bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals
Authors: Martín Guiomar , Márquez Yamile , Mantica Federica , Duque Paula , Irimia Manuel 
Published: January 2021

Abstract
Background
Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing.

Results
We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion.

Conclusions
Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.
The reality of informed consent: empirical studies on patient comprehension—systematic review
Authors: Pietrzykowski Tomasz , Smilowska Katarzyna 
Published: January 2021

Abstract
Background
Informed consent is a basic concept of contemporary, autonomy-based medical practice and facilitates a shared decision-making model for relations between physicians and patients. Thus, the extent to which patients can comprehend the consent they grant is essential to the ethical viability of medicine as it is pursued today. However, research on patients’ comprehension of an informed consent’s basic components shows that their level of understanding is limited.

Methods
Systemic searches of the PubMed and Web of Science databases were performed to identify the literature on informed consent, specifically patients’ comprehension of specific informed consent components.

Results
In total, 14 relevant articles were retrieved. In most studies, few clinical trial participants correctly responded to items that examined their awareness of what they consented to. Participants demonstrated the highest level of understanding (over 50%) regarding voluntary participation, blinding (excluding knowledge about investigators’ blinding), and freedom to withdraw at any time. Only a small minority of patients demonstrated comprehension of placebo concepts, randomisation, safety issues, risks, and side effects.

Conclusions
We found that participants’ comprehension of fundamental informed consent components was low, which is worrisome because this lack of understanding undermines an ethical pillar of contemporary clinical trial practice and questions the viability of patients’ full and genuine involvement in a shared medical decision-making process.
Controlling of two destructive zooplanktonic predators in Chlorella mass culture with surfactants
Authors: Wen Xiaobin , Zhang Aoqi , Zhu Xiaoyan , Liang Lin , Huo Yan , Wang Kaixuan , Yu Youzhi , Geng Yahong , Ding Yi , Li Yeguang 
Published: January 2021

Abstract
Background
Predatory flagellates and ciliates are two common bio-contaminants which frequently cause biomass losses in Chlorella mass culture. Efficient and targeted ways are required to control these contaminations in Chlorella mass cultivation aiming for biofuel production especially.

Results
Five surfactants were tested for its ability to control bio-contaminations in Chlorella culture. All five surfactants were able to eliminate the contaminants at a proper concentration. Particularly the minimal effective concentrations of sodium dodecyl benzene sulfonate (SDBS) to completely eliminate Poterioochromonas sp. and Hemiurosomoida sp. were 8 and 10 mg L−1, respectively, yet the photosynthesis and viability of Chlorella was not significantly affected. These results were further validated in Chlorella mass cultures in 5, 20, and 200 m2 raceway ponds.

Conclusions
A chemical method using 10 mg L−1 SDBS as pesticide to control predatory flagellate or ciliate contamination in Chlorella mass culture was proposed. The method helps for a sustained microalgae biomass production and utilization, especially for biofuel production.
Efficacy of plasma exchange for antineutrophil cytoplasmic antibody-associated systemic vasculitis: a systematic review and meta-analysis
Authors: Yamada Yosuke , Harada Makoto , Hara Yuuta , Iwabuchi Ryohei , Hashimoto Koji , Yamamoto Shuhei , Kamijo Yuji 
Published: January 2021

Abstract
Objective
To assess through systematic review and meta-analysis whether plasma exchange (PE) is associated with prognosis in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) patients.

Methods
A systematic search of PubMed, MEDLINE, Embase, and CENTRAL databases from inception to 17 June 2020 was conducted. Ongoing or unpublished trials were also searched in ClinicalTrials.gov and the World Health Organization trials portal. Randomised controlled trials (RCTs) comparing PE vs. non-PE in AAV patients (microscopic polyangiitis [MPA], granulomatosis with polyangiitis [GPA], or eosinophilic granulomatosis with polyangiitis [EGPA]) were included. The combined risk ratio (RR) was calculated by the random-effects model using the Mantel-Haenszel method. Heterogeneity was measured using the I2 statistic. Primary outcomes were mortality, clinical remission (CR), and adverse events (AEs).

