bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Underwater Macroplastic Monitoring Using Echo Sounding
Authors: Broere Sophie , van Emmerik Tim , González-Fernández Daniel , Luxemburg Willem , de Schipper Matthieu , Cózar Andrés , van de Giesen Nick 
Published: July 2021

Plastics originating from land are mainly transported to the oceans by rivers. The total plastic transport from land to seas remains uncertain because of difficulties in measuring and the lack of standard observation techniques. A large focus in observations is on plastics floating on the water surface. However, an increasing number of observations suggest that large quantities of plastics are transported in suspension, below the water surface. Available underwater plastic monitoring methods use nets or fish traps that need to be deployed below the surface and are labor-intensive. In this research, we explore the use of echo sounding as an innovative low-cost method to quantify and identify suspended macroplastics. Experiments under controlled and natural conditions using a low-cost off-the-shelf echo sounding device show that plastic items can be detected and identified up to 7 m below the river surface. Eight different debris items (metal can, cup, bottles, food wrappers, food container) were characterized based on their reflection signature. Reflectance from plastic items diverged significantly from organic material and non-plastic anthropogenic debris. During a multi-day trial field expedition in the Guadalete river, Spain, we found that between 0.8 and 6.3 m depth considerable quantities of plastics are transported. As most plastic monitoring and removal strategies focus on the upper layer below the surface (up to approximately 1.5 m depth), a substantial share of the total plastic transport may be neglected. With this paper we 1) demonstrate that echo sounding is a promising tool for underwater plastic monitoring, and 2) emphasize the importance of an improved understanding of the existing plastic loads below the surface.
Long-Term Evolution of Greenhouse Gas Emissions From Global Reservoirs
Authors: Yan Xingcheng , Thieu Vincent , Garnier Josette 
Published: July 2021

The contribution of artificial reservoirs to greenhouse gas (GHG) emissions has been emphasized in previous studies. In the present study, we collected and updated data on GHG emission rates from reservoirs at the global scale, and applied a new classification method based on the hydrobelt concept. Our results showed that CH4 and CO2 emissions were significantly different in the hydrobelt groups (p &lt; 0.01), while no significant difference was found for N2O emissions, possibly due to their limited measurements. We found that annual GHG emissions (calculated as C or N) from global reservoirs amounted to 12.9 Tg CH4-C, 50.8 Tg CO2-C, and 0.04 Tg N2O-N. Furthermore, GHG emissions (calculated as CO2 equivalents) were also estimated for the 1950–2017 period based on the cumulative number and surface area of global reservoirs in the different hydrobelts. The highest increase rate in both the number of reservoirs and their surface area, which occurred from 1950 to the 1980s, led to an increase in GHG emissions from reservoirs. Since then, the increase rate of reservoir construction, and hence GHG emissions, has slowed down. Moreover, we also examined the potential impact of reservoir eutrophication on GHG emissions and found that GHG emissions from reservoirs could increase by 40% under conditions in which total phosphorus would double. In addition, we showed that the characteristics of reservoirs (e.g., geographical location) and their catchments (e.g., surrounding terrestrial net primary production, and precipitation) may influence GHG emissions. Overall, a major finding of our study was to provide an estimate of the impact of large reservoirs during the 1950–2017 period, in terms of GHG emissions. This should help anticipate future GHG emissions from reservoirs considering all reservoirs being planned worldwide. Besides using the classification per hydrobelt and thus reconnecting reservoirs to their watersheds, our study further emphasized the efforts to be made regarding the measurement of GHG emissions in some hydrobelts and in considering the growing number of reservoirs.
Prediction of BRCA Gene Mutation in Breast Cancer Based on Deep Learning and Histopathology Images
Authors: Wang Xiaoxiao , Zou Chong , Zhang Yi , Li Xiuqing , Wang Chenxi , Ke Fei , Chen Jie , Wang Wei , Wang Dian , Xu Xinyu , Xie Ling , Zhang Yifen 
Published: July 2021

