bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transformation of multicolour flow cytometry data with OTflow prevents misleading multivariate analysis results and incorrect immunological conclusions
Authors: Folcarelli Rita , van Staveren Selma , Tinnevelt Gerjen , Cadot Emily , Vrisekoop Nienke , Buydens Lutgarde , Koenderman Leo , Jansen Jeroen , van den Brink Oscar F. 
Published: July 2021

AbstractThe rapid evolution of the flow cytometry field, currently allowing the measurement of 30–50 parameters per cell, has led to a marked increase in deep multivariate information. Manual gating is insufficient to extract all this information. Therefore, multivariate analysis (MVA) methods have been developed to extract information and efficiently analyze the high‐density multicolour flow cytometry (MFC) data. To aid interpretation, MFC data are often logarithmically transformed before MVA. We studied the consequences of different transformations of flow cytometry data in datasets containing negative intensities caused by background subtractions and spreading error, as logarithmic transformation of negative data is impossible. Transformations such as logicle or hyperbolic arcsine transformations allow linearity around zero, whereas higher (positive and negative) intensities are logarithmically transformed. To define the linear range, a parameter (or cofactor) must be chosen. We show how the chosen transformation parameter has great impact on the MVA results. In some cases, peak splitting is observed, producing two distributions around zero in an actual homogeneous population. This may be misinterpreted as the presence of multiple cell populations. Moreover, when performing arbitrary transformation before MVA analysis, biologically relevant and statistically significant information might be missed. We present a new algorithm, Optimal Transformation for flow cytometry data (OTflow), which uses various statistical methods to optimally choose the parameter of the transformation and prevent artifacts such as peak splitting. Arbitrary or unconsidered transformation can lead to wrong conclusions for the MVA cluster methods, dimensionality reduction methods, and classification methods. We recommend transformation of flow cytometry data by using OTflow‐defined parameters estimated per channel, in order to prevent peak splitting and other artifacts in the data.
Facile N‐Formylation of Amines on Magnetic Fe3O4−CuO Nanocomposites
Authors: Mishra Kanchan , Datta Khanal Hari , Rok Lee Yong 
Published: July 2021

AbstractA facile, eco‐friendly, efficient, and recyclable heterogeneous catalyst is synthesized by immobilizing copper impregnated on mesoporous magnetic nanoparticles. The surface chemistry analysis of Fe3O4−CuO nanocomposites (NCs) by XRD and XPS demonstrates the synergistic effect between Fe3O4 and CuO nanoparticles, providing mass‐transfer channels for the catalytic reaction. TEM images clearly indicate the impregnation of CuO onto mesoporous Fe3O4. This hydrothermally synthesized eco‐friendly and highly efficient Fe3O4−CuO NCs are applied as a magnetically retrievable heterogeneous catalyst for the N‐formylation of wide range of aliphatic, aromatic, polyaromatic and heteroaromatic amines using formic acid as a formylating agent at room temperature. The catalytic activity of the NCs for N‐formylation is attributable to the synergistic effect between Fe3O4 and CuO nanoparticles. The N‐formylated product is further employed for the synthesis of biologically active quinolone moieties.
Simultaneous solid–liquid separation and primary purification of clavulanic acid from fermentation broth of Streptomyces clavuligerus using salting‐out extraction system
Authors: Wang Xu‐Dong , Hu Chun‐Yan , Qin Chao , Dong Yue‐Sheng , Ying Guo‐Qing , Xiu Zhi‐Long , Su Zhi‐Guo 
Published: July 2021

