bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Endophytes from Vitis vinifera L. – Metabolomics Characterization of Plant‐Endophyte Crosstalk
Authors: Stranska Milena , Lovecka Petra , Vrchotova Blanka , Uttl Leos , Bechynska Kamila , Behner Adam , Hajslova Jana 
Published: October 2021

AbstractBacterial endophytes are known to protect Vitis vinifera L. against various harmful effects of the environment and support its growth. However, for the most part, biochemical responses of such co‐existence have not yet been fully elucidated. In this work, we aimed to characterize the activities of endophytic consortia in a plant‐endophyte extract by measuring five indicators of colonization (overall endophyte metabolic activity, microbial ACC deaminase activity, ability to solubilize phosphorus, ability to convert atmospheric nitrogen to ammonia ions, and ability to produce growth promoting indole acetic acid), and find relationships between these activities and metabolome. The V. vinifera canes for the metabolomics fingerprinting were extracted successively with water and methanol, and analysed by ultra‐high performance liquid chromatography coupled with high resolution mass spectrometry. For data processing, the MS‐DIAL – MS‐CleanR – MS‐FINDER software platform was used, and the data matrix was processed by PCA and PLS‐DA multivariate statistical methods. The metabolites that were upregulated with the heavy endophyte colonization were mainly chlorins, phenolics, flavonoid and terpenoid glycosides, tannins, dihydropyranones, sesquiterpene lactones, and long‐chain unsaturated fatty acids.
Synchronous gastric cancer and carcinoma in situ of the pancreas
Authors: Inoue Masashi , Hakoda Keishi , Sawada Hiroyuki , Hotta Ryuichi , Ohmori Ichiro , Miyamoto Kazuaki , Toyota Kazuhiro , Sadamoto Seiji , Takahashi Tadateru 
Published: October 2021

AbstractAbnormal findings in the pancreatic duct without a mass may require serial pancreatic juice aspiration cytological examination. In cases of synchronous gastric cancer and stage 0 pancreatic cancer, spleen‐preserving pancreatectomy may have advantage.
Ten years of battle with multiple recurrences of pediatric skull base chondrosarcoma: A case report
Authors: Ariamanesh Mona , Tafrishi Rana , Dehghani Mansoureh , Bakhshai Mehdi , Javadinia Seyed Alireza , Hosseini Seyyed Morteza , Nematshahi Mohammad , Welsh James S. , Porouhan Pejman 
Published: October 2021

AbstractIn children and adolescents presenting with skull base sarcoma, treatment strategies will face challenging decisions due to the unique chemoresistant pathologies, limitations imposed by the not‐yet fully mature anatomical structures, and the small surgical site.
Self‐reported quality of life as a predictor of mortality in renal cell carcinoma
Authors: Alam Ridwan , Patel Hiten D. , Su Zhuo T. , Cheaib Joseph G. , Ged Yasser , Singla Nirmish , Allaf Mohamad E. , Pierorazio Phillip M. 
Published: October 2021

BackgroundThis study evaluated the utility of self‐reported quality of life (QOL) metrics in predicting mortality among all‐comers with renal cell carcinoma (RCC) and externally tested the findings in a registry of patients with small renal masses.MethodsThe Surveillance, Epidemiology, and End Results–Medicare Health Outcomes Survey (SEER‐MHOS) captured QOL metrics composed of mental component summary (MCS) and physical component summary (PCS) scores. Regression models assessed associations of MCS and PCS with all‐cause, RCC‐specific, and non–RCC‐specific mortality. Harrell's concordance statistic (the C‐index) and the Akaike information criterion (AIC) determined predictive accuracy and parsimony, respectively. Findings were tested in the prospective Delayed Intervention and Surveillance for Small Renal Masses (DISSRM) registry.ResultsIn SEER‐MHOS, 1494 patients had a median age of 73.4 years and a median follow‐up time of 5.6 years. Each additional MCS and PCS point reduced the hazard of all‐cause mortality by 1.3% (95% CI, 0.981‐0.993; P < .001) and 2.3% (95% CI, 0.971‐0.984; P < .001), respectively. Models with QOL metrics demonstrated higher predictive accuracy (C‐index, 72.3% vs 70.1%) and parsimony (AIC, 9376.5 vs 9454.5) than models without QOL metrics. QOL metrics exerted a greater effect on non–RCC‐specific mortality than RCC‐specific mortality. External testing in the DISSRM registry confirmed these findings with similar results for all‐cause mortality.ConclusionsModels with self‐reported QOL metrics predicted all‐cause mortality in patients with RCC with higher accuracy and parsimony than those without QOL metrics. Physical health was a stronger predictor of mortality than mental health. The findings support the incorporation of QOL metrics into prognostic models and patient counseling for RCC.
ezTrack—A Step‐by‐Step Guide to Behavior Tracking
Authors: Pennington Zachary T. , Diego Keziah S. , Francisco Taylor R. , LaBanca Alexa R. , Lamsifer Sophia I. , Liobimova Olga , Shuman Tristan , Cai Denise J. 
Published: October 2021

