bluuebunny/crossref_metadata_2025 huggingface dataset:
Aqueous Oxytetracycline and Norfloxacin Sonocatalytic Degradation in the Presence of Peroxydisulfate with Multilayer Sheet-Like Zinc Oxide
Authors: Hsiao Shui-Shu , Wang Pei-Hua , Nguyen Nhat-Thien , Le Thuy-Trang , Chen Chih-Kuei , Chen Shiao-Shing , Chang Chang-Tang
Published: January 2021

Multilayer ZnO sheet-like flakes were synthesized by a simple method of precipitation and characterized by the techniques of X-Ray Diffraction (XRD) and Scanning Electron Microscopy (SEM). The findings are proven that the SEM images show the overall morphology of a single sheet-like
ZnO nanostructure made from uniformly thick nano-sheets. In an aqueous environment, the acoustic ability of the prepared material was assessed using ultrasound (US) radiation to degrade oxytetracycline (OTC) and norfloxacin (NF). To increase the degradation efficiency, a US/ZnO/peroxodisulfate
system was developed by introducing ammonium persulfate ((NH4)2S2O8) and sodium persulfate (Na2S2O8), exhibiting excellent synergistic effects. Result show the decomposition efficiency for NF removal with Na2S2O8
(64%) appeared to be slightly better than with (NH4)2S2O8 (56%). By contrast, the ultrasonic catalytic efficiency of Na2S2O8 (98%) was slightly better than that of (NH4)2S2O8
(94%) for OTC removal. The addition of scavengers to the US/ZnO/peroxodisulfate system through the NF and OTC results in the largest effect of holes. The degradation is considered to be often caused by holes. In this system, the Na2S2O8 can have two roles to
increase the rate of degradation: (1) The SO4− formed by Na2S2O8 under ultrasonic irradiation directly degraded to norfloxacin on ZnO surface; and (2) S2O82- behaved as an electron acceptor, inhibiting
recombination of electron hole pairs, enabling the development of more ·OH. Therefore, the synergistic effect significantly increases US/ZnO/peroxodisulfate sonocatalytic activity (Hu, S.B., et al., 2017. Aqueous norfloxacin sonocatalytic degradation with multilayer flower-like ZnO
in the presence of peroxydisulfate. Ultrasonics Sonochemistry, 38(1), pp.446–454).
Ambient Temperature Is an Independent Risk Factor for Acute Tonsillitis Incidence
Authors: Chen Jian , Zhang Yibo , Zhang Xin , Jiang Yingfang , Huang Yibo
Published: January 2021

Objective:

Acute tonsillitis is a common disease in otorhinolaryngology. Meteorological factors can affect the incidence of many infectious diseases. This study aims to analyze the correlation between acute tonsillitis and meteorological conditions.

Materials and Methods:

We collected the meteorological data, including daily temperature, humidity, and fine particulate matter (PM2.5) of Shanghai, China, from 2014 to 2015. The monthly number of acute tonsillitis cases in our hospital was also calculated and used as the outcome variable. The associations between them were evaluated, respectively.

Results:

The average number of patients diagnosed with acute tonsillitis in our hospital per month was 68.67 ± 18.67 from 2014 to 2015. The average temperature, humidity, and PM2.5 of Shanghai during the defined period was 16.84 °C ± 7.80 °C, 75.93% ± 5.45%, and 52.38 ± 14.23 μg/m3, respectively. The temperature was significantly positively associated with the acute tonsillitis cases number both in Pearson correlation analysis ( R = 0.423, P = .039) and in multivariate regression analysis (coefficient =2.194, P = .012). However, no correlation between the acute tonsillitis cases number and relative humidity or PM2.5 was found through a multivariate regression model ( P = .225 and P = .243), respectively.