BackgroundBreast cancer is one of the most common cancers and the leading cause of death from cancer among women worldwide. The genetic predisposition to breast cancer may be associated with a mutation in particular genes such as gene BRCA1/2. Patients who carry a germline pathogenic mutation in BRCA1/2 genes have a significantly increased risk of developing breast cancer and might benefit from targeted therapy. However, genetic testing is time consuming and costly. This study aims to predict the risk of gBRCA mutation by using the whole-slide pathology features of breast cancer H&amp;E stains and the patients’ gBRCA mutation status.MethodsIn this study, we trained a deep convolutional neural network (CNN) of ResNet on whole-slide images (WSIs) to predict the gBRCA mutation in breast cancer. Since the dimensions are too large for slide-based training, we divided WSI into smaller tiles with the original resolution. The tile-based classification was then combined by adding the positive classification result to generate the combined slide-based accuracy. Models were trained based on the annotated tumor location and gBRCA mutation status labeled by a designated breast cancer pathologist. Four models were trained on tiles cropped at 5×, 10×, 20×, and 40× magnification, assuming that low magnification and high magnification may provide different levels of information for classification.ResultsA trained model was validated through an external dataset that contains 17 mutants and 47 wilds. In the external validation dataset, AUCs (95% CI) of DL models that used 40×, 20×, 10×, and 5× magnification tiles among all cases were 0.766 (0.763–0.769), 0.763 (0.758–0.769), 0.750 (0.738–0.761), and 0.551 (0.526–0.575), respectively, while the corresponding magnification slides among all cases were 0.774 (0.642–0.905), 0.804 (0.676–0.931), 0.828 (0.691–0.966), and 0.635 (0.471–0.798), respectively. The study also identified the influence of histological grade to the accuracy of the prediction.ConclusionIn this paper, the combination of pathology and molecular omics was used to establish the gBRCA mutation risk prediction model, revealing the correlation between the whole-slide histopathological images and gRCA mutation risk. The results indicated that the prediction accuracy is likely to improve as the training data expand. The findings demonstrated that deep CNNs could be used to assist pathologists in the detection of gene mutation in breast cancer.
M1 Macrophage-Derived Nanovesicles Repolarize M2 Macrophages for Inhibiting the Development of Endometriosis
Authors: Li Qiuju , Yuan Ming , Jiao Xue , Huang Yufei , Li Jing , Li Dong , Ji Miaomiao , Wang Guoyun 
Published: July 2021

BackgroundEndometriosis is a common nonmalignant gynecological disorder that affects 10–15% women of reproductive age and causes several symptoms that result in decreased quality of life and a huge social burden. In recent decades, extracellular vesicles (EVs) have gained attention as a potential therapeutic tool; however, the therapeutic effects of EVs against endometriosis have not been reported. Accordingly, in this study, we investigated the feasibility of nanovesicles (NVs) derived from M1 macrophages (M1NVs) in treating endometriosis.MethodsM1NVs were prepared by serial extrusion. Co-culture assays were performed to investigate changes in tube formation and migration/invasion of eutopic endometrial stroma cells (ESCs) obtained from patients with endometriosis (EM-ESCs). A mouse model of endometriosis was established, and mice were treated with phosphate-buffered saline, M0NVs, or M1NVs to evaluate the efficacy and safety of M1NV for treating endometriosis.ResultsM1NVs directly or indirectly inhibited the migration and invasion of EM-ESCs and reduced tube formation. In the mouse model, M1NVs suppressed the development of endometriosis through reprogramming of M2 macrophages, without causing damage to the organs.ConclusionsM1NVs inhibit the development of endometriosis directly, or through repolarizing macrophages from M2 to M1 phenotype. Hence, administration of M1NVs may represent a novel method for the treatment of endometriosis.
Admission Systolic Blood Pressure and In-hospital Mortality in Acute Type A Aortic Dissection: A Retrospective Observational Study
Authors: Yang Guifang , Peng Wen , Zhou Yang , He Huaping , Pan Xiaogao , Li Xizhao , Chai Xiangping 
Published: July 2021