AbstractTracking animal behavior by video is one of the most common tasks in neuroscience. Previously, we have validated ezTrack, a free, flexible, and easy‐to‐use software for the analysis of animal behavior. ezTrack's Location Tracking Module can be used for the positional analysis of an individual animal and is applicable to a wide range of behavioral tasks. Separately, ezTrack's Freeze Analysis Module is designed for the analysis of defensive freezing behavior. ezTrack supports a range of desirable tools, including options for cropping and masking portions of the field of view, defining regions of interest, producing summary data for specified portions of time, algorithms to remove the influence of electrophysiology cables and other tethers, batch processing of multiple videos, and video down‐sampling. Moreover, ezTrack produces a range of interactive plots and visualizations to promote users' confidence in their results. In this protocols paper, we provide step‐by‐step instructions for the use of ezTrack, from tips for recording behavior to instructions for using the software for video analysis. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.This article was corrected on 4 August 2022. See the end of the full text for details.Basic Protocol 1: Software environment installationBasic Protocol 2: Using the Location Tracking ModuleBasic Protocol 3: Using the Freeze Analysis Module
Modified Cross‐Linking, Ligation, and Sequencing of Hybrids (qCLASH) to Identify MicroRNA Targets
Authors: Gay Lauren A. , Turner Peter C. , Renne Rolf 
Published: October 2021

AbstractThis protocol was designed to identify microRNA (miRNA) targetomes from smaller‐input samples by performing a simplified workflow of the Cross‐Linking and Sequencing of Hybrids (CLASH) technique developed in the Tollervey group. In this ribonomics‐based technique, Cross‐Linking and Immunoprecipitation (CLIP) of Argonaute (Ago) is combined with an RNA ligase reaction that yields covalently bound “hybrids” between miRNAs and their target RNAs. While this iteration of CLIP identifies “high‐confidence” or “unambiguous” miRNA targets, the added ligation step is highly inefficient and therefore requires large numbers of cultured cells. To make this powerful approach applicable to smaller cell numbers, we created qCLASH, incorporating a workflow that performs all enzymatic reactions on bead‐bound complexes and omits gel purification of immunoprecipitated Ago complexes associated with major loss of RNA. At a sequencing depth of 100 million reads per library, which is highly feasible with rapidly decreasing sequencing costs, qCLASH, when used with three biological replicates, results in thousands of high‐confidence miRNA targets. qCLASH was first developed to identify viral miRNA targetomes of endothelial cells infected with Kaposi's sarcoma−associated herpesvirus. Since then, qCLASH has been applied to Epstein‐Barr virus− and MHV68‐infected cells, and more recently to metastatic melanoma and breast cancer cells. Currently, protocols are under development to apply qCLASH to human solid tumor specimens. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol: Quick Cross‐Linking and Sequencing of Hybrids (qCLASH)Support Protocol: Optimization of Ago immunoprecipitation
Multi‐probe FISH Analysis of Immunophenotyped Chronic Lymphocytic Leukemia by Imaging Flow Cytometry
Authors: Hui Henry Y. L. , Stanley Jason , Clarke Kathryn , Erber Wendy N. , Fuller Kathryn A. 
Published: October 2021

