterior center‐edge angle through the medial one‐third (r = −.62, P = .0003; r = −.57, P = .001) and one‐quarter (r = −.60, P = .0005; r = −.55, P = .002) of the femoral head and anterior center‐edge angle after virtual osteotomy (r = −.67, P = .0005; r = −.62, P = .0003). Measuring preoperative parameters reflecting pelvic morphology enables surgeons to predict postoperative anterior coverage and range of motion in curved periacetabular osteotomy cases.
Effects of exogenous compound sprays on cherry cracking: skin properties and gene expression
Authors: Correia Sofia , Santos Marlene , Glińska Sława , Gapińska Magdalena , Matos Manuela , Carnide Valdemar , Schouten Rob , Silva Ana Paula , Gonçalves Berta 
Published: February 2020

AbstractBACKGROUNDCherry fruit cracking is a costly problem for cherry growers. The effect of repeated sprayings (gibberellic acid – GA3; abscisic acid – ABA; salicylic acid – SA; glycine betaine – GB, and Ascophyllum nodosum – AN) combined with CaCl2, on ‘Sweetheart’ cherry fruit‐cracking characteristics was investigated. Cracking was quantified in terms of cracking incidence, crack morphology, confocal scanning laser microscopy, cuticular wax content, cell‐wall modification, and cuticular wax gene expression.RESULTSAll spray treatments reduced cracking compared with an untreated control (H2O), with fewer cheek cracks. The least cracking incidence was observed for ABA + CaCl2‐ and GB + CaCl2‐treated fruits, indicating an added benefit compared to spraying with CaCl2 alone. In addition, GB + CaCl2‐treated fruits showed higher fruit diameter. ABA + CaCl2 and GB + CaCl2 sprays showed higher wax content and higher cuticle and epidermal thickness compared with the control, including increased expression of wax synthase (ABA + CaCl2) and expansin 1 (GB + CaCl2).CONCLUSIONIn general, factors that improve the cuticle thickness appear to be important at the fruit‐coloring stage. At the fruit‐ripening stage, larger cell sizes of the epidermis, hypodermis, and parenchyma cells lower cracking incidence, indicating the importance of flexibility and elasticity of the epidermis. © 2020 Society of Chemical Industry
Simultaneous determination of six alkaloids in tobacco and tobacco products by direct analysis of real‐time triple quadrupole mass spectrometry with a modified pretreatment method
Authors: Li Chao , Li E'xian , Ma Ming , Liu Xiuming , You Junheng , Wu Yiqin , Jiang Wei , Liu Zhihua , Qin Yunhua 
Published: February 2020

AbstractIn order to determine six alkaloids (mass fraction) of nicotine, nornicotine, myosmine, anatabine, anabasine, and nicotyrine in tobacco and tobacco products quickly, accurately, and simultaneously, a novel method based on direct analysis of real‐time model in situ ionization technique combined tandem mass spectrometry with a modified sample pretreatment was established, in which experimental parameters such as the type and amount of extraction solvent and injection rate were optimized, respectively. The samples of five commercial cigarettes and five kinds of tobacco leaves were analyzed by the established method, and the determined values were compared with those obtained using a gas chromatography with mass spectrometry method: (1) Under optimized conditions (30 mL ultrapure water as extraction solvent and with extraction rate of 0.6 mm/s), analysis could be completed within 10 min. (2) The linear range of the method was 0.002–2000 μg/g with, the recovery ranged from 86.8 to 105.6%, and the limit of detection and the limit of quantification were 0.004–0.835 μg/g and 0.013–2.787 μg/g, respectively. (3) The relative standard deviation between direct analysis of real‐time method and the gas chromatography with mass spectrometry method was 0.34–8.83%. The established method is rapid, reliable, and suitable for the ultrafast determination of six alkaloids in tobacco and tobacco products.
Mental Health and Dysphonia: Which Comes First, and Does That Change Care Utilization?
Authors: Jordan Victoria A. , Cohen Seth , Lunos Scott , Horvath Keith J. , Sieger Gretchen , Misono Stephanie 
Published: February 2020

ObjectivesVoice patients with voice disorders have a high prevalence of distress and mental health (MH) comorbidities, but it is unknown to what extent distress precedes or follows voice disorder diagnoses. Objectives were to compare 1) proportions of voice patients with MH diagnoses who received MH diagnoses first versus voice‐related diagnoses first, 2) voice‐related diagnoses and care utilization, and 3) time to specialty evaluation in each group.MethodsPatients with voice and MH diagnoses were identified using International Classification of Diseases, Ninth and Tenth Revisions codes in a large health system data repository from January 2005 through July 2017. Sociodemographics, comorbidities, MH‐ and voice‐related diagnoses, and voice‐related care utilization were analyzed using descriptive statistics and multivariable regression modeling.ResultsAmong the 11,419 patients with both voice and MH diagnoses, 63% (n = 7,251) received MH diagnoses prior to voice diagnoses, compared with 37% with a voice diagnosis first (P < 0.0001). The latter group received more specific voice‐related diagnoses (e.g., laryngeal cancer [odds ratio (OR) 4.27], benign laryngeal neoplasm [OR 1.60]), and were more likely to ever see an otolaryngologist than those receiving MH diagnoses first (P < 0.0001).ConclusionMost patients with voice and MH diagnoses received a MH diagnosis first. Patients who receive MH diagnoses first appeared to have different voice‐related healthcare compared to those who received voice diagnoses first.Level of EvidenceNALaryngoscope, 130:1243–1248, 2020
Lysosome and Inflammatory Defects in GBA1‐Mutant Astrocytes Are Normalized by LRRK2 Inhibition
Authors: Sanyal Anwesha , DeAndrade Mark P. , Novis Hailey S. , Lin Steven , Chang Jianjun , Lengacher Nathalie , Tomlinson Julianna J. , Tansey Malú G. , LaVoie Matthew J. 
Published: February 2020