Results
Four RCTs comparing PE vs. no PE (N = 827) and 1 RCT comparing PE vs. pulse steroid treatment (N = 137) were included. All participants were MPA or GPA patients (no EGPA patients). PE was not associated with main primary outcomes compared with no PE (mortality RR 0.93 [95% confidence interval {CI} 0.70–1.24], I2 = 0%; CR RR 1.02 [95% CI 0.91–1.15], I2 = 0%; and AE RR 1.10 [95% CI 0.73–1.68], I2 = 37%) or pulse steroid (mortality RR 0.99 [95% CI 0.71–1.37]; CR [the Birmingham Vasculitis Activity score] mean difference − 0.53 [95% CI − 1.40–0.34]; and AE RR 1.05 [95% CI 0.74–1.48]). Focusing on the early treatment phases, PE was associated with a reduction in end-stage renal disease incidence compared with both no PE (PE 1/43 vs. no PE 10/41; RR 0.14 [0.03–0.77] at 3 months) and pulse steroid (PE 11/70 vs. pulse steroid 23/67; RR 0.46 [0.24–0.86] at 3 months).

Conclusion
We carried out a systematic review and meta-analysis targeting all AAV patients, including MPA, GPA, and EGPA. In AAV patients, performing PE was not associated with the risk of mortality, CR, and AE. No RCT exists evaluating the efficacy of PE for EGPA; hence, this is required in the future. The results may affect the development of guidelines for AAV and may indicate the direction of future clinical research on AAV.

Trial registration
UMIN R000045239, PROSPERO CRD42020182566.
72-h diurnal RNA-seq analysis of fully expanded third leaves from maize, sorghum, and foxtail millet at 3-h resolution
Authors: Lai Xianjun , Bendix Claire , Zhang Yang , Schnable James C. , Harmon Frank G. 
Published: January 2021

Abstract
Objectives
The purpose of this data set is to capture the complete diurnal (i.e., daily) transcriptome of fully expanded third leaves from the C4 panacoid grasses sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica) with RNA-seq transcriptome profiling. These data are the cornerstone of a larger project that examined the conservation and divergence of gene expression networks within these crop plants. This data set focuses on temporal changes in gene expression to identify the network architecture responsible for daily regulation of plant growth and metabolic activities. The power of this data set is fine temporal resolution combined with continuous sampling over multiple days.

Data description
The data set is 72 individual RNA-seq samples representing 24 time course samples each for sorghum, maize, and foxtail millet plants cultivated in a growth chamber under equal intervals of light and darkness. The 24 samples are separated by 3-h intervals so that the data set is a fine scale 72-h analysis of gene expression in the leaves of each plant type. FASTQ files from Illumina sequencing are available at the National Center for Biotechnology Information Sequence Read Archive.
iTRAQ-based proteomic analysis reveals the molecule mechanism of reducing higher alcohols in Chinese rice wine by nitrogen compensation
Authors: Huang Guidong , Ren Hong , Wang Ali , Wan Xinran , Wu Ziying , Zhong Xianfeng 
Published: January 2021

Abstract
Purpose
Higher alcohol is a by-product of the fermentation of wine, and its content is one of the most important parameters that affect and are used to appraise the final quality of Chinese rice wine. Ammonium compensation is an efficient and convenient method to reduce the content of higher alcohols, but the molecule mechanism is poorly understood. Therefore, an iTRAQ-based proteomic analysis was designed to reveal the proteomic changes of Saccharomyces cerevisiae to elucidate the molecular mechanism of ammonium compensation in reducing the content of higher alcohols.