AbstractClavulanic acid (CA) is usually used together with other β‐lactam antibiotics as combination drugs to inhibit bacterial β‐lactamases, which is mainly produced from the fermentation of microorganism such as Streptomyces clavuligerus. Recently, it is still a challenge for downstream processing of low concentration and unstable CA from fermentation broth with high solid content, high viscosity, and small cell size. In this study, an integrated process was developed for simultaneous solid–liquid separation and primary purification of CA from real fermentation broth of S. clavuligerus using salting‐out extraction system (SOES). First, different SOESs were investigated, and a suitable SOES composed of ethanol/phosphate was chosen and further optimized using the pretreated fermentation broth. Then, the optimal system composed of 20% ethanol/15% K2HPO4 and 10% KH2PO4 w/w was used to direct separation of CA from untreated fermentation broth. The result showed that the partition coefficient (K) and recovery yield (Y) of CA from untreated fermentation broth were 29.13 and 96.8%, respectively. Simultaneously, the removal rates of the cells and proteins were 99.8% and 63.3%, respectively. Compared with the traditional method of membrane filtration or liquid–liquid extraction system, this developed SOES showed the advantages of simple operation, shorter operation time, lower process cost and higher recovery yield of CA. These results demonstrated that the developed SOES could be used as an attractive alternative for the downstream processing of CA from real fermentation broth.
A hierarchical integrative group least absolute shrinkage and selection operator for analyzing environmental mixtures
Authors: Boss Jonathan , Rix Alexander , Chen Yin‐Hsiu , Narisetty Naveen N. , Wu Zhenke , Ferguson Kelly K. , McElrath Thomas F. , Meeker John D. , Mukherjee Bhramar 
Published: July 2021

AbstractEnvironmental health studies are increasingly measuring multiple pollutants to characterize the joint health effects attributable to exposure mixtures. However, the underlying dose‐response relationship between toxicants and health outcomes of interest may be highly nonlinear, with possible nonlinear interaction effects. Existing penalized regression methods that account for exposure interactions either cannot accommodate nonlinear interactions while maintaining strong heredity or are computationally unstable in applications with limited sample size. In this article, we propose a general shrinkage and selection framework to identify noteworthy nonlinear main and interaction effects among a set of exposures. We design the hierarchical integrative group least absolute shrinkage and selection operator (HiGLASSO) to (a) impose strong heredity constraints on two‐way interaction effects (hierarchical), (b) incorporate adaptive weights without necessitating initial coefficient estimates (integrative), and (c) induce sparsity for variable selection while respecting group structure (group LASSO). We prove sparsistency of the proposed method and apply HiGLASSO to an environmental toxicants dataset from the LIFECODES birth cohort, where the investigators are interested in understanding the joint effects of 21 urinary toxicant biomarkers on urinary 8‐isoprostane, a measure of oxidative stress. An implementation of HiGLASSO is available in the higlasso R package, accessible through the comprehensive R archive network.
Interactions between the hippocampus and fronto‐parietal regions during memory encoding in early childhood
Authors: Geng Fengji , Xu Wenwen , Riggins Tracy 
Published: July 2021

AbstractThe neural mechanisms underlying memory encoding have received much attention in the literature. Research in adults and school‐age children suggest that the hippocampus and cortical regions in both frontal and parietal areas are involved in successful formation of memories. Overall, the hippocampus has been shown to interact with fronto‐parietal regions to collaboratively support successful memory encoding for both individual items as well as item details (such as the source or color in which the item was originally encountered). To date, only one study has investigated neural regions engaged during memory encoding in children younger than 8 years of age, which is unfortunate since early childhood is a period of dramatic improvement in memory. This previous study indicated that both the hippocampus and cortical regions are involved during the encoding of subsequently remembered item details (i.e., sources). However, this study reported few interactions between these regions, and it did not explore item memory at a more general level. To fill these gaps, this article reanalyzed data from the previous report, aiming to examine the neural correlates of item memory during encoding in early childhood (4–8 years) and interactions between the hippocampus and fronto‐parietal regions during encoding. Consistent with research in older individuals, both the hippocampus and fronto‐parietal regions were found to participate in item memory encoding. Additionally, functional connectivity between hippocampus and fronto‐parietal regions was significantly related to both subsequent item memory and subsequent source memory. Taken together, these findings suggest that not only the activation of individual brain regions (hippocampus and fronto‐parietal regions) but also the functional connections between these regions are important for memory encoding. These data add to the growing literature providing insight into how the hippocampus and cortical regions interact to support memory during development.
Spontaneous pneumomediastinum and pneumothorax in COVID‐19 patients: A tertiary care experience
Authors: Shaikh Nissar , Al Ameri Gamal , Shaheen Muhsen , Abdaljawad Wael I. , Al Wraidat Mohammad , Al Alawi Abdul Aziz S. , Ali Husain S. , Mohamed Ahmed S. , Daeri Hazem , Khatib Mohamad Y. , Elshafei Moustafa S. , Nashwan Abdulqadir J. 
Published: July 2021