AbstractBackgroundAutosomal recessive mutations in the glucocerebrosidase gene, Beta‐glucocerebrosidase 1 (GBA1), cause the lysosomal storage disorder Gaucher's disease. Heterozygous carriers of most GBA1 mutations have dramatically increased Parkinson's disease (PD) risk, but the mechanisms and cells affected remain unknown. Glucocerebrosidase expression is relatively enriched in astrocytes, yet the impact of its mutation in these cells has not yet been addressed.ObjectivesEmerging data supporting non‐cell‐autonomous mechanisms driving PD pathogenesis inspired the first characterization of GBA1‐mutant astrocytes. In addition, we asked whether LRRK2, likewise linked to PD and enriched in astrocytes, intersected with GBA1 phenotypes.MethodsUsing heterozygous and homozygous GBA1 D409V knockin mouse astrocytes, we conducted rigorous biochemical and image‐based analyses of lysosomal function and morphology. We also examined basal and evoked cytokine response at the transcriptional and secretory levels.ResultsThe D409V knockin astrocytes manifested broad deficits in lysosomal morphology and function, as expected. This, however, is the first study to show dramatic defects in basal and TLR4‐dependent cytokine production. Albeit to different extents, both the lysosomal dysfunction and inflammatory responses were normalized by inhibition of LRRK2 kinase activity, suggesting functional intracellular crosstalk between glucocerebrosidase and LRRK2 activities in astrocytes.ConclusionsThese data demonstrate novel pathologic effects of a GBA1 mutation on inflammatory responses in astrocytes, indicating the likelihood of broader immunologic changes in GBA‐PD patients. Our findings support the involvement of non‐cell‐autonomous mechanisms contributing to the pathogenesis of GBA1‐linked PD and identify new opportunities to correct these changes with pharmacological intervention. © 2020 International Parkinson and Movement Disorder Society
Inclusion‐body myositis and primary Sjögren syndrome: mechanisms for shared etiologies
Authors: Limaye Vidya S. , Cash Kathy , Smith Caroline , Koszyca Barbara , Patel Sandy , Greenberg Steven A. , Hissaria Pravin 
Published: February 2020

AbstractHerein we report a case of sporadic inclusion‐body myositis (sIBM) occurring at an unusually young age in a patient with primary Sjögren syndrome, and use the case to explore possible shared mechanisms for disease susceptibility. Possible factors may include the association of both conditions with the 8.1 ancestral haplotype; the presence of anti‐cN1A antibodies, which, although considered specific for sIBM, are also seen in pSS; and the shared association with T‐cell large granular lymphocyte leukemia (T‐LGLL). Further evaluation of this patient did in fact reveal underlying T‐LGLL and mechanisms by which T cells in sIBM may escape immune regulation and contribute to disease phenotype are explored. Despite myofiber infiltration with CD8‐positive T cells in sIBM, and, although sIBM is traditionally considered treatment‐refractory, we report a significant response to the anti‐CD20 monoclonal antibody, rituximab, and discuss possible mechanisms by which this response may be mediated.
Aclonifen targets solanesyl diphosphate synthase, representing a novel mode of action for herbicides
Authors: Kahlau Sabine , Schröder Florian , Freigang Jörg , Laber Bernd , Lange Gudrun , Passon Daniel , Kleeßen Sabrina , Lohse Marc , Schulz Arno , von Koskull‐Döring Pascal , Klie Sebastian , Gille Sascha 
Published: February 2020

AbstractBACKGROUNDAclonifen is a unique diphenyl ether herbicide. Despite its structural similarities to known inhibitors of the protoporphyrinogen oxidase (e.g. acifluorfen, bifenox or oxadiazon), which result in leaf necrosis, aclonifen causes a different phenotype that is described as bleaching. This also is reflected by the Herbicide Resistance Action Committee (HRAC) classification that categorizes aclonifen as an inhibitor of pigment biosynthesis with an unknown target.RESULTSA comprehensive Arabidopsis thaliana RNAseq dataset comprising 49 different inhibitor treatments and covering 40 known target pathways was used to predict the aclonifen mode of action (MoA) by a random forest classifier. The classifier predicts for aclonifen a MoA within the carotenoid biosynthesis pathway similar to the reference compound norflurazon that inhibits the phytoene desaturase. Upon aclonifen treatment, the phytoene desaturation reaction is disturbed, resulting in a characteristic phytoene accumulation in vivo. However, direct enzyme inhibition by the herbicide was excluded for known herbicidal targets such as phytoene desaturase, 4‐hydroxyphenylpyruvate dioxygenase and homogentisate solanesyltransferase. Eventually, the solanesyl diphosphate synthase (SPS), providing one of the two homogentisate solanesyltransferase substrate molecules, could be identified as the molecular target of aclonifen. Inhibition was confirmed using biochemical activity assays for the A. thaliana SPSs 1 and 2. Furthermore, a Chlamydomonas reinhardtii homolog was used for co‐crystallization of the enzyme–inhibitor complex, showing that one inhibitor molecule binds at the interface between two protein monomers.CONCLUSIONSolanesyl diphosphate synthase was identified as the target of aclonifen, representing a novel mode of action for herbicides. © 2020 Society of Chemical Industry