Background: Evidence between admission systolic blood pressure (SBP) and in-hospital deaths in acute type A aortic dissection (AAD) patients is inadequate. Here, we examined the relationship between SBP and in-hospital deaths in AAD patients.Methods: 703 AAD patients were enrolled from January 2014 to December 2018. The independent and dependent variables targeted were admission SBP and in-hospital deaths, respectively. Gender, age, body mass index (BMI), chronic renal insufficiency, smoking, hypertension, diabetes, laboratory indicators, and management were used as covariates.Results: The 703 participants had a mean age of 50.48 ± 11.35. About 76.24% of the participants were male. After adjusting for confounders, there was a negative correlation between AAD patients' admission SBP and in-hospital deaths (OR = 0.88, 95%CI 0.80–0.96). Consequently, a non-linear relationship of point 120 (mmHg) was detected between admission SBP and in-hospital deaths for AAD patients. Confidence intervals and effect sizes of the right (SBP &gt;120 mmHg) and left (SBP ≤ 120 mmHg) sides of the inflection point were 0.96 (0.85–1.09) and 0.67 (0.51–0.88), respectively. The change in the male population and non-diabetes people was more pronounced according to subgroup analysis.Conclusions: Correlation between admission SBP and in-hospital mortality of AAD patients is non-linear. SBP negatively correlated with in-hospital mortality when ≤120 mmHg.
Evaluation of Positive End-Expiratory Pressure Strategies in Patients With Coronavirus Disease 2019–Induced Acute Respiratory Distress Syndrome
Authors: Pan Chun , Lu Cong , She Xiaobin , Ren Haibo , Wei Huazhang , Xu Liang , Huang Yingzi , Xia Jia'an , Yu Yuetian , Chen Lu , Du Bin , Qiu Haibo 
Published: July 2021

Background: Different positive end-expiratory pressure (PEEP) strategies are available for subjects with coronavirus disease 2019 (COVID-19)–induced acute respiratory distress syndrome (ARDS) requiring invasive mechanical ventilation. We aimed to evaluate three conventional PEEP strategies on their effects on respiratory mechanics, gas exchanges, and hemodynamics.Methods: This is a prospective, physiologic, multicenter study conducted in China. We recruited 20 intubated subjects with ARDS and confirmed COVID-19. We first set PEEP by the ARDSnet low PEEP–fraction of inspired oxygen (FIO2) table. After a recruitment maneuver, PEEP was set at 15, 10, and 5 cm H2O for 10 min, respectively. Among these three PEEP levels, best-compliance PEEP was the one providing the highest respiratory system compliance; best-oxygenation PEEP was the one providing the highest PaO2 (partial pressure of arterial oxygen)/FIO2.Results: At each PEEP level, we assessed respiratory mechanics, arterial blood gas, and hemodynamics. Among three PEEP levels, plateau pressure, driving pressure, mechanical power, and blood pressure improved with lower PEEP. The ARDSnet low PEEP–FIO2 table and the best-oxygenation strategies provided higher PEEP than the best-compliance strategy (11 ± 6 cm H2O vs. 11 ± 3 cm H2O vs. 6 ± 2 cm H2O, p = 0.001), leading to higher plateau pressure, driving pressure, and mechanical power. The three PEEP strategies were not significantly different in gas exchange. The subgroup analysis showed that three PEEP strategies generated different effects in subjects with moderate or severe ARDS (n = 12) but not in subjects with mild ARDS (n = 8).Conclusions: In our cohort with COVID-19–induced ARDS, the ARDSnet low PEEP/FIO2 table and the best-oxygenation strategies led to higher PEEP and potentially higher risk of ventilator-induced lung injury than the best-compliance strategy.Clinical Trial Registration:www.ClinicalTrials.gov, identifier: NCT04359251.
Expression and Pathogenic Analysis of Integrin Family Genes in Systemic Sclerosis
Authors: Xu Dan , Li Ting , Wang Ruikang , Mu Rong 
Published: July 2021

Objectives: Emerging evidence shows that integrin members are involved in inflammation and fibrosis in systemic sclerosis (SSc). This study aimed at evaluating the expression of integrin family genes in the skin tissue from SSc patients and exploring the potential pathogenic mechanism.Methods: We utilized the public datasets of SSc skin tissue from the Gene Expression Omnibus (GEO) database to analyze the expression and clinical significance of integrin family genes in SSc. The expression of integrin members in skin tissue was also assessed by immunohistochemistry. In addition, functional enrichment and pathway analysis were conducted.Results: Compared with healthy controls, the mRNA and protein levels of ITGA5, ITGB2, and ITGB5 were upregulated in the skin of SSc patients. Further analysis indicated that the mRNA expression levels of ITGA5, ITGB2, and ITGB5 were positively correlated with modified Rodnan skin thickness score (mRSS). Functional enrichment and pathway analysis showed that integrin members may play multiple roles in the pathogenesis of SSc. Among them, ITGA5, ITGB2, and ITGB5 might synergistically promote SSc through affecting extracellular matrix (ECM) turnover, ECM–receptor interaction, focal adhesion, and leukocyte trans-endothelial migration, while ITGA5 and ITGB5 also might affect angiogenesis and endothelial cell function. In addition, ITGA5, ITGB2, and ITGA5 were associated with different pathways, respectively. ITGA5 was uniquely enriched for actin organization, while ITGB5 was for TGF-β signaling and ITGB2 for immune cell activation.Conclusion: Our results implied that the abnormal expression of integrin family genes including ITGA5, ITGB2, and ITGB5 may participate in multiple pathological processes in SSc. Further investigations are required for confirming this speculation.
Effect of Dietary Amylose/Amylopectin Ratio on Intestinal Health and Cecal Microbes’ Profiles of Weaned Pigs Undergoing Feed Transition or Challenged With Escherichia coli Lipopolysaccharide
Authors: Yang Can , Wang Min , Tang XiaoWu , Yang HuanSheng , Li FengNa , Wang YanCan , Li Jianzhong , Yin YuLong 
Published: July 2021