Conclusion:

The high temperature was associated with an increased incidence of acute tonsillitis.
What Factors Influence an Officer’s Decision to Shoot? The Promise and Limitations of Using Public Data
Authors: Wheeler Andrew P. , Phillips Scott W. , Worrall John L. , Bishopp Stephen A.
Published: January 2021

We analyze a set of 207 Dallas Police Department officer-involved shooting incidents in reference to 1,702 instances in which officers from the same agency drew their firearms but did not shoot at the suspect. We find that situational factors of whether the suspect was armed and whether an officer was injured were the best predictors of the decision to shoot. We also find that African Americans are less likely than Whites to be shot. It is important to collect data on encounters in which weapons are and are not discharged. Analyses examining only shootings is fundamentally limited in assessing racial bias.
Mineralogy of volcanic calciocarbonatites from the Trig Point Hill debris flow, Kerimasi volcano, Tanzania: implications for the altered natrocarbonatite hypothesis
Authors: Mitchell Roger H. , Dawson J. Barry
Published: January 2021

A major debris flow, the Trig Point Hill flow, originating from Kerimasi volcano (Tanzania) contains numerous blocks of extrusive/pyroclastic carbonatites similar to those exposed at the rim of the currently inactive crater. The blocks of calcite carbonatite consist of: (1) large clasts of corroded and altered coarse grained calcite; (2) primary prismatic inclusion bearing phenocrystal calcite; and (3) a matrix consisting primarily of fine-grained prismatic calcite. The large clasts are inclusion free and exhibit a ‘corduroy-like’ texture resulting from solution along cleavage planes. The resulting voids are filled by brown Fe–Mn hydroxides/oxides and secondary calcite. The prismatic or lath-shaped phenocrystal calcite is not altered and contains melt inclusions consisting principally of primary Na–Ca carbonates which contain earlier-formed crystals of monticellite, periclase, apatite, Mn–Mg-magnetite, Mn–Fe-sphalerite and Nb-perovskite. Individual Na–Ca carbonate inclusions are of uniform composition, and the overall range of all inclusions analysed (wt.%) is from 28.7 to 35.9 CaO; 16.7–23.6 Na2O; 0.5–2.8 K2O, with minor SO3(1.1–2.2) and SrO (0.34–1.0). The Na–Ca carbonate compositions are similar to that of shortite, although this phase is not present. The Na–Ca carbonates are considered to be primary deuteric phases and not secondary minerals formed after nyerereite. Monticellite shows limited compositional variation and contains 2–4 wt.% MnO and 12 wt.% FeO and is Mn-poor relative to monticellite in Oldoinyo Lengai natrocarbonatite. Periclase is Fe-bearing with up to 13 wt.% FeO. Spinels are Cr-free, Mn-poor and belong to the magnetite–magnesioferrite series in contrast to Mn-rich spinels of the magnetite–jacobsite series occurring in Oldoinyo Lengai natrocarbonatite. The matrix in which the ‘corduroy’ clasts and phenocrystal calcite are set consists of closely packed small prisms of calcite lacking melt inclusions, with interstitial fine-grained apatite, baryte, strontianite and minor fluorite. Pore spaces are filled with secondary Mn–Fe hydroxides/oxides, anhydrite and gypsum. The hypothesis that flow-aligned calcite in volcanic calciocarbonatites from Kerimasi, Tinderet, Homa and Catanda is altered nyerereite is discussed and it is considered that these calcite are either primary phases or altered melilite. The nyerereite alteration hypothesis is discussed with respect to the volumetric and compositional aspects of pseudomorphism by dissolution–precipitation replacement mechanisms. This study concludes that none of the volcanic calciocarbonatites containing flow-aligned calcite phenocrysts are altered natrocarbonatite.
The clinical value of cardiopulmonary exercise testing in the modern era
Authors: Laveneziana Pierantonio , Di Paolo Marcello , Palange Paolo
Published: January 2021

Cardiopulmonary exercise testing (CPET) has long been used as diagnostic tool for cardiac diseases. During recent years CPET has been proven to be additionally useful for 1) distinguishing between normal and abnormal responses to exercise; 2) determining peak oxygen uptake and level of disability; 3) identifying factors contributing to dyspnoea and exercise limitation; 4) differentiating between ventilatory (respiratory mechanics and pulmonary gas exchange), cardiovascular, metabolic and peripheral muscle causes of exercise intolerance; 5) identifying anomalies of ventilatory (respiratory mechanics and pulmonary gas exchange), cardiovascular and metabolic systems, as well as peripheral muscle and psychological disorders; 6) screening for coexistent ischaemic heart disease, peripheral vascular disease and arterial hypoxaemia; 7) assisting in planning individualised exercise training; 8) generating prognostic information; and 9) objectively evaluating the impact of therapeutic interventions.