Methods
The iTRAQ proteomic analysis method was used to analyze a blank group and an experimental group with an exogenous addition of 200 mg/L (NH4)2HPO4 during inoculation. The extracted intracellular proteins were processed by liquid chromatography-mass spectrometry and identified using bioinformatics tools. Real-time quantitative polymerase chain reaction was used to verify the gene expression of differentially expressed proteins.

Results
About 4062 proteins, including 123 upregulated and 88 downregulated proteins, were identified by iTRAQ-based proteomic analysis. GO and KEGG analysis uncovered that significant proteins were concentrated during carbohydrate metabolism, such as carbon metabolism, glyoxylate, and dicarboxylate metabolism, pyruvate metabolism, and the nitrogen metabolism, such as amino acid synthesis and catabolism pathway. In accordance with the trend of differential protein regulation in the central carbon metabolism pathway and the analysis of carbon metabolic flux, a possible regulatory model was proposed and verified, in which ammonium compensation facilitated glucose consumption, regulated metabolic flow direction into tricarboxylic acid, and further led to a decrease in higher alcohols. The results of RT-qPCR confirmed the authenticity of the proteomic analysis results at the level of gene.

Conclusion
Ammonium assimilation promoted by ammonium compensation regulated the intracellular carbon metabolism of S. cerevisiae and affected the distribution of metabolic flux. The carbon flow that should have gone to the synthesis pathway of higher alcohols was reversed to the TCA cycle, thereby decreasing the content of higher alcohols. These findings may contribute to an improved understanding of the molecular mechanism for the decrease in higher alcohol content through ammonium compensation.
A large Middle Devonian eubrachythoracid ‘placoderm’ (Arthrodira) jaw from northern Gondwana
Authors: Jobbins Melina , Rücklin Martin , Argyriou Thodoris , Klug Christian 
Published: January 2021

AbstractFor the understanding of the evolution of jawed vertebrates and jaws and teeth, ‘placoderms’ are crucial as they exhibit an impressive morphological disparity associated with the early stages of this process. The Devonian of Morocco is famous for its rich occurrences of arthrodire ‘placoderms’. While Late Devonian strata are rich in arthrodire remains, they are less common in older strata. Here, we describe a large tooth-bearing jaw element of Leptodontichthys ziregensis gen. et sp. nov., an eubrachythoracid arthrodire from the Middle Devonian of Morocco. This species is based on a large posterior superognathal with a strong dentition. The jawbone displays features considered synapomorphies of Late Devonian eubrachythoracid arthrodires, with one posterior and one lateral row of conical teeth oriented postero-lingually. μCT-images reveal internal structures including pulp cavities and dentinous tissues. The posterior orientation of the teeth and the traces of a putative occlusal contact on the lingual side of the bone imply that these teeth were hardly used for feeding. Similar to Compagopiscis and Plourdosteus, functional teeth were possibly present during an earlier developmental stage and have been worn entirely. The morphological features of the jaw element suggest a close relationship with plourdosteids. Its size implies that the animal was rather large.ZooBank LSID: urn:lsid:zoobank.org:pub:B707FB56-74A8-42C2-8BA0-D5BE1F32AB4A.
A classification method for social information of sellers on social network
Authors: Cui Haoliang , Shao Shuai , Niu Shaozhang , Shi Chengjie , Zhou Lingyu 
Published: January 2021

AbstractSocial e-commerce has been a hot topic in recent years, with the number of users increasing year by year and the transaction money exploding. Unlike traditional e-commerce, the main activities of social e-commerce are on social network apps. To classify sellers by the merchandise, this article designs and implements a social network seller classification scheme. We develop an app, which runs on the mobile phones of the sellers and provides the operating environment and automated assistance capabilities of social network applications. The app can collect social information published by the sellers during the assistance process, uploads to the server to perform model training on the data. We collect 38,970 sellers’ information, extract the text information in the picture with the help of OCR, and establish a deep learning model based on BERT to classify the merchandise of sellers. In the final experiment, we achieve an accuracy of more than 90%, which shows that the model can accurately classify sellers on a social network.
On a more accurate Hilbert-type inequality in the whole plane with the general homogeneous kernel
Authors: Huang Xingshou , Yang Bicheng 
Published: January 2021

