bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human attention‐inspired volume reconstruction method on serial section electron microscopy images
Authors: Zhou Fangxu , Shen Lijun , Chen Bohao , Chen Xi , Hua Han 
Published: March 2021

AbstractThe alignment of a 2D microscopic image stack to create a 3D image volume is an indispensable aspect of serial section electron microscopy (EM) technology, which could restore the original 3D integrity of biological tissues destroyed by chemical fixation and physical dissection. However, due to the similar texture intrasection and complex variations intersections of neural images, previous registration methods usually failed to yield reliable correspondences. And this also led to misalignment and impeded restoring the z‐axis anatomical continuity of the neuron volume. In this article, inspired by human behaviors in finding correspondences, which use the topological relationship of image contents, we developed a spatial attention‐based registration method for serial EM images to improve registration accuracy. Our approach combined the U‐Net framework with spatial transformer networks (STN) to regress corresponding transformation maps in an unsupervised training fashion. The spatial attention (SA) module was incorporated into the U‐Net architecture to increase the distinctiveness of image features by modeling its topological relationship. Experiments are conducted on both simulated and real data sets (MAS and RegCremi). Quantitative and qualitative comparisons demonstrate that our approach results in state of art accuracy (using the evaluation index of NCC, SSIM, Dice, Landmark error) and providing smooth and reliable transformation with less texture blur and unclear boundary than existing techniques. Our method is able to restore image stacks for visualization and quantitative analysis of EM image sequences.
Investigation of fabrication conditions for VO2 thin films by MOD using carbon thermal reduction
Authors: Fujishiro Yuhi , Kawahara Masami , Samura Tsuyoshi , Tachiki Takashi , Uchida Takashi 
Published: March 2021

AbstractVanadium dioxide (VO2) thin films were fabricated by metal‐organic decomposition (MOD). To utilize a carbon thermal reduction for obtaining a VO2 composition, the precursor films were fabricated at the temperature Tp from 300°C to 380°C in a N2 atmosphere. From the measurement results of XRD, diffraction peaks indicating VO2 phase were observed with a wide range of firing temperatures from Tf = 560°C to 620°C. Furthermore, the peaks indicating VO2 phase were also observed with a wide range of firing time from tf = 15–45 min. Regarding the surface morphology of the films, the nanoparticles of 100–200 nm were densely packed although small spaces existed between the particles. The R‐T characteristics of the films indicated the phase transition with a rapid resistance change of about three orders of magnitude and hysteresis loop. From these experimental results, it was found that wide windows of firing conditions for fabricating VO2 thin film can be obtained in the MOD process using the carbon thermal reduction.
Low spatial autocorrelation in mountain biodiversity data and model residuals
Authors: Chevalier Mathieu , Mod Heidi , Broennimann Olivier , Di Cola Valeria , Schmid Sarah , Niculita‐Hirzel Hélène , Pradervand Jean‐Nicolas , Schmidt Benedikt R. , Ursenbacher Sylvain , Pellissier Loïc , Guisan Antoine 
Published: March 2021