As such, CPET is an essential part of patients' clinical assessment. This article belongs to the special series on the “Ventilatory efficiency and its clinical prognostic value in cardiorespiratory disorders”, addressed to clinicians, physiologists and researchers, and aims at encouraging them to get acquainted with CPET in order to help and orient the clinical decision concerning individual patients.
Chronic lung diseases: prospects for regeneration and repair
Authors: Barnes Peter J. , Anderson Gary P. , Fagerås Malin , Belvisi Maria G.
Published: January 2021

COPD and idiopathic pulmonary fibrosis (IPF) together represent a considerable unmet medical need, and advances in their treatment lag well behind those of other chronic conditions. Both diseases involve maladaptive repair mechanisms leading to progressive and irreversible damage. However, our understanding of the complex underlying disease mechanisms is incomplete; with current diagnostic approaches, COPD and IPF are often discovered at an advanced stage and existing definitions of COPD and IPF can be misleading. To halt or reverse disease progression and achieve lung regeneration, there is a need for earlier identification and treatment of these diseases. A precision medicine approach to treatment is also important, involving the recognition of disease subtypes, or endotypes, according to underlying disease mechanisms, rather than the current “one-size-fits-all” approach. This review is based on discussions at a meeting involving 38 leading global experts in chronic lung disease mechanisms, and describes advances in the understanding of the pathology and molecular mechanisms of COPD and IPF to identify potential targets for reversing disease degeneration and promoting tissue repair and lung regeneration. We also discuss limitations of existing disease measures, technical advances in understanding disease pathology, and novel methods for targeted drug delivery.
Feasibility and integration of an intensive emergency pediatric care curriculum in Armenia
Authors: Baghdassarian Aline , Best Al M. , Virabyan Anushavan , Alexanian Claire , Shekherdimian Shant , Santen Sally A. , Simonyan Hambartzum
Published: January 2021

Background

Emergency pediatric care curriculum (EPCC) was developed to address the need for pediatric rapid assessment and resuscitation skills among out-of-hospital emergency providers in Armenia. This study was designed to evaluate the effectiveness of EPCC in increasing physicians’ knowledge when instruction transitioned to local instructors. We hypothesize that (1) EPCC will have a positive impact on post-test knowledge, (2) this effect will be maintained when local trainers teach the course, and (3) curriculum will satisfy participants.

Methods

This is a quasi-experimental, pre-test/post-test study over a 4-year period from October 2014‑November 2017. Train-the-trainer model was used. Primary outcomes are immediate knowledge acquisition each year and comparison of knowledge acquisition between two cohorts based on North American vs local instructors. Descriptive statistics was used to summarize results. Pre-post change and differences across years were analyzed using repeated measures mixed models.

Results

Test scores improved from pretest mean of 51% (95% CI 49.6 to 53.0%) to post-test mean of 78% (95% CI 77.0 to 79.6%, p < 0.001). Average increase from pre- to post-test each year was 27% (95% CI 25.3 to 28.7%). Improvement was sustained when local instructors taught the course (p = 0.74). There was no difference in improvement when experience in critical care, EMS, and other specialties were compared (p = 0.23). Participants reported satisfaction and wanted the course repeated. In 2017, EPCC was integrated within the Emergency Medicine residency program in Armenia.

Discussion

This program was effective at impacting immediate knowledge as well as participant satisfaction and intentions to change practice. This knowledge acquisition and reported satisfaction remained constant even when the instruction was transitioned to the local instructors after 2 years. Through a partnership between the USA and Armenia, we provided OH-EPs in Armenia with an intensive educational experience to attain knowledge and skills necessary to manage acutely ill or injured children in the out-of-hospital setting.

Conclusions

EPCC resulted in significant improvement in knowledge and was well received by participants. This is a viable and sustainable model to train providers who have otherwise not had formal education in this field.
SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
Authors: Aguirre-Plans Joaquim , Meseguer Alberto , Molina-Fernandez Ruben , Marín-López Manuel Alejandro , Jumde Gaurav , Casanova Kevin , Bonet Jaume , Fornes Oriol , Fernandez-Fuentes Narcis , Oliva Baldo
Published: January 2021

Background

Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities.