AbstractBy the use of the weight coefficients, the idea of introduced parameters and the technique of real analysis, a more accurate Hilbert-type inequality in the whole plane with the general homogeneous kernel is given, which is an extension of the more accurate Hardy–Hilbert’s inequality. An equivalent form is obtained. The equivalent statements of the best possible constant factor related to several parameters, the operator expressions and a few particular cases are considered.
Engaging primary care providers in managing pediatric eating disorders: a mixed methods study
Authors: Lebow Jocelyn , Narr Cassandra , Mattke Angela , Gewirtz O’Brien Janna R. , Billings Marcie , Hathaway Julie , Vickers Kristin , Jacobson Robert , Sim Leslie 
Published: January 2021

AbstractBackgroundThe primary care setting offers an attractive opportunity for, not only the identification of pediatric eating disorders, but also the delivery of evidence-based treatment. However, constraints of this setting pose barriers for implementing treatment. For interventions to be successful, they need to take into consideration the perspectives of stakeholders. As such, the purpose of this study was to examine in-depth primary care providers’ perspective of challenges to identifying and managing eating disorders in the primary care setting.MethodsThis mixed methods study surveyed 60 Pediatric and Family Medicine providers across 6 primary care practices. Sixteen of these providers were further interviewed using a qualitative, semi-structured interview.ResultsProviders (n= 60, response rate of 45%) acknowledged the potential of primary care as a point of contact for early identification and treatment of pediatric eating disorders. They also expressed that this was an area of need in their practices. They identified numerous barriers to successful implementation of evidence-based treatment in this setting including scarcity of time, knowledge, and resources.ConclusionsInvestigations seeking to build capacities in primary care settings to address eating disorders must address these barriers.
A comparative study of methods for determining Intravoxel incoherent motion parameters in cervix cancer
Authors: Wang Xue , Song Jiao , Zhou Shengfa , Lu Yi , Lin Wenxiao , Koh Tong San , Hou Zujun , Yan Zhihan 
Published: January 2021

Abstract
Background
To compare different fitting methods for determining IVIM (Intravoxel Incoherent Motion) parameters and to determine whether the use of different IVIM fitting methods would affect differentiation of cervix cancer from normal cervix tissue.

Methods
Diffusion-weighted echo-planar imaging of 30 subjects was performed on a 3.0 T scanner with b-values of 0, 30, 100, 200, 400, 1000 s/mm2. IVIM parameters were estimated using the segmented (two-step) fitting method and by simultaneous fitting of a bi-exponential function. Segmented fitting was performed using two different cut-off b-values (100 and 200 s/mm2) to study possible variations due to the choice of cut-off. Friedman’s test and Student’s t-test were respectively used to compare IVIM parameters derived from different methods, and between cancer and normal tissues.

Results
No significant difference was found between IVIM parameters derived from the segmented method with b-value cutoff of 200 s/mm2 and the simultaneous fitting method (P>0.05). Tissue diffusivity (D) and perfusion fraction (f) were significantly lower in cervix cancer than normal tissue (P< 0.05).

Conclusions
IVIM parameters derived using fitting methods with small cutoff b-values could be different, however, the segmented method with b-value cutoff of 200 s/mm2 are consistent with the simultaneous fitting method and both can be used to differentiate between cervix cancer and normal tissue.
Successful treatment of G-CSF-related aortitis with prednisolone during preoperative chemotherapy for breast cancer: a case report
Authors: Koyama Yoichi , Adachi Kayo , Yagi Mio , Go Yoko , Orimoto Kyoko , Kawai Saori , Uenaka Natsuki , Okazaki Miki , Asaoka Mariko , Teraoka Saeko , Ueda Ai , Miyahara Kana , Kawate Takahiko , Kaise Hiroshi , Yamada Kimito , Ishikawa Takashi 
Published: January 2021

Abstract
Background
With the introduction of dose-dense therapy, the use of primary pegfilgrastim (PEG-G) has been increasing in breast cancer treatment. A rare side effect of PEG-G is aortitis. We describe a case of PEG-G-induced aortitis.