AbstractImaging flow cytometry is an automated method that enables cells and fluorescent signals to be visualized and quantified. Here, we describe a new imaging flow cytometry method whereby fluorescence in situ hybridization (FISH) is integrated with cell phenotyping. The method, called “immuno‐flowFISH,” provides an exciting new dimension for the analysis of genomic changes in cytological samples (e.g., blood, bone marrow). Cells are analyzed in suspension without any requirement for prior cell isolation or separation. Multiple antibodies and FISH probes, each with a unique fluorophore, can be added and many thousands of cells analyzed. Specific cell populations are identified by their antigenic profile and then analyzed for the presence of chromosomal defects. Immuno‐flowFISH was applied to the assessment of chronic lymphocytic leukemia (CLL), a mature B‐cell neoplasm where chromosomal abnormalities predict prognosis and treatment requirements. This integrated immunophenotyping and multi‐probe FISH strategy could detect both structural and numerical chromosomal changes involving chromosomes 12 and 17 in CLL cells. Given that many thousands of cells were analyzed and the leukemic cells were positively identified by their immunophenotype, this multi‐probe method adds precision to the cytogenomic analysis of CLL. © 2021 Wiley Periodicals LLC.
Winter cover crops reduce the soil seed bank and infestations of Italian ryegrass in no‐tillage system
Authors: Cechin Joanei , Schmitz Maicon Fernando , Torchelsen Jonathan Schwanz , Durigon Miria Rosa , Agostinetto Dirceu , Vargas Leandro 
Published: October 2021

AbstractItalian ryegrass (Lolium perenne spp. multiflorum Lam.) is a troublesome weed commonly found in winter cereals. Winter cover crops represent an alternative for weed suppression, reducing weed soil seed banks, and future infestations. The aim of this study was to evaluate the suppression of winter cover crops on reducing the soil seed bank and infestations of Italian ryegrass in fields managed under no‐tillage system. Field experiment was carried out during three consecutive years, in a strip‐plot design with four blocks, containing the winter cover crops. Wheat (Triticum aestivum), canola (Brassica napus), barley (Hordeum vulgare), common vetch (Vicia sativa), cereal rye (Secale cereale), feral radish (Raphanus sativus), and black oat (Avena strigosa) were sown in each strip (block) under no‐tillage system and compared with weedy fallow. Seed bank was quantified at 0.0‐ to 0.05‐ and 0.05‐ to 0.10‐m depths, whereas Italian ryegrass infestations were measured with a sample frame of 0.0625 m2. Greater suppression and lower soil seed bank were reported in plots managed with cereal rye, common vetch, black oat, and feral radish, reducing up to 80% in the first year, and up to 96% after 3 yr of continuous management in comparison to weedy fallow. Italian ryegrass infestations increased four‐ to six‐fold when managed with canola. High suppressor potential of Italian ryegrass occurred for cover crops with biomass dry accumulation greater than 8.7 tons ha−1, especially to plants with a height upper to 1 m, plant characteristics essential to reduce strongly Italian ryegrass infestations and ensure weed‐free fields throughout the time.
New Technologies are Needed to Improve the Recycling and Upcycling of Waste Plastics
Authors: Ragauskas Arthur J. , Huber George W. , Wang Jia , Guss Adam , O'Neill Hugh M. , Lin Carol Sze Ki , Wang Yanqin , Wurm Frederik R. , Meng Xianzhi 
Published: October 2021

AbstractIn their Editorial to the Special Issue on The Chemistry of Waste Plastics Upcycling, the Guest Editors Adam Guss, George Huber, Carol Lin, Xianzhi Meng, Hugh O'Neill, Arthur Ragauskas, Jia Wang, Yanqin Wang, and Frederik Wurm highlight some of the increasingly urgent efforts being made by chemists to address challenges related to the fate of plastics at the end of, their useful lives and the valorization of plastic waste.
Can artificial ecological islands alter the biodiversity of macroinvertebrate? A case study in Fujin National Wetland Park, the Sanjiang Plain, China
Authors: Yuan Zi‐Ao , Liu Xin‐xin , Du Hai‐rong , Zhang Ming‐Hai 
Published: October 2021

Abstract

Many policies and studies globally have highlighted the pivotal role of wetland ecosystems regarding wetland biota and their ecological status. With the strengthening of wetland ecosystem management legislation and policy, wetland restoration should also consider increasing habitat diversity to improve biota. We explore whether the construction of artificial ecological islands can increase the diversity of and macroinvertebrates before assessing the effects of actively constructing islands via human intervention on wetland protection.

We discuss changes in macroinvertebrate diversity (i) with and without islands, (ii) at different water‐level gradients surrounding the islands, (ⅲ) on different island substrates, and (ⅳ) at different time scales. We used ANOVA, ANOSIM, and cluster analysis to test the differences.