AbstractIntroductionCOVID‐19 can occasionally complicate into spontaneous pneumothorax (SP) and/or spontaneous pneumomediastinum (SM). This study aims at exploring the occurrence of SP and or SM, risk factors, and outcomes in COVID‐19 patients.Materials and MethodsAll patients with COVID‐19, which complicated into SP and/or SM at Hamad Medical Corporation (the principal public healthcare provider in Qatar) from March to September 2020, were retrospectively enrolled. The clinical diagnosis was confirmed by CXR and CT. Between‐group comparisons were performed by using Chi‐square and t‐test. Differences were considered statistically significant at P ≤ .05.ResultsA total of 1100 patients were admitted, and 43 patients developed SP, SP + SM, or SM. Most patients were males (42/97.9%), and the most common comorbidity was diabetes mellitus (13/30.2%). All patients had acute respiratory distress syndrome (ARDS), and most patients had low lung compliance at the time of developing SP or SM. Twenty‐two of the patients developed SP (51.2%), 11 patients had both SP and SM (25.6%), and 10 patients had SM only (23.3%). There was no significant difference in the development of SP or SM and patients' gender or blood group or whether patients were on invasive or noninvasive ventilation or even the mortality (P > .05). Lung compliance was significantly (P < .05) lower in patients complicated with SP and or SM. Patients with SP required significantly higher (P < .001) chest drain insertion.ConclusionPatients with severe COVID‐19 pneumonia can complicate into SP and SM. These complications are more common in male diabetic patients. Patients with ARDS and having low lung compliance are at a higher risk of developing SP, SP + SM, or SM.
Multidecadal variability of the Tonle Sap Lake flood pulse regime
Authors: Chen Aifang , Liu Junguo , Kummu Matti , Varis Olli , Tang Qiuhong , Mao Ganquan , Wang Jie , Chen Deliang 
Published: July 2021

AbstractTonle Sap Lake (TSL) is one of the world's most productive lacustrine ecosystems, driven by the Mekong River's seasonal flood pulse. This flood pulse and its long‐term dynamics under the Mekong River basin's (MRB) fast socio‐economic development and climate change need to be identified and understood. However, existing studies fall short of sufficient time coverage or concentrate only on changes in water level (WL) that is only one of the critical flood pulse parameters influencing the flood pulse ecosystem productivity. Considering the rapidly changing hydroclimatic conditions in the Mekong basin, it is crucial to systematically analyse the changes in multiple key flood pulse parameters. Here, we aim to do that by using observed WL data for 1960–2019 accompanied with several parameters derived from a Digital Bathymetry Model. Results show significant declines of WL and inundation area from the late 1990s in the dry season and for the whole year, on top of increased subdecadal variability. Decreasing (increasing) probabilities of high (low) inundation area for 2000–2019 have been found, in comparison to the return period of inundation area for 1986–2000 (1960–1986). The mean seasonal cycle of daily WL in dry (wet) season for 2000–2019, compared to that for 1986–2000, has shifted by 10 (5) days. Significant correlations and coherence changes between the WL and large‐scale circulations (i.e., El Niño‐Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO) and Indian Ocean Dipole (IOD)), indicate that the atmospheric circulations could have influenced the flood pulse in different time scales. Also, the changes in discharge at the Mekong mainstream suggest that anthropogenic drivers may have impacted the high water levels in the lake. Overall, our results indicate a declining flood pulse since the late 1990s.
Hidden blood loss and its risk factors in patients undergoing conventional laparoscopic surgery and laparoendoscopic single‐site surgery for ovarian cystectomy
Authors: Chen Qiuyu , Zhu Sennan , Wang Danhan , Chen Miaomiao , Zhao Yu , Zhang Qiong 
Published: July 2021

