bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome evolution and the emergence of pathogenicity in avian Escherichia coli
Authors: Mageiros Leonardos , Méric Guillaume , Bayliss Sion C. , Pensar Johan , Pascoe Ben , Mourkas Evangelos , Calland Jessica K. , Yahara Koji , Murray Susan , Wilkinson Thomas S. , Williams Lisa K. , Hitchings Matthew D. , Porter Jonathan , Kemmett Kirsty , Feil Edward J. , Jolley Keith A. , Williams Nicola J. , Corander Jukka , Sheppard Samuel K. 
Published: February 2021

AbstractChickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
Sludge amendment accelerating reclamation process of reconstructed mining substrates
Authors: Li Dan , Yin Ningning , Xu Ruiwei , Wang Liping , Zhang Zhen , Li Kang 
Published: February 2021

AbstractWe constructed a mining soil restoration system combining plant, complex substrate and microbe. Sludge was added to reconstructed mine substrates (RMS) to accelerate the reclamation process. The effect of sludge on plant growth, microbial activity, soil aggregate stability, and aggregation-associated soil characteristics was monitored during 10 years of reclamation. Results show that the height and total biomass of ryegrass increases with reclamation time. Sludge amendment increases the aggregate binding agent content and soil aggregate stability. Soil organic carbon (SOC) and light-fraction SOC (LFOC) in the RMS increase by 151% and 247% compared with those of the control, respectively. A similar trend was observed for the glomalin-related soil protein (GRSP). Stable soil aggregate indexes increase until the seventh year. In short, the variables of RMS determined after 3–7 years insignificantly differ from those of the untreated sample in the tenth-year. Furthermore, significant positive correlations between the GRSP and SOC and GRSP and soil structure-related variables were observed in RMS. Biological stimulation of the SOC and GRSP accelerates the recovery of the soil structure and ecosystem function. Consequently, the plant–complex substrate–microbe ecological restoration system can be used as an effective tool in early mining soil reclamation.
Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation
Authors: Duan Mingzheng , Bao Haiying , Bau Tolgor 
Published: February 2021

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.
Optical characterization of non-thermal plasma jet energy carriers for effective catalytic processing of industrial wastewaters
Authors: Naz M. Y. , Shukrullah S. , Rehman S. U. , Khan Y. , Al-Arainy A. A. , Meer R. 
Published: February 2021

AbstractAn argon plasma jet was sustained in open air and characterized for its chemical composition. The optically characterized plasma jet was used to treat industrial wastewater containing mixed textile dyes and heavy metals. Since plasma jet produces UV-radiations, the photocatalytic TiO2 was used to enhance plasma treatment efficiency especially for degradation of dyes. Mixed anatase and rutile phases of TiO2 (5.2–8.5 nm) were produced through surfactant assisted sol–gel approach. The emission spectrum confirmed the presence of excited argon, OH, excited nitrogen, excited oxygen, ozone and nitric oxide in the plasma jet. The spectral lines of excited Ar, NO, O3, OH−, N2, $${\mathrm{N}}_{2}^{+}$$

N

2

+

, O, $${\mathrm{O}}_{2}^{+}$$

O

2

+

and O+ species were observed at wavelength of 695–740 nm, 254.3 nm, 307.9 nm, 302–310 nm, 330–380 nm, 390–415 nm, 715.6 nm, 500–600 nm and 400–500 nm. These reactive species decompose the organic pollutants and separate the heavy metals from the water samples. The conductivity of plasma exposed water samples increased while pH and hardness decreased. The atomic absorption spectrophotometry analysis confirmed the presence of heavy metals in the samples, which were effectively removed through plasma treatment. Finally, the effect of plasma treatment on Staphylococcus aureus strains was more pronounced than Escherichia coli strains.
Bacterial bile duct colonization in perihilar cholangiocarcinoma and its clinical significance
Authors: Bednarsch Jan , Czigany Zoltan , Heij Lara Rosaline , Luedde Tom , van Dam Ronald , Lang Sven Arke , Ulmer Tom Florian , Hornef Mathias Walter , Neumann Ulf Peter 
Published: February 2021