Results

Here, we present the SPServer, a web server that applies the Split-Statistical Potentials to analyze protein folds and protein interfaces. SPServer provides global scores as well as residue/residue-pair profiles presented as score plots and maps. This level of detail allows users to: (1) identify potentially problematic regions on protein structures; (2) identify disrupting amino acid pairs in protein interfaces; and (3) compare and analyze the quality of tertiary and quaternary structural models.

Conclusions

While there are many web servers that provide scoring functions to assess the quality of either protein folds or PPI structures, SPServer integrates both aspects in a unique easy-to-use web server. Moreover, the server permits to locally assess the quality of the structures and interfaces at a residue level and provides tools to compare the local assessment between structures.

Server address

https://sbi.upf.edu/spserver/.
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes
Authors: Ruiz-Perez Carlos A. , Conrad Roth E. , Konstantinidis Konstantinos T.
Published: January 2021

Background

High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. Although several approaches exist for genome annotation, these are typically not designed for easy incorporation into analysis pipelines, do not combine results from different annotation databases or offer easy-to-use summaries of metabolic reconstructions, and typically require large amounts of computing power for high-throughput analysis not available to the average user.

Results

Here, we introduce MicrobeAnnotator, a fully automated, easy-to-use pipeline for the comprehensive functional annotation of microbial genomes that combines results from several reference protein databases and returns the matching annotations together with key metadata such as the interlinked identifiers of matching reference proteins from multiple databases [KEGG Orthology (KO), Enzyme Commission (E.C.), Gene Ontology (GO), Pfam, and InterPro]. Further, the functional annotations are summarized into Kyoto Encyclopedia of Genes and Genomes (KEGG) modules as part of a graphical output (heatmap) that allows the user to quickly detect differences among (multiple) query genomes and cluster the genomes based on their metabolic similarity. MicrobeAnnotator is implemented in Python 3 and is freely available under an open-source Artistic License 2.0 from https://github.com/cruizperez/MicrobeAnnotator.

Conclusions

We demonstrated the capabilities of MicrobeAnnotator by annotating 100 Escherichia coli and 78 environmental Candidate Phyla Radiation (CPR) bacterial genomes and comparing the results to those of other popular tools. We showed that the use of multiple annotation databases allows MicrobeAnnotator to recover more annotations per genome compared to faster tools that use reduced databases and is computationally efficient for use in personal computers. The output of MicrobeAnnotator can be easily incorporated into other analysis pipelines while the results of other annotation tools can be seemingly incorporated into MicrobeAnnotator to generate summary plots.
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism
Authors: Ye Yilin , Wang Jian , Xu Yunwan , Wang Yi , Pan Youdong , Song Qi , Liu Xing , Wan Ji
Published: January 2021

Background

Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learning algorithms and mass spectrometry data have indeed showed improvement on the average predicting power for class I HLA-peptide interaction. However, their prediction performances show great variability over individual HLA alleles and peptides with different lengths, which is particularly the case for HLA-C alleles due to the limited amount of experimental data. To meet the increasing demand for attaining the most accurate HLA-peptide binding prediction for individual patient in the real-world clinical studies, more advanced deep learning framework with higher prediction accuracy for HLA-C alleles and longer peptides is highly desirable.

Results

We present a pan-allele HLA-peptide binding prediction framework—MATHLA which integrates bi-directional long short-term memory network and multiple head attention mechanism. This model achieves better prediction accuracy in both fivefold cross-validation test and independent test dataset. In addition, this model is superior over existing tools regarding to the prediction accuracy for longer ligand ranging from 11 to 15 amino acids. Moreover, our model also shows a significant improvement for HLA-C-peptide-binding prediction. By investigating multiple-head attention weight scores, we depicted possible interaction patterns between three HLA I supergroups and their cognate peptides.

Conclusion

Our method demonstrates the necessity of further development of deep learning algorithm in improving and interpreting HLA-peptide binding prediction in parallel to increasing the amount of high-quality HLA ligandome data.
Reduced translation efficiency due to novel splicing variants in 5′ untranslated region and identification of novel cis-regulatory elements in canine and human BRCA2
Authors: Yoshikawa Yasunaga , Kozuma Hajime , Morimatsu Masami , Sugawara Kaori , Orino Koichi
Published: January 2021

Background

Breast cancer 2, early onset (BRCA2) is a tumor suppressor gene. The protein encoded by this gene plays an important role in homologous recombination (HR)-mediated DNA repair. Deleterious mutations in BRCA2 and downregulation of its expression have been associated with tumorigenesis in dogs and humans. Thus, regulation of BRCA2 expression level is important for maintaining homeostasis in homologous recombination.