AbstractObjectiveTo quantify the volume of hidden blood loss (HBL) between conventional laparoscopic surgery (CLS) and laparoendoscopic single‐site surgery (LESS) for ovarian cyst and to explore its risk factors.MethodsA total of 310 patients who underwent CLS or LESS were enrolled in this study. The Nadler formula and Gross formula were used to calculate each patient's estimated blood volume and total blood loss, multiple linear regression analysis was applied to identify the risk factors.ResultsThe HBL in LESS was more than in CLS (P = 0.000). Operative time (p = 0.015), pre‐hematocrit (P = 0.002), pre‐hemoglobin (P = 0.015), and pelvic adhesions (P = 0.037) were positively correlated with HBL in CLS. Intraoperative bleeding (P = 0.026), operative time (P = 0.000), pre‐hematocrit (P = 0.042), CA125 (P = 0.047), and cyst volume (P = 0.012) were independent risk factors for HBL in LESS.ConclusionA large amount of HBL occurs in ovarian cystectomy surgery and cannot be ignored in clinical work; fully and correctly understanding HBL and exploring its causes can ensure the safety and improve the prognosis of patients.
Effects of shading and micro‐spray of canopy on photosynthetic characteristics, quality and yield of drip‐irrigated grapes*
Authors: Zheng Ming , Bai Yungang , Zhang Jianghui , Liu Hongbo , Cai Junshe , Bai Shijian , Ding Bangxin , Ding Ping 
Published: July 2021

AbstractGrapes are prone to midday depression of photosynthesis (MDP) under the action of high temperature and strong light, which can reduce the accumulation of organic matter, resulting in a decline in yield and quality. In this study, the grapes in Shanshan County, Xinjiang, China, were taken as an example to implement shading and micro‐spray measures. Shading degrees of 0, 15 and 30% were combined with micro‐spray flow rates of 20, 30 and 40 L h−1. Nine treatments and one control treatment (the control treatment is without shading and mist spraying) were designed through a combination of the shading and micro‐spray conditions. The photosynthetic prediction model of the multivariate nonlinear model was constructed and had high simulation accuracy. The decline of air temperature at the top of the canopy increased as the degree of shading and the amount of micro‐spray increased; MDP could be eliminated under the combined conditions of shading and micro‐spray. The mean daily net CO2 assimilation rate (An) increased by more than 0.53 μmol m−2 s−1. The combination of shading and micro‐spray conditions significantly increased fruit size and promoted greenness. The WP1 (15% and 40 L h−1) treatment had the highest mean daily An and the largest fruit volume. The vitamin C (VC) content of WP1 treatment was the highest, 4.13 mg kg−1, which was 1.2 times that of the control (CK) treatment. The yield of the WP1 treatment was the highest, which was 19.7% higher than that of the CK treatment. Thus, the WP1 treatment was the optimal treatment for promoting the An of grape leaves and improving the fruit quality of grapes. This research could provide a reference for improving the photosynthesis, fruit quality and yield of grapes and alleviating the photosynthetic MDP of crops.
Long noncoding RNA DARS‐AS1 regulates TP53 ubiquitination and affects ovarian cancer progression by modulation miR‐194‐5p/RBX1 axis
Authors: Zhou Ming , Cheng Hao , Fu Yulan , Zhang Jun 
Published: July 2021

AbstractBackgroundOvarian cancer is a malignant tumor with a poor prognosis, its underlying mechanism is still unclear.ObjectiveIn this study, long noncoding RNA DARS‐AS1 was studied to identify its function in the development of ovarian cancer.MethodsPerform functional experiments to detect the effects of DARS‐AS1 on the proliferation, apoptosis, and migration of ovarian cancer cells A2780. The luciferase report, immunoprecipitation (IP) experiment, and ubiquitination level determination verify that RBX1 ubiquitination and mediate the degradation of tumor suppressor gene TP53.ResultsKnockdown of DARS‐AS1 can inhibit cell proliferation, migration, and apoptosis, and the application of miR‐194‐5p inhibitors can prevent this process. Luciferase and IP experiments showed that DARS‐AS1 regulates the expression of RBX1 by binding to miR‐194‐5p, and RBX1 mediates its degradation through ubiquitination of TP53.
The Clevo case: A timeline of IFRS “Reluctance”
Authors: Hsu Yu‐Lin , Reid Gavin C. 
Published: July 2021