The macroinvertebrate communities had spatially heterogeneous distributions which changes over time due to both natural and anthropogenic stresses. The establishment of islands significantly increased the community composition and biodiversity of the macroinvertebrate. Water depth and substrate affect community composition of macrozoobenthos. The abundance and diversity of macroinvertebrates can influence the biodiversity of their predators (fish and waterbirds). Potentially, the construction of islands could provide some cobenefits for the conservation of wetland fauna.

Synthesis and applications. Establishing artificial ecological islands in broad open‐water areas and increasing water‐level gradient and substrate diversity can increase microhabitat availability and habitat heterogeneity. These changes can adapt to different ecological niches of aquatic organisms, increase biodiversity, and have a positive effect on the ecological restoration of inland freshwater marshes and wetlands.
Solid State Characterization of One‐ and Two‐Electron Oxidized CuII‐salen Complexes with para‐Substituents: Geometric Structure‐Magnetic Property Relationship
Authors: Takeyama Tomoyuki , Suzuki Takashi , Kikuchi Misa , Kobayashi Misato , Oshita Hiromi , Kawashima Kyohei , Mori Seiji , Abe Hitoshi , Hoshino Norihisa , Iwatsuki Satoshi , Shimazaki Yuichi 
Published: October 2021

AbstractOne‐ and two‐electron oxidized CuII complexes of Schiff base ligands with para‐substituted phenolate moieties were synthesized and characterized. The crystal structure of the one‐electron oxidized methylthio‐substituted complex [Cu(MeS‐salen)]SbCl6 revealed the intermolecular π‐π stacking interaction of the two phenolate moieties with those of the neighboring complex cations to form the one‐dimensional chain. Such a π‐π stacking interaction could not be detected in the two‐electron oxidized complex [Cu(MeS‐salen)](SbCl6)2 and the oxidized methoxy‐substituted complexes [Cu(MeO‐salen)](SbF6)n (n=1, 2). Magnetic study of [Cu(MeO‐salen)]SbF6 showed a weak antiferromagnetic interaction between the CuII ion and phenoxyl radical unpaired electron spins, while [Cu(MeS‐salen)]SbCl6 showed a ferromagnetism. Both of the two‐electron oxidized complexes exhibited a relatively strong magnetic interaction between the two radical electrons, while the signs of the electron spins are different.
Pd, Cu and Bimetallic PdCu NPs Supported on CNTs and Phosphine‐Functionalized Silica: One‐Pot Preparation, Characterization and Testing in the Semi‐Hydrogenation of Alkynes
Authors: Sánchez‐Resa Daniel , Delgado Jorge A. , Fernández‐Martínez Maria Dolores , Didelot Chloé , De Mallmann Aimery , Szeto Kaï C. , Taoufik Mostafa , Claver Carmen , Godard Cyril 
Published: October 2021

AbstractTriphenylphosphine stabilized Pd, Cu and PdCu nanocatalysts supported on carbon nanotubes (CNTs) or phosphorus functionalised silica (P−SiO2) were prepared via a one‐pot methodology. The series of P−SiO2 supported catalysts evidenced metal particle sizes of metallic nanoparticles (M‐NPs) between 1 and 2.4 nm, smaller than their equivalents on CNTs (2.4–2.6 nm). Such a difference in particle size as a function of the support and the metallic composition indicated the more pronounced mediation of the CNTs support during the formation of the M‐NPs when compared to the P−SiO2 support. The series of supported catalysts were tested in the semi‐hydrogenation of alkynes providing differences in reactivity which might be correlated with the size and composition of the M‐NPs and the nature of corresponding support. The carbon supported catalysts displayed in general higher activities than those supported on silica and the bimetallic catalyst PdCu/CNTs were the most selective for the case of alkyl substituted alkynes. This catalyst could moreover be recycled several times without loss of activity nor selectivity.
Tracing evolutionary decoupling of oral and pharyngeal jaws in cichlid fishes
Authors: Ronco Fabrizia , Salzburger Walter 
Published: October 2021