AbstractSpatial autocorrelation (SAC) is a common feature of ecological data where observations tend to be more similar at some geographic distance(s) than expected by chance. Despite the implications of SAC for data dependencies, its impact on the performance of species distribution models (SDMs) remains controversial, with reports of both strong and negligible impacts on inference. Yet, no study has comprehensively assessed the prevalence and the strength of SAC in the residuals of SDMs over entire geographic areas. Here, we used a large‐scale spatial inventory in the western Swiss Alps to provide a thorough assessment of the importance of SAC for (1) 850 species belonging to nine taxonomic groups, (2) six predictors commonly used for modeling species distributions, and (3) residuals obtained from SDMs fitted with two algorithms with the six predictors included as covariates. We used various statistical tools to evaluate (1) the global level of SAC, (2) the spatial pattern and spatial extent of SAC, and (3) whether local clusters of SAC can be detected. We further investigated the effect of the sampling design on SAC levels. Overall, while environmental predictors expectedly displayed high SAC levels, SAC in biodiversity data was rather low overall and vanished rapidly at a distance of ~5–10 km. We found low evidence for the existence of local clusters of SAC. Most importantly, model residuals were not spatially autocorrelated, suggesting that inferences derived from SDMs are unlikely to be affected by SAC. Further, our results suggest that the influence of SAC can be reduced by a careful sampling design. Overall, our results suggest that SAC is not a major concern for rugged mountain landscapes.
CD5 levels define functionally heterogeneous populations of naïve human CD4+ T cells
Authors: Sood Aditi , Lebel Marie‐Ève , Dong Mengqi , Fournier Marilaine , Vobecky Suzanne J. , Haddad Élie , Delisle Jean‐Sébastien , Mandl Judith N. , Vrisekoop Nienke , Melichar Heather J. 
Published: March 2021

AbstractStudies in murine models show that subthreshold TCR interactions with self‐peptide are required for thymic development and peripheral survival of naïve T cells. Recently, differences in the strength of tonic TCR interactions with self‐peptide, as read‐out by cell surface levels of CD5, were associated with distinct effector potentials among sorted populations of T cells in mice. However, whether CD5 can also be used to parse functional heterogeneity among human T cells is less clear. Our study demonstrates that CD5 levels correlate with TCR signal strength in human naïve CD4+ T cells. Further, we describe a relationship between CD5 levels on naïve human CD4+ T cells and binding affinity to foreign peptide, in addition to a predominance of CD5hi T cells in the memory compartment. Differences in gene expression and biases in cytokine production potential between CD5lo and CD5hi naïve human CD4+ T cells are consistent with observations in mice. Together, these data validate the use of CD5 surface levels as a marker of heterogeneity among human naïve CD4+ T cells with important implications for the identification of functionally biased T‐ cell populations that can be exploited to improve the efficacy of adoptive cell therapies.
Rhodium‐Catalyzed [3+2]‐Annulation of ortho‐Diazoquinones with Enol Ethers: Diversity‐Oriented Total Synthesis of Aflatoxin B2
Authors: Paymode Dinesh J. , Sharma Indrajeet 
Published: March 2021

AbstractA simple and efficient approach for synthesizing substituted and fused polycyclic 2,3‐dihydrobenzofurans has been developed through a Rh‐catalyzed [3+2]‐annulation of ortho‐diazoquinones with enol ethers. This methodology has a broad substrate scope and has been employed for the concise total synthesis of natural product aflatoxin B2.
Bioaccumulation, Metabolism, and Biomarker Responses in Hyriopsis cumingii Exposed to 4-Mono-Chlorinated Dibenzothiophene
Authors: Zhu Ziqing , Shi Jiaqi , Huang Xinxin , Zhang Xuesheng , Li Yucheng , Qin Li , Zhang Rui , Liu Bingxiang 
Published: March 2021