Results

In this study, the mechanisms that regulate the expression of BRCA2 were proposed. Novel splicing variants were identified in the 5′ untranslated region (UTR) of canine and human BRCA2 in canine testis, canine ovary, and canine and human cultured cell lines. In cultured cells, the ratio of BRCA2 splicing variants at the 5′ UTR was altered by serum starvation. These novel splicing variants, excluding one of the canine splicing variants, were found to reduce the translational efficiency. Additionally, the DNA sequence in human BRCA2 intron 1 harbored novel cis-regulatory elements. Three silencer and two enhancer cis-regulatory elements were identified in human BRCA2 intron 1.

Conclusions

This study demonstrates that BRCA2 expression level is regulated via 5′ UTR splicing variants and that the BRCA2 intron 1 region harbors cis-regulatory elements.
A novel method for isolation and culture of primary swine gastric epithelial cells
Authors: Bautista-Amorocho Henry , Silva-Sayago Jorge Alexander , Goyeneche-Patino Diego A. , Pérez-Cala Tania Liseth , Macías-Gómez Fabio , Arango-Viana Juan Carlos , Martínez Alonso
Published: January 2021

Background

Culturing primary epithelial cells has a major advantage over tumor-derived or immortalized cell lines as long as their functional phenotype and genetic makeup are mainly maintained. The swine model has shown to be helpful and reliable when used as a surrogate model for human diseases. Several porcine cell lines have been established based on a variety of tissues, which have shown to extensively contribute to the current understanding of several pathologies, especially cancer. However, protocols for the isolation and culture of swine gastric epithelial cells that preserve cell phenotype are rather limited. We aimed to develop a new method for establishing a primary epithelial cell culture from the fundic gland region of the pig stomach.

Results

Mechanical and enzymatic dissociation of gastric tissue was possible by combining collagenase type I and dispase II, protease inhibitors and antioxidants, which allowed the isolation of epithelial cells from the porcine fundic glands showing cell viability > 90% during the incubation period. Gastric epithelial cells cultured in RPMI 1640, DMEM-HG and DMEM/F12 media did not contribute enough to cell adhesion, cluster formation and cell proliferation. By contrast, William’s E medium supplemented with growth factors supports confluency and proliferation of a pure epithelial cell monolayer after 10 days of incubation at 37 °C, 5% CO2. Mucin-producing cell phenotype of primary isolates was confirmed by PAS staining, MUC1 by immunohistochemistry, as well as the expression of MUC1 and MUC20 genes by RT-PCR and cDNA sequencing. Swine gastric epithelial cells also showed origin-specific markers such as cytokeratin cocktail (AE1/AE3) and cytokeratin 18 (CK-18) using immunohistochemical and immunofluorescence methods, respectively.

Conclusions

A new method was successfully established for the isolation of primary gastric epithelial cells from the fundic gland zone through a swine model based on a combination of tissue-specific proteases, protease inhibitors and antioxidants after mechanical cell dissociation. The formulation of William’s E medium with growth factors for epithelial cells contributes to cell adhesion and preserves functional primary cells phenotype, which is confirmed by mucin production and expression of typical epithelial markers over time.
ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus
Authors: Johnston Dayle , Kim JaeWoo , Taylor Jeremy F. , Earley Bernadette , McCabe Matthew S. , Lemon Ken , Duffy Catherine , McMenamy Michael , Cosby S. Louise , Waters Sinéad M.
Published: January 2021

Background

Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues.

Results

Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci.

Conclusions

The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.
Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)
Authors: Feng Shan , Fang Hongcheng , Liu Xia , Dong Yuhui , Wang Qingpeng , Yang Ke Qiang
Published: January 2021

Background

Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance, the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.

Results

The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4–23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14,525 DELs were identified, including 10,645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.