AbstractEvolutionary innovations can facilitate diversification if the novel trait enables a lineage to exploit new niches or by expanding character space. The elaborate pharyngeal jaw apparatus of cichlid fishes is often referred to as an evolutionary “key innovation” that has promoted the spectacular adaptive radiations in these fishes. This goes back to the idea that the structural and functional independence of the oral and pharyngeal jaws for food capturing and food processing, respectively, permitted each jaw type to follow independent evolutionary trajectories. This “evolutionary decoupling” is thought to have facilitated novel trait combinations and, hence, ecological specialization, ultimately allowing more species to coexist in sympatry. Here, we test the hypotheses of evolutionary decoupling of the oral and pharyngeal jaws in the massive adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on phylogenetic comparative analyses of oral jaw morphology and lower pharyngeal jaw shape across most of the ∼240 cichlid species occurring in that lake, we show that the two jaws evolved coupled along the main axes of morphological variation, yet most other components of these trait complexes evolved largely independently over the course of the radiation. Further, we find limited correlations between the two jaws in both overall divergence and evolutionary rates. Moreover, we show that the two jaws were evolutionary decoupled at a late stage of the radiation, suggesting that decoupling contributed to micro-niche partitioning and the associated rapidly increasing trophic diversity during this phase.
Mobility as a driver of severe acute respiratory syndrome coronavirus 2 in cancer patients during the second coronavirus disease 2019 pandemic wave
Authors: Fong Dominic , Mair Maximilian J. , Lanthaler Florian , Alber Monika , Mitterer Manfred 
Published: October 2021

AbstractWe retrospectively analyzed the epidemiological characteristics of cancer patients with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection and their correlations with publicly available mobility data. Between 19 October 2020 and 28 February 2021, 4754 patient visits were carried out, and 1454 treatments have been applied at the Haemato‐Oncology Day Hospital Merano. Additional measures to prevent local SARS‐CoV‐2 transmission included a specific questionnaire for coronavirus disease 2019 (COVID‐19) symptoms as well as a SARS‐CoV‐2 real‐time polymerase‐chain reaction (RT‐PCR) 2 days prior to any intravenous or subcutaneous therapy. Community mobility was assessed through publicly available mobile phone tracking data from Google; 106/719 (14.7%) cancer patients have been tested positive for SARS‐CoV‐2 by PCR during the second wave compared to 5/640 (0.8%) within the first wave (P < .001); 66/106 (62%) had solid tumors, and 40/106 (38%) had hematological malignancies; 90/106 (85%) patients received ongoing antitumor therapies. Mortality rate of COVID‐19 positive cancer patients (7/106; 6.6%) was higher compared to the overall population (731/46 421; 1.6%; P < .001). Strict control measures at our department led to a significantly lower test positivity rate compared to the general population, resulting in a reduction of 58.5% of new SARS‐CoV‐2 cases. Over time, infection rates and community mobility correlated in the first and second wave after initiating and lifting restrictions. Our findings underscore the importance of strict preventive control measures including testing and contact tracing in vulnerable subpopulations such as cancer patients, particularly if social restriction policies are being lifted. Smartphone‐based mobility data may help to guide policy makers to prevent a vulnerable population like cancer patients from virus transmission.
Expression of the HOXA gene family and its relationship to prognosis and immune infiltrates in cervical cancer
Authors: Ge Fenfen , Tie Weiwei , Zhang Junli , Zhu Yingying , Fan Yingying 
Published: October 2021

AbstractBackgroundThe homeobox A cluster (HOXA) gene family is participated in multiple biological functions in human cancers. To date, little is known about the expression profile and clinical significance of HOXA genes in cervical cancer.MethodsWe downloaded RNASeq data of cervical cancer from The Cancer Genome Atlas (TCGA) database. The difference in HOXA family expression was analyzed using independent samples t test. Cox proportional hazard regression analysis was used to assess the effect of HOXA family expression on survival, and a nomogram predicting survival was generated. We assessed the infiltration difference in immune cells and expression difference of immunity biomarkers between two groups with different expression level of HOXA genes through Immune Cell Abundance Identifier (ImmuCellAI) and independent samples t test, respectively.ResultsOur results showed that the HOXA1 gene was upregulated, while the HOXA10 and HOXA11 were downregulated in cervical cancer. Downregulation of HOXA1 was related to a poor outcome for cervical cancer patient. We also identified a significantly increased abundance of T helper 2 cells (Th2) and higher expression of PD‐L1 in cervical cancer patients with lower expression of HOXA10 and HOXA11. The gene set enrichment analysis (GSEA) results indicated that HOXA1 and HOXA11 were involved in immune responses pathways and participated in the activation of a variety of classic signaling pathways related to the progression of human cancer.ConclusionThis study comprehensively analyzed different HOXA genes applying public database to determine their expression patterns, potential diagnostic, prognostic, and treatment values in cervical cancer.