Abstract
Polychlorinated dibenzothiophenes (PCDTs) are sulfur analogues of polychlorinated dibenzofurans with prevalent occurrence in aquatic environments and potential ecological risks. However, data on the behavior and toxicity of PCDTs in aquatic organisms remain scarce. In the present study, the bioaccumulation, metabolism, and oxidative damage of 4-mono-chlorinated dibenzothiophene (4-mono-CDT) in freshwater mussel (Hyriopsis cumingii) were investigated after exposure to 4-mono-CDT in semistatic water. The uptake rates, depuration rates, half-lives, and bioconcentration factors of 4-mono-CDT in hepatopancreas, gill, and muscle tissues ranged from 0.492 to 1.652 L d−1 g−1 dry weight, from 0.117 to 0.308 d−1, from 2.250 to 5.924 d, and from 2.903 to 8.045 × 103 L kg−1 dry weight, respectively. A dechlorinated metabolite (dibenzothiophene) was detected in hepatopancreas tissue, indicating that dechlorination was the main metabolic pathway of 4-mono-CDT. As the exposure time increased, the activities of superoxide dismutase, catalase, and glutathione peroxidase were induced or inhibited in the different experimental groups. The malondialdehyde content increased with increasing 4-mono-CDT dose and exposure time. A higher concentration of 4-mono-CDT corresponded to a greater integrated biomarker response in each tissue and greater oxidative damage. The antioxidant enzymes in hepatopancreas were more sensitive to 4-mono-CDT than those in gill. The results provide useful information on the behavior and ecotoxicity of PCDTs in freshwater mussels. Environ Toxicol Chem 2021;40:1871–1880. © 2021 SETAC
Abstract
4-mono-chlorinated dibenzothiophene accumulated in mussel and a dechlorinated metabolite was detected in mussel hepatopancreas. Moreover, it could trigger tissue oxidative damage. SOD = superoxide dismutase; CAT = catalase; GPx = glutathione peroxidase; MDA = malondialdehyde; IBR = integrated biomarker response.
Reproducing diabetic retinopathy features using newly developed human induced‐pluripotent stem cell‐derived retinal Müller glial cells
Authors: Couturier Aude , Blot Guillaume , Vignaud Lucile , Nanteau Céline , Slembrouck‐Brec Amélie , Fradot Valérie , Acar Niyazi , Sahel José‐Alain , Tadayoni Ramin , Thuret Gilles , Sennlaub Florian , Roger Jerome E , Goureau Olivier , Guillonneau Xavier , Reichman Sacha 
Published: March 2021

AbstractMuller glial cells (MGCs) are responsible for the homeostatic and metabolic support of the retina. Despite the importance of MGCs in retinal disorders, reliable and accessible human cell sources to be used to model MGC‐associated diseases are lacking. Although primary human MGCs (pMGCs) can be purified from post‐mortem retinal tissues, the donor scarcity limits their use. To overcome this problem, we developed a protocol to generate and bank human induced pluripotent stem cell‐derived MGCs (hiMGCs). Using a transcriptome analysis, we showed that the three genetically independent hiMGCs generated were homogeneous and showed phenotypic characteristics and transcriptomic profile of pMGCs. These cells expressed key MGC markers, including Vimentin, CLU, DKK3, SOX9, SOX2, S100A16, ITGB1, and CD44 and could be cultured up to passage 8. Under our culture conditions, hiMGCs and pMGCs expressed low transcript levels of RLPB1, AQP4, KCNJ1, KCJN10, and SLC1A3. Using a disease modeling approach, we showed that hiMGCs could be used to model the features of diabetic retinopathy (DR)‐associated dyslipidemia. Indeed, palmitate, a major free fatty acid with elevated plasma levels in diabetic patients, induced the expression of inflammatory cytokines found in the ocular fluid of DR patients such as CXCL8 (IL‐8) and ANGPTL4. Moreover, the analysis of palmitate‐treated hiMGC secretome showed an upregulation of proangiogenic factors strongly related to DR, including ANG2, Endoglin, IL‐1β, CXCL8, MMP‐9, PDGF‐AA, and VEGF. Thus, hiMGCs could be an alternative to pMGCs and an extremely valuable tool to help to understand and model glial cell involvement in retinal disorders, including DR.
A Dynamic Aspartate‐to‐Alanine Aminotransferase Ratio Provides Valid Predictions of Incident Severe Liver Disease
Authors: Åberg Fredrik , Danford Christopher J. , Thiele Maja , Talbäck Mats , Rasmussen Ditlev Nytoft , Jiang Z. Gordon , Hammar Niklas , Nasr Patrik , Ekstedt Mattias , But Anna , Puukka Pauli , Krag Aleksander , Sundvall Jouko , Erlund Iris , Salomaa Veikko , Stål Per , Kechagias Stergios , Hultcrantz Rolf , Lai Michelle , Afdhal Nezam , Jula Antti , Männistö Satu , Lundqvist Annamari , Perola Markus , Färkkilä Martti , Hagström Hannes 
Published: March 2021