BackgroundDietary amylose/amylopectin ratio (DAR) plays an important role in piglets’ intestinal health. It is controversial whether diarrhea could be relieved by changing DAR in weaning piglets.MethodsSixty (Landrace × Yorkshire) castrated male pigs (initial body weight (BW) 6.51 ± 0.64 kg) were randomly allocated to five groups (one pig per cage and 12 replicates per group) according to their BW. Piglets received diets with different DARs (0.00, 0.20, 0.40, 0.60, and 0.80) for 29 days. Feed transition occurs at day 15. The piglets were challenged with lipopolysaccharides (Escherichia coliLPS, 100 μg/kg BW) on day 29 by intraperitoneal injection at 12 h before slaughter. Chyme was collected for pH value, short-chain fatty acid (SCFA), and cecal microbe analysis using 16S rRNA gene sequencing; mucosa was sampled for detecting gene expression.ResultsRate and degree of diarrhea were higher when DAR was 0.40 than when it was 0.20 and 0.80 during the third week (P&lt; 0.05). The chyme pH value in the cecum was higher (P&lt; 0.05) in 0.20 DAR than in 0.00 and 0.80 DARs, but with no significant difference compared with 0.40 and 0.60 DARs (P&gt; 0.05). Cecal isobutyric acid and isovaleric acid concentrations were higher in 0.20 than in other groups (P&lt; 0.01). Cecal SCFAs such as acetic acid, propionic acid, and total SCFA, concentrations were higher in 0.40 DAR than in 0.00, 0.60, and 0.80 DARs (P&lt; 0.05), but with no significant difference when compared with 0.20 (P&gt; 0.05). Cecal crypt depth was lower (P&lt; 0.05) in 0.80 than in other groups, but not 0.40. Claudin mRNA expression in the mucosa of the ileum was higher in 0.20 than in other groups (P&lt; 0.01). The alpha diversity of cecal microbe representative by goods coverage was higher in group 0.40 when compared with group 0.20 (P&lt; 0.05). At the genus level, the abundances of theRuminococcaceae_NK4A214_groupandAnaerotruncuswere higher but that ofCetobacteriumwas lower in the cecal chyme of group 0.20 than that of group 0.60 (P&lt; 0.05), with no significant difference compared with other groups (P&gt; 0.05). The diarrhea rate during the third week was negatively correlated with the abundances ofRikenellaceae_RC9_gut_groupandX.Eubacterium_coprostanoligenes_group(P&lt; 0.05).ConclusionCompared with diet high in amylose or amylopectin, diet with DAR 0.40 showed a worse degree of diarrhea in weaned piglets during feed transition. But the intestinal health will be improved the week after the microbes and metabolites are regulated by DAR.
The Role of Edema in Subacute Lesion Progression After Treatment of Acute Ischemic Stroke
Authors: Konduri Praneeta , van Kranendonk Katinka , Boers Anna , Treurniet Kilian , Berkhemer Olvert , Yoo Albert J. , van Zwam Wim , Oostenbrugge Robert van , van der Lugt Aad , Dippel Diederik , Roos Yvo , Bot Joost , Majoie Charles , Marquering Henk ,   the MR CLEAN Trial Investigators (Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands)
Published: July 2021