Conclusions

The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.
Chromatin loop anchors contain core structural components of the gene expression machinery in maize
Authors: Deschamps Stéphane , Crow John A. , Chaidir Nadia , Peterson-Burch Brooke , Kumar Sunil , Lin Haining , Zastrow-Hayes Gina , May Gregory D.
Published: January 2021

Background

Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity.

Results

Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions.

Conclusions

Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.
Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response
Authors: Zhang Hao , Yu Zhenjia , Yao Xiaodie , Chen Jingli , Chen Xing , Zhou Huiwen , Lou Yuxia , Ming Feng , Jin Yue
Published: January 2021

Background

Auxin is critical to plant growth and development, as well as stress responses.Small auxin-up RNA(SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of fewSAURgenes is known owing to functional redundancy among the many family members.

Results

In this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs fromAnthoceros angustus,Marchantia polymorpha,Physcomitrella patens,Selaginella moellendorffii,Ginkgo biloba,Gnetum montanum,Amborella trichopoda,Arabidopsis thaliana,Oryza sativa,Zea mays,Glycine max,Medicago truncatulaandSetaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta,SAURfamily have appeared very large expansion. The number ofSAURgene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed thatSAURgenes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis ofSAURgenes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade.

Conclusions

This study provides insights into the evolution and function of theSAURgene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions ofSAURfamily members should employ a clade as the study unit.
Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)
Authors: Wu Huanhuan , Zheng Lei , Qanmber Ghulam , Guo Mengzhen , Wang Zhi , Yang Zuoren
Published: January 2021

Background

The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton.

Results

In this study, 108, 55, and 52PHDgenes were identified inG. hirsutum,G. raimondii, andG. arboreum, respectively. A total of 297PHDgenes from three cotton species,Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis forGhPHDgenes.GhPHDgenes were unevenly distributed on each chromosome. However, moreGhPHDgenes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, andGhPHDgenes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance ofGhPHDgene family. Expression pattern analysis based on RNA-seq data showed that mostGhPHDgenes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions ofGhPHDsin plant growth and development. Moreover, analysis ofcis-acting elements revealed thatGhPHDsmay respond to a variety of abiotic and phytohormonal stresses. In this regard, someGhPHDgenes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated thatGhPHDsare essential for plant growth and development, whileGhPHDgenes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions.

Conclusion

This study will provide useful information to facilitate further research related to the vital roles ofGhPHDgene family in plant growth and development.
Circulatory collapse during wound closure in spine surgery with an unknown cause: a possible adverse effect of topical application of vancomycin?
Authors: Zhang Xiaoqing , Zhai Wenwen , Li Min , Guo Xiangyang
Published: January 2021

Background

Vancomycin (VCM) is effective in fighting Gram-positive bacteria related severe infections, and topical application of VCM powder is widely used in orthopedic surgery to prevent wound infection. However, VCM could lead to infusion rate-dependent antibody-and complement-independent anaphylaxis reaction by inducing direct release of histamine.

Case presentation

We retrospectively analyzed seven cases of severe hypotension and shock during wound closure or immediately after orthopedic surgery with unidentifiable reasons. We found that these cases were all associated with local application of VCM powder during wound closure process. Two patients experienced sudden cardiac arrest. Most of the cases (6/7) with circulatory collapse were discharged without severe sequelae. While one case with application of 3 g VCM developed cardiac arrest and remained in a coma due to hypoxic-hypoxic encephalopathy. The clinical presentations and the time of the shock onset were considered to be related with a VCM induced anaphylaxis reaction. However, as this was a retrospective study, and there was no laboratory examination performed, the conclusion was made upon differential diagnosis based on clinical manifestations and the timing of the shock.

Conclusions

Local application of VCM may not be as safe as was once believed and may lead to a related anaphylaxis. As VCM induced infusion-rate dependent, non-IgE mediated anaphylaxis is characterized by delayed occurrence, severe hypotension and even circulatory collapse, surgeons and anesthesiologists should be extra vigilant during and after VCM application.
Analysis for interaction between interleukin-35 genes polymorphisms and risk factors on susceptibility to coronary heart disease in the Chinese Han population
Authors: Li Hu , Liu Ying-Xue , Huang Jin-Yan , Zhu Yu-Feng , Wang Kui
Published: January 2021

Background

The relationship between IL-35 genes polymorphism and susceptibility to coronary heart disease has not been tested in the largest Han population in China. The aim of this study was to explore the effect of single nucleotide polymorphisms (SNPs) of interleukin-35 (IL-35) genes and its relationship with environment on the risk of coronary heart disease (CHD).