The aspartate‐to‐alanine aminotransferase ratio (AAR) is associated with liver fibrosis, but its predictive performance is suboptimal. We hypothesized that the association between AAR and liver disease depends on absolute transaminase levels and developed and validated a model to predict liver‐related outcomes in the general population. A Cox regression model based on age, AAR, and alanine aminotransferase (ALT) level (dynamic AAR [dAAR]) using restricted cubic splines was developed in Finnish population‐based health‐examination surveys (FINRISK, 2002‐2012; n = 18,067) with linked registry data for incident liver‐related hospitalizations, hepatocellular carcinoma, or liver death. The model was externally validated for liver‐related outcomes in a Swedish population cohort (Swedish Apolipoprotein Mortality Risk [AMORIS] subcohort; n = 126,941) and for predicting outcomes and/or prevalent fibrosis/cirrhosis in biopsied patients with nonalcoholic fatty liver disease (NAFLD), chronic hepatitis C, or alcohol‐related liver disease (ALD). The dynamic AAR model predicted liver‐related outcomes both overall (optimism‐corrected C‐statistic, 0.81) and in subgroup analyses of the FINRISK cohort and identified persons with >10% risk for liver‐related outcomes within 10 years. In independent cohorts, the C‐statistic for predicting liver‐related outcomes up to a 10‐year follow‐up was 0.72 in the AMORIS cohort, 0.81 in NAFLD, and 0.75 in ALD. Area‐under‐the‐curve (AUC) for detecting prevalent cirrhosis was 0.80‐0.83 in NAFLD, 0.80 in hepatitis C, but only 0.71 in ALD. In ALD, model performance improved when using aspartate aminotransferase instead of ALT in the model (C‐statistic, 0.84 for outcome; AUC, 0.82 for prevalent cirrhosis). Conclusion: A dAAR score provides prospective predictions for the risk of incident severe liver outcomes in the general population and helps detect advanced liver fibrosis/cirrhosis. The dAAR score could potentially be used for screening the unselected general population and as a trigger for further liver evaluations.
Modelling interannual variations in catchment evapotranspiration considering vegetation and climate seasonality using the Budyko framework
Authors: Wang Yaqin , Luo Yi , Shafeeque Muhammad , Zhou Meilin , Li Hongyu 
Published: March 2021

AbstractThe Budyko framework is an efficient tool for investigating catchment water balance, focusing on the effects of seasonal changes in climate (S) and vegetation cover (M) on catchment evapotranspiration (ET). However, the effects of vegetation seasonality on ET remain largely unknown. The present study explored these effects by modelling interannual variations in ET considering vegetation and climate seasonality using the Budyko framework. Reconstructed 15‐day GIMMS NDVI3g timeseries data from 1982 to 2015 were used to estimate M and extract the relative duration of the vegetation growing season (GL) in the Yellow River Basin (YRB). To characterize S, seasonal variations in precipitation and potential ET were extracted using a Gaussian algorithm. Analysis of the observed datasets for 19 catchments revealed that interannual variation in the catchment parameter ϖ (in Fuh's equation) was significantly and positively correlated with M and GL. Conversely, ϖ was significantly but negatively correlated with S. Furthermore, stepwise linear regression was used to calibrate the empirical formula of ϖ for these three dimensionless parameters. Following validation, based on observations in the remaining 11 catchments, ϖ was integrated into Fuh's equation to accurately estimate annual ET. Over 79% subcatchments showed an upward trend (0.9 mm yr−1), whereas fewer than 21% subcatchments showed a downward trend (−0.5 mm yr−1) across YRB. In the central region of the middle reach, ET increased with increased M, prolonged GL, and decreased S, whereas in the source region of YRB, ET decreased with decreased M and shortened GL. Our study provides an alternative method to estimate interannual ET in ungauged catchments and offers a novel perspective to investigate hydrological responses to vegetation and climate seasonality in the long‐term.
Mycorrhizal stress alleviation in Senecio bonariensis Hook & Arn growing in urban polluted soils
Authors: Bompadre María Josefina , Benavidez Matías , Colombo Roxana Paula , Silvani Vanesa Analía , Godeas Alicia Margarita , Scotti Adalgisa , Pardo Alejandro Guillermo , Fernández Bidondo Laura 
Published: March 2021