Case presentation
The patient was a 43-year-old woman with stage IIA breast cancer. Due to the subtype of triple-negative breast cancer, preoperative dose-dense epirubicin–cyclophosphamide chemotherapy was started. PEG-G was administered on day 3 after the first cycle of epirubicin–cyclophosphamide chemotherapy. On day 11, she had a fever (39.4 °C) and an elevated C-reactive protein level (27.1 mg/dL). Emergency computed tomography revealed diffused wall thickening of the aortic arch without any other signs of infection. Despite administering antibiotics, her general condition and laboratory findings deteriorated until day 18. Based on these observations, she was diagnosed with PEG-G-induced aortitis. Antibiotics were discontinued, and she was treated with prednisolone thereafter. Subsequently, her clinical symptoms and laboratory findings improved around day 39. A second computed tomography scan revealed a decrease in the aortic arch wall thickening, and she was discharged on day 43.

Conclusions
We successfully treated PEG-G-induced aortitis using prednisolone. Although this side effect is rare, cancer patients receiving PEG-G for chemotherapy should be monitored for aortic inflammation.
Influence of trees and associated variables on soil organic carbon: a review
Authors: Devi Angom Sarjubala 
Published: January 2021

AbstractThe level of soil organic carbon (SOC) fluctuates in different types of forest stands: this variation can be attributed to differences in tree species, and the variables associated with soil, climate, and topographical features. The present review evaluates the level of SOC in different types of forest stands to determine the factors responsible for the observed variation. Mixed stands have the highest amount of SOC, while coniferous (both deciduous-coniferous and evergreen-coniferous) stands have greater SOC concentrations than deciduous (broadleaved) and evergreen (broadleaved) tree stands. There was a significant negative correlation between SOC and mean annual temperature (MAT) and sand composition, in all types of forest stands. In contrast, the silt fraction has a positive correlation with SOC, in all types of tree stands. Variation in SOC under different types of forest stands in different landscapes can be due to differences in MAT, and the sand and silt fraction of soil apart from the type of forests.
The relationship of the serum endocan level with the CHA2DS2-VASc score in patients with paroxysmal atrial fibrillation
Authors: Ceyhun Gökhan 
Published: January 2021

AbstractBackgroundIn this study considering the relationship between serum endocan and CHA2DS2-VASc score, we assumed that endocan level could be a new biomarker for stroke risk in patients with paroxysmal atrial fibrillation (PAF). It was examined that endocan could be an alternative to determine the risk of stroke and anticoagulation strategy in patients with PAF. The CHA2DS2-VASc scores were calculated for 192 patients with PAF, and their serum endocan levels were measured. The patients were divided into two groups as those with low to moderate (0-1) and those with high (≥ 2) CHA2DS2-VASc scores, and the endocan levels were compared between these two groups.ResultsThe serum endocan level was significantly higher in the high CHA2DS2-VASc score group (p< 0.001). In the multivariate logistic regression analysis, endocan, C-reactive protein, and low-density lipoprotein were found to be independent determinants of the CHA2DS2-VASc score. The predictive value of endocan was analyzed using the ROC curve analysis, which revealed that endocan predicted a high stroke risk (CHA2DS2-VASc ≥ 2) at 82.5% sensitivity and 71.2% specificity at the cutoff value of 1.342.ConclusionThis study indicates that endocan is significantly associated with CHA2DS2-VASc score. We demonstrated that endocan could be a new biomarker for the prediction of a high stroke risk among patients diagnosed with PAF.