Methods

We performed Hardy–Weinberg equilibrium test on the control group. The relationship between the four SNPs of IL-35 genes and the risk of coronary heart disease was studied by multivariate logistic regression. The best interaction was identified with generalized multifactor dimensionality reduction (GMDR). Logistic regression was used for investigation on association between four SNPs and CHD risk.

Results

Logistic regression analysis showed that the C allele of rs428253 and the G allele of rs2243115 were independently correlated with increased risk of CHD, and adjusted ORs (95% CI) were 1.91 (1.28–2.64) and 1.80 (1.30–2.23), respectively. However, there was no significant association between CHD and rs4740 or rs568408. GMDR model indicated a best model for CHD risk consisted of rs428253 and current smoking, which scored 10/10 for both the sign test and cross-validation consistency (p = 0.010). Therefore, this overall multi-dimensional model had the highest cross-validation consistency, regardless of how the data were divided. This provided an evidence of gene–environment interaction effects. We also found that current smokers with rs428253-GC/CC genotype have the highest CHD risk, compared to never smokers with rs428253-GG genotype, OR (95% CI) = 3.04 (1.71–4.41), after adjustment for age, gender, hypertension, T2DM and alcohol consumption status.

Conclusions

In this study, the C allele of rs428253 and the G allele of rs2243115, and the interaction rs428253 and current smoking were correlated with increased risk of CHD.
Partial anomalous pulmonary venous return after orthotopic heart transplantation case report
Authors: A. Salas de Armas Ismael , Patel Manish K. , Akkanti Bindu , Salazar Jorge , Kar Biswajit , Gregoric Igor D.
Published: January 2021

Background

Partial anomalous pulmonary venous return (PAPVR) is a congenital heart defect. Reports of repair and treatment in pediatric cases have been published, but incidence of PAPVR in adults is not common. To our knowledge, there has not been a diagnosis of left-sided PAPVR after a heart transplant an in adult patient.

Case presentation

A 62-year-old patient with ischemic cardiomyopathy and systolic heart failure underwent orthotopic heart transplantation. The immediate post-operative course was remarkable for an elevated cardiac index and pulmonary artery pressures as well as decreased systemic vascular resistance. The post-operative echocardiogram did not reveal an intra-cardiac shunt. However, computed tomographic angiography (CTA) showed a left superior pulmonary vein draining into the innominate vein. Operative repair of the left superior pulmonary venous connection to the left atrial appendage was completed under cardiopulmonary bypass with beating heart. Her hemodynamics improved immediately, and she had an unremarkable postoperative course.

Conclusions

While uncommon, any patient with a high cardiac output and abnormal hemodynamics after heart transplant should be evaluated for the existence of a shunt. While not a part of all traditional preoperative imaging protocols, a chest CTA should be considered if PAPVR is suspected as it can both diagnose the condition and enable a plot of the corrective course of surgical action.
Ankle brachial index as a surrogate to vascular imaging in evaluation of peripheral artery disease in patients with type 2 diabetes
Authors: Ugwu Ejiofor , Anyanwu Anthony , Olamoyegun Michael
Published: January 2021

Background

Peripheral artery disease (PAD) is common in persons with type 2 diabetes (T2DM) and contributes significantly to cardiovascular morbidity and mortality. Controversy exists regarding the utility of ankle brachial index (ABI) for clinical diagnosis of PAD in persons with diabetes. The aim of this study was to evaluate the reliability of ABI for diagnosis of PAD in patients with T2DM using duplex ultrasonography (DUS) as the gold standard.

Results

A total of 319 legs from 163 patients comprising of 156 subjects with intact legs and 7 patients who had undergone unilateral lower limb amputations were studied. The mean age of the participants was 56.1 ± 17.3 years. One hundred and ninety-five legs (61.1%) had sonographically confirmed PAD which was mild, moderate and severe in 40%, 41.5% and 18.5% respectively. The accuracy of ABI in detecting PAD was 76.7% for mild stenosis, 91.7% for moderate stenosis and 93.1% for severe stenosis. The sensitivity of ABI improved with increasing severity of arterial stenosis, reaching 100% in severe cases. ABI demonstrated good agreement with DUS [kappa = 0.65 (95% CI 0.49–0.88), P < 0.001].