AbstractLoss of biodiversity and accumulation of contaminants in urban soils and water bodies cause serious issues in metropolitan areas. The Matanza‐Riachuelo river basin (metropolitan area of Buenos Aires, Argentina) is one of the most environmentally degraded regions in the world. Senecio bonariensis Hook & Arn (Asteraceae) grows in the periodically flooded soils of this wetland. This plant concentrates potentially toxic trace elements (PTEs) in its tissues and establishes symbiosis with arbuscular mycorrhizal (AM) fungi that collaborate with PTE phytostabilization in soils. The objective of this work was to evaluate tolerance and stress alleviation of AM‐colonized S. bonariensis when transplanting and exposing to highly polluted environmental conditions of the river basin. Plants were initially inoculated with different AM strains and maintained in greenhouse conditions. After 6 mo, they were transplanted to the field. These plants showed a more equal distribution between shoot and root biomass production in comparison to field spontaneous S. bonaerensis plants. Plants in earlier contact with native soil inoculum showed positive correlation with phosphorus content and a significant increase of vesicle frequency. Plants belatedly contacted with native inoculum in the field (control) showed a higher catalase level that was positively correlated with the total colonization frequency and chlorophyll content. The ability to establish symbiosis with Rhizophagus intraradices (strain GC3), commonly used in the formulation of biofertilizers, was also analyzed. Plants inoculated with GC3 at the beginning of the assay showed lower colonization and were less efficient in the field. The preservation of spontaneous native plants with ornamental value and bioaugmentation of their associated microbiome can contribute to the stabilization of contaminants in soils.
Neutrophil-derived extracellular vesicles modulate the phenotype of naïve human neutrophils
Authors: Amjadi Maya F , Avner Benjamin S , Greenlee-Wacker Mallary C , Horswill Alexander R , Nauseef William M 
Published: March 2021

AbstractNeutrophils (PMN) regulate inflammation in many ways, including communication with other immune cells via extracellular vesicles (EVs). EVs released by human neutrophils activated with N-formylmethionyl-leucyl-phenylalanine (fMLF) (PMN-fMLF EVs) had an outside-out orientation and contained functionally important neutrophil plasma membrane proteins, including flavocytochrome b558, and enzymatically active granule proteins, elastase, and myeloperoxidase. Treatment of naïve PMN with PMN-fMLF EVs primed fMLF-stimulated NADPH oxidase activity, increased surface expression of the complement receptors CD11b/CD18 and CD35, the specific granule membrane protein CD66, and flavocytochrome b558, and promoted phagocytosis of serum-opsonized Staphylococcus aureus. The primed oxidase activity reflected increased surface expression of flavocytochrome b558 and phosphorylation of SER345 in p47phox, two recognized mechanisms for oxidase priming. Taken together, these data demonstrate that stimulated PMN released EVs that altered the phenotype of naïve phagocytes by priming of the NADPH oxidase activity and augmenting phagocytosis, two responses that are integral to optimal PMN host defense.
Systematic inhibitor selectivity between PARP1 and PARP2 enzymes: Molecular implications for ovarian cancer personalized therapy
Authors: Zuo Xueqian , Zhao Haibo , Li Dan 
Published: March 2021