Background:Ischemic lesions commonly continue to progress even days after treatment, and this lesion growth is associated with unfavorable functional outcome in acute ischemic stroke patients. The aim of this study is to elucidate the role of edema in subacute lesion progression and its influence on unfavorable functional outcome by quantifying net water uptake.Methods:We included all 187 patients from the MR CLEAN trial who had high quality follow-up non-contrast CT at 24 h and 1 week. Using a CT densitometry-based method to calculate the net water uptake, we differentiated total ischemic lesion volume (TILV) into edema volume (EV) and edema-corrected infarct volume (ecIV). We calculated these volumes at 24 h and 1 week after stroke and determined their progression in the subacute period. We assessed the effect of 24-h lesion characteristics on EV and ecIV progression. We evaluated the influence of edema and edema-corrected infarct progression on favorable functional outcome after 90 days (modified Rankin Scale: 0–2) after correcting for potential confounders. Lastly, we compared these volumes between subgroups of patients with and without successful recanalization using the Mann–WhitneyU-test.Results:Median TILV increased from 37 (IQR: 18–81) ml to 68 (IQR: 30–130) ml between 24 h and 1 week after stroke, while the net water uptake increased from 22 (IQR: 16–26)% to 27 (IQR: 22–32)%. The TILV progression of 20 (8.8–40) ml was mostly caused by ecIV with a median increase of 12 (2.4–21) ml vs. 6.5 (2.7–15) ml of EV progression. Larger TILV, EV, and ecIV volumes at 24 h were all associated with more edema and lesion progression. Edema progression was associated with unfavorable functional outcome [aOR: 0.53 (0.28–0.94) per 10 ml;p-value: 0.05], while edema-corrected infarct progression showed a similar, non-significant association [aOR: 0.80 (0.62–0.99);p-value: 0.06]. Lastly, edema progression was larger in patients without successful recanalization, whereas ecIV progression was comparable between the subgroups.Conclusion:EV increases in evolving ischemic lesions in the period between 1 day and 1 week after acute ischemic stroke. This progression is larger in patients without successful recanalization and is associated with unfavorable functional outcome. However, the extent of edema cannot explain the total expansion of ischemic lesions since edema-corrected infarct progression is larger than the edema progression.
Platelet-to-Lymphocyte Ratio Is Associated With Favorable Response to Neoadjuvant Chemotherapy in Triple Negative Breast Cancer: A Study on 120 Patients
Authors: Lusho Sejdi , Durando Xavier , Mouret-Reynier Marie-Ange , Kossai Myriam , Lacrampe Nathalie , Molnar Ioana , Penault-Llorca Frederique , Radosevic-Robin Nina , Abrial Catherine 
Published: July 2021

IntroductionTriple negative breast cancer (TNBC) is highly heterogeneous, but still most of the patients are treated by the anthracycline/taxane-based neoadjuvant therapy (NACT). Tumor-infiltrating lymphocytes (TILs) are a strong predictive and prognostic biomarker in TNBC, however are not always available. Peripheral blood counts, which reflect the systemic inflammatory/immune status, are easier to obtain than TILs. We investigated whether baseline white cell or platelet counts, as well as, Neutrophil-to-Lymphocyte Ratio (NLR) or Platelet-to-Lymphocyte Ratio (PLR) could replace baseline TILs as predictive or prognostic biomarkers in a series of TNBC treated by standard NACT.Patients and MethodsOne hundred twenty patients uniformly treated by FEC/taxane NACT in a tertiary cancer care center were retrospectively analyzed. The presence of pathological complete response (pCR: ypT0/Tis, ypN0) or the presence of pCR and/small residual disease (ypT0/Tis/T1ab, ypN0) were considered as good responses in data analysis. Baseline/pre-NACT blood count, NLR, PLR and TILs were evaluated as predictors of response, distant recurrence rate and distant recurrence-free survival (DRFS).ResultsTILs ≥30% and ≥1.5% were best predictors of pCR and distant recurrence risk, respectively (p = 0.007, p = 0.012). However, in this cohort, pCR status was not significantly associated with recurrence. Only the ensemble of patients with pCR and small residual disease had lower recurrence risk and longer survival DRFS (p = 0.042, p = 0.024, respectively) than the rest of the cohort (larger residual disease). The only parameter which could predict the pCR/small residual disease status was PLR: patients with values lower than 133.25 had significantly higher chance of reaching that status after NACT (p = 0.045). However, no direct correlation could be established between baseline PLR and metastatic recurrence. No correlation either was found between TIL and individual blood counts, or between TILs and NLR or PLR.ConclusionIn this cohort, TILs retained their pCR predictive value; however PLR was a better predictor of the ensemble of responses which had good outcome in terms of less distant recurrences or longer DRFS (pCR or small residual disease). Thus, baseline PLR is worth further, prospective investigation together with baseline TILs, as it might indicate a good TNBC response to NACT when TILs are unavailable.