AbstractThere is an ongoing policy debate over whether the adoption of IFRS should be mandatory. All Taiwanese listed companies had to adopt IFRS from 2013, but they could choose to adopt earlier in 2012. Surprisingly, given cross‐national comparisons, not one Taiwanese company adopted early. This is an extreme example of policy “reluctance.” We explore this unique setting, by analyzing a leading reluctant Taiwanese company, Clevo. It was widely known as a potential early adopter but withdrew at the last minute. This paper illustrates how a firm which perceived net benefits would be incentivized to adopt IFRS early, but then how uncertainties in regulations could stall such intentions. Through discussing how the accounting regulators responded to this firm's actions (and vice versa), this paper helps us to understand better the prerequisites for effective policy design and corporate decision‐making in the context of IFRS adoption and implementation. This paper, using a qualitative research method, will also add to exiting IFRS literature which mainly focuses on quantitative analysis.
Efficacy of endoscopic large balloon dilation extended for 2 minutes in bile duct stone removal: A multicenter retrospective study
Authors: Nakahara Kazunari , Michikawa Yosuke , Suetani Keigo , Sato Junya , Igarashi Yosuke , Sekine Akihiro , Kobayashi Shinjiro , Matsuda Koji , Otsubo Takehito , Itoh Fumio 
Published: July 2021

AbstractBackground/PurposeThere is no evidence regarding the optimal balloon dilation time during endoscopic papillary large balloon dilation (EPLBD). The study aim was to evaluate the efficacy of 2‐minute extended balloon dilation for EPLBD.MethodsTwo hundred and five patients who underwent EPLBD during endoscopic retrograde cholangiopancreatography (ERCP) for bile duct stones at three tertiary centers were included in the analysis. Clinical outcomes and the adverse events were compared between the 0‐minute group (n = 94, balloon deflated immediately after waist disappearance) and the 2‐minute group (n = 111, balloon dilation maintained for 2 minutes after waist disappearance). The risk factors of post‐ERCP pancreatitis (PEP) after EPLBD were assessed.ResultsThere were no significant differences in the stone removal rates and hospitalization periods between the two groups. However, the total ERCP procedure time was significantly shorter in the 2‐minute group (40.6 vs 48.9 min, P = .03). The incidence of PEP was 7.4% in the 0‐minute group and significantly lower at 0.9% in the 2‐minute group (P = .04). Multivariate analysis identified without 2‐minute extended EPLBD as a significant risk factor of PEP (OR: 9.9, P = .045).ConclusionsExtension of EPLBD for 2 minutes helped prevent PEP and shortened the procedure time.
Phosphoproteomic analysis of duck egg yolk provides novel insights into its characteristics and biofunctions
Authors: Arshad Rida , Meng Yaqi , Qiu Ning , Geng Fang , Mine Yoshinori , Keast Russell , Zhu Chunxia 
Published: July 2021

AbstractBACKGROUNDAlthough the importance of phosphorylation in the function of proteins is known, investigation of the protein phosphorylation of duck egg yolk (DEY) is still very limited. This study aimed to conduct a detailed phosphoproteomic study of DEY using immobilized metal affinity chromatography and ultra‐high liquid chromatography tandem mass spectrometry.RESULTSA total of 253 phosphorylation sites assigned to 66 phosphoproteins were identified in DEY, of which VTG‐1, VTG‐2, and fibrinogen alpha chain were found to be the highly phosphorylated proteins in DEY. The biological functions of the identified phosphoproteins were illuminated through gene ontology analysis, which showed that they were mainly involved in binding, catalytic, immune response, and metabolic activity. S‐X‐E and S‐X‐S were found to be the most conserved serine motifs of phosphorylation in DEY. The comparison of DEY phosphoproteins with those of chicken egg yolk (CEY) revealed that differences mostly involved molecular functions and biological processes. The comparison also revealed a higher phosphorylation level in DEY proteins.CONCLUSIONThe higher phosphorylation level in DEY proteins than that in CEY proteins are supposed to help enhance duck growth performance and biological activities (e.g. antibacterial and antioxidant ability) for better adapting the humid environment the duck lived. © 2021 Society of Chemical Industry.