AbstractHuman poly(ADP‐ribose) polymerases (PARPs) are a class of nuclear enzymes involved in the pathogenesis of diverse gynecologic tumors. The PARP1 and PARP2 are the two most documented members in PARP family, which have been approved as the druggable targets of ovarian and cervical cancers. Selective targeting of the two enzymes with small‐molecule inhibitors is a great challenge due to the high conservation in catalytic domain and active site. Here, we investigate the systematic selectivity profile of sophisticated PARP inhibitors between the two enzymes. Computational methods are used to model/optimize the complex structures of inhibitor ligands with PARP1/2 catalytic domains and then to estimate the theoretical Fenzymatic assays exhibit a good consistence with theoretical selectivity over six tested inhibitor samples (rc2 = 0.857). It is revealed that the inhibitor selectivity is conferred from the exquisite difference in the residue composition and structural architecture of both the local activity sites and the whole catalytic domains of the two enzymes. In particular, the TMZ50 and ME0328 show strong selectivity between PARP1 and PARP2, but only the former has a potent activity on the two enzymes, whereas the latter can only inhibit the enzymes moderately. These compounds can be considered as potential lead molecular entities to develop new specific PARP‐selective inhibitor drugs for personalized therapy combating gynecologic cancers.
Radiomics Models Based on Apparent Diffusion Coefficient Maps for the Prediction of High‐Grade Prostate Cancer at Radical Prostatectomy: Comparison With Preoperative Biopsy
Authors: Han Chao , Ma Shuai , Liu Xiang , Liu Yi , Li Changxin , Zhang Yaofeng , Zhang Xiaodong , Wang Xiaoying 
Published: March 2021

BackgroundIt is feasible to use magnetic resonance (MR)‐based radiomics to distinguish high‐grade from low‐grade prostate cancer (PCa), but radiomics model performance based on fully automated segmentation remains unknown.PurposeTo develop and test radiomics models based on manually or automatically gained masks on apparent diffusion coefficient (ADC) maps to predict high‐grade (Gleason score ≥ 4 + 3) PCa at radical prostatectomy (RP).Study TypeRetrospective.PopulationA total of 176 patients (94 high‐grade PCa and 82 low‐grade PCa) with complete RP, preoperative biopsy, and multiparametric magnetic resonance imaging (mpMRI) were retrospectively recruited and randomly divided into training (N = 123) and test (N = 53) cohorts.Field Strength/SequenceUsing a 3.0‐T MR scanner, ADC maps were calculated from diffusion‐weighted imaging (b values = 0, 1400 s/mm2, echo planar imaging).AssessmentTwo radiologists segmented the whole prostate gland and the most index prostate lesion. Automatic segmentation of the prostate and the lesion were performed. Four radiomics models were constructed using four masks (manual/automatic prostate gland/PCa lesion segmentation). According to the standard reference of the RP histopathologic assessment, the performance of each radiomics models was compared with that of biopsy and Prostate Imaging Reporting and Data System version 2.1 (PI‐RADS) assessment.Statistical TestsA receiver operating characteristic curve analysis was employed to estimate the area under the curve (AUC) values of the models. The AUCs of the four models, biopsy, and PI‐RADS assessment were compared using the DeLong test.ResultsThe four radiomics models yielded AUCs of 0.710, 0.731, 0.726, and 0.709 in the test cohort, respectively; biopsy and PI‐RADS assessment yielded AUCs of 0.793 and 0.680, respectively. No significant differences were found among model, biopsy, and PI‐RADS assessment comparisons (P = 0.132–0.988).Data ConclusionTo distinguish high‐grade from low‐grade PCa, radiomics models based on automatic segmentation on ADC maps exhibit approximately the same diagnostic efficacy as manual segmentation and biopsy, highlighting the possibility of a fully automatic workflow combining automated segmentation with radiomics analysis.Evidence Level4Technical EfficacyStage 2