Conclusion

In comparison to DUS, the ABI demonstrated good reliability for diagnosis of PAD in high risk T2DM patients. The utility of this simple and non-invasive procedure should therefore be maximized in clinical practice.
Time to peak bilirubin concentration and advanced AKI were associated with increased mortality in rheumatic heart valve replacement surgery patients with severe postoperative hyperbilirubinemia: a retrospective cohort study
Authors: Chen Xiaolan , Bai Ming , Zhao Lijuan , Yu Yan , Yue Yuan , Sun Shiren , Chen Xiangmei
Published: January 2021

Background

Hyperbilirubinemia after heart valve surgery (HVS) with cardiopulmonary bypass is frequently observed and associated with worse outcomes. We investigated the characteristics and prognosis of patients with severe hyperbilirubinemia after HVS for rheumatic heart disease (RHD) to identify the clinical outcomes and potential risk factors.

Methods

Between 2015 and 2018, patients who underwent HVS in the cardiac surgery intensive care unit of our hospital were retrospectively screened. Risk factors for acute kidney injury (AKI), the requirement for continuous renal replacement therapy (CRRT), and in-hospital and long-term mortality were identified by univariate and multivariate analyses. The patient survival proportion was graphically presented with the Kaplan–Meier method.

Results

A total of 149 patients who underwent HVS for RHD and had severe postoperative hyperbilirubinemia were included. Of the included patients, 80.5% developed postoperative AKI, and 18.1% required CRRT. The in-hospital mortality was 30.2%. Backward logistic regression analysis showed that the time to peak TB concentration (odds ratio [OR] 1.557, 95% confidence interval [CI] 1.259–1.926;P < 0.001) and advanced AKI (stage 2 and 3 AKI) (OR 19.408, 95% CI 6.553–57.482;P < 0.001) were independent predictors for in-hospital mortality. The cutoff value of the time to peak TB levels for predicting in-hospital mortality was 5 postoperative days.

Conclusions

Severe postoperative hyperbilirubinemia is a life-threatening complication in patients who undergo HVS for RHD. Patients whose bilirubin levels continued to increase past the 5th postoperative day and who had advanced AKI (stages 2 and 3) were associated with a higher risk of mortality.
Overexpression of P-glycoprotein, MRP2, and CYP3A4 impairs intestinal absorption of octreotide in rats with portal hypertension
Authors: Sun Xiaoyu , Tang Shunxiong , Hou Binbin , Duan Zhijun , Liu Zhen , Li Yang , He Shoucheng , Wang Qiuming , Chang Qingyong
Published: January 2021

Background

Portal hypertension (PH) is the main cause of complications and death in liver cirrhosis. The effect of oral administration of octreotide (OCT), a drug that reduces PH by the constriction of mesenteric arteries, is limited by a remarkable intestinal first-pass elimination.

Methods

The bile duct ligation (BDL) was used in rats to induce liver cirrhosis with PH to examine the kinetics and molecular factors such as P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cytochrome P450 3A4 (CYP3A4) influencing the intestinal OCT absorption via in situ and in vitro experiments on jejunal segments, transportation experiments on Caco-2 cells and experiments using intestinal microsomes and recombinant human CYP3A4. Moreover, RT-PCR, western blot, and immunohistochemistry were performed.

Results

Both in situ and in vitro experiments in jejunal segments showed that intestinal OCT absorption in both control and PH rats was largely controlled by P-gp and, to a lesser extent, by MRP2. OCT transport mediated by P-gp and MRP2 was demonstrated on Caco-2 cells. The results of RT-PCR, western blot, and immunohistochemistry suggested that impaired OCT absorption in PH was in part due to the jejunal upregulation of these two transporters. The use of intestinal microsomes and recombinant human CYP3A4 revealed that CYP3A4 metabolized OCT, and its upregulation in PH likely contributed to impaired drug absorption.

Conclusions

Inhibition of P-gp, MRP2, and CYP3A4 might represent a valid option for decreasing intestinal first-pass effects on orally administered OCT, thereby increasing its bioavailability to alleviate PH in patients with cirrhosis.