AbstractAbdominal infections including cholangitis represent a major problem in patients with perihilar cholangiocarcinoma (pCCA). Thus, we investigated bacterial colonization of the bile ducts and determined its impact on postoperative outcome focusing on abdominal infections. A cohort of 95 pCCA patients who underwent surgery between 2010 and 2019 with available intraoperative microbial bile cultures were analyzed regarding bile duct colonization and postoperative abdominal infection by group comparisons and logistic regressions. 84.2% (80/95) showed bacterial colonization of the bile ducts and 54.7% (52/95) developed postoperative abdominal infections. Enterococcus faecalis (38.8%, 31/80), Enterococcus faecium (32.5%, 26/80), Enterobacter cloacae (16.3%, 13/80) and Escherichia coli (11.3%, 9/80) were the most common bacteria colonizing the bile ducts and Enterococcus faecium (71.2%, 37/52), Enterococcus faecalis (30.8%, 16/52), Enterobacter cloacae (25.0%, 13/52) and Escherichia coli (19.2%, 10/52) the most common causes of postoperative abdominal infection. Further, reduced susceptibility to perioperative antibiotic prophylaxis (OR = 10.10, p = .007) was identified as independent predictor of postoperative abdominal infection. Bacterial colonization is common in pCCA patients and reduced susceptibility of the bacteria to the intraoperative antibiotic prophylaxis is an independent predictor of postoperative abdominal infections. Adapting antibiotic prophylaxis might therefore have the potential to improve surgical outcome pCCA patients.
An under-ice bloom of mixotrophic haptophytes in low nutrient and freshwater-influenced Arctic waters
Authors: Søgaard Dorte H. , Sorrell Brian K. , Sejr Mikael K. , Andersen Per , Rysgaard Søren , Hansen Per Juel , Skyttä Annaliina , Lemcke Signe , Lund-Hansen Lars Chresten 
Published: February 2021

AbstractThe pelagic spring bloom is essential for Arctic marine food webs, and a crucial driver of carbon transport to the ocean depths. A critical challenge is understanding its timing and magnitude, to predict its changes in coming decades. Spring bloom onset is typically light-limited, beginning when irradiance increases or during ice breakup. Here we report an acute 9-day under-ice algal bloom in nutrient-poor, freshwater-influenced water under 1-m thick sea ice. It was dominated by mixotrophic brackish water haptophytes (Chrysochromulina/Prymnesium) that produced 5.7 g C m−2new production. This estimate represents about half the annual pelagic production, occurring below sea ice with a large contribution from the mixotrophic algae bloom. The freshwater-influenced, nutrient-dilute and low light environment combined with mixotrophic community dominance implies that phagotrophy played a critical role in the under-ice bloom. We argue that such blooms dominated by potentially toxic mixotrophic algae might become more common and widespread in the future Arctic Ocean.
Using electrical impedance tomography for rapid determination of starch and soluble sugar contents in Rosa hybrida
Authors: Qian Ji , Zhou Juan , Di Bao , Liu Yang , Zhang Gang , Yang Xin 
Published: February 2021

AbstractSoluble sugars and starches are important metabolites of plant life and physiological markers of plant stress response. There is an urgent need to develop a non-destructive and rapid method for determining plant starch and soluble sugar contents. Electrical impedance tomography (EIT) technology has been used to determine the physiological state and cold resistance of select plant tissues. However, so far there have been no reports on the use of EIT for the rapid estimation of soluble sugar and starch contents. In this study, EIT was used to obtain reconstructed voltage values and estimate starch and soluble sugar contents in the stems of three Rosa hybrida cultivars during February to May, which were grown in the Specimen Park (38° 50′ N, 115° 26′ E) of Hebei Agricultural University, Baoding City, Hebei Province, China. Stems from two of the cultivars were used for establishing regression models for starch and soluble sugar contents as functions of reconstructed voltage values. The third cultivar was used to test the accuracy of the regression models. The quadratic regression model was best for determining soluble sugar content and the logarithmic regression model was best for determining starch content. Thus, this research provided technical support for using EIT to analyze changes in physiological parameters and to rapidly estimate physiological indexes of plants. More studies were now needed to validate the results in this paper.
Prevalence and molecular characterization of glucose-6-phosphate dehydrogenase deficiency in the Lue ethnic group of northern Thailand
Authors: Sathupak Suwapat , Leecharoenkiat Kamonlak , Kampuansai Jatupol 
Published: February 2021

AbstractGlucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most common enzyme disorders. Prevalence and variant distribution of G6PD deficiency can vary in different regions and among differing ethnic groups. To reveal the G6PD frequency and molecular characterization among the Lue ethnic group of northern Thailand, blood samples of 296 unrelated individuals collecting from 6 Lue villages were analyzed. The observed G6PD enzyme activity ranged from 0.11 to 20.60 U/g Hb. Overall, 13.51% (40/296) of the individuals were identified as having G6PD deficiency status. The prevalence in males was 14.28% (20/140), while that of females was 12.82% (20/156). The most common G6PD variants in the Lue were the Kaiping 1388G > A (5.40%) and Canton 1376G > T (6.42%) types. Observed prevalence and variant types of the G6PD gene in the Lue population are similar to that of the Tai-Kadai speaking ethnic groups in southern China, which is consistent with their historically close line of ancestry. However, the founder effect that occurred during the Lue’s transboundary migration from China to Thailand showed its impact upon different patterns of G6PD distribution among each Lue village.
Neutrophil degranulation interconnects over-represented biological processes in atrial fibrillation
Authors: Kawasaki Makiri , Meulendijks Eva R. , van den Berg Nicoline W. E. , Nariswari Fransisca A. , Neefs Jolien , Wesselink Robin , Baalman Sarah W. E. , Jongejan Aldo , Schelfhorst Tim , Piersma Sander R. , Pham Thang V. , van Boven Wim J. P. , Driessen Antoine H. G. , Jimenez Connie R. , de Groot Joris R. 
Published: February 2021

AbstractDespite our expanding knowledge about the mechanism underlying atrial fibrillation (AF), the interplay between the biological events underlying AF remains incompletely understood. This study aimed to identify the functionally enriched gene-sets in AF and capture their interconnection via pivotal factors, that may drive or be driven by AF. Global abundance of the proteins in the left atrium of AF patients compared to control patients (n = 3/group), and the functionally enriched biological processes in AF were determined by mass-spectrometry and gene set enrichment analysis, respectively. The data were validated in an independent cohort (n = 19–20/group). In AF, the gene-sets of innate immune system, metabolic process, cellular component disassembly and ion homeostasis were up-regulated, while the gene-set of ciliogenesis was down-regulated. The innate immune system was over-represented by neutrophil degranulation, the components of which were extensively shared by other gene-sets altered in AF. In the independent cohort, an activated form of neutrophils was more present in the left atrium of AF patients with the increased gene expression of neutrophil granules. MYH10, required for ciliogenesis, was decreased in the atrial fibroblasts of AF patients. We report the increased neutrophil degranulation appears to play a pivotal role, and affects multiple biological processes altered in AF.
MDM4 inhibition: a novel therapeutic strategy to reactivate p53 in hepatoblastoma
Authors: Woodfield Sarah E. , Shi Yan , Patel Roma H. , Chen Zhenghu , Shah Aayushi P. , Srivastava Rohit K. , Whitlock Richard S. , Ibarra Aryana M. , Larson Samuel R. , Sarabia Stephen F. , Badachhape Andrew , Starosolski Zbigniew , Ghaghada Ketan B. , Sumazin Pavel , Annis D. Allen , López-Terrada Dolores , Vasudevan Sanjeev A. 
Published: February 2021

AbstractHepatoblastoma (HB) is the most common pediatric liver malignancy. High-risk patients have poor survival, and current chemotherapies are associated with significant toxicities. Targeted therapies are needed to improve outcomes and patient quality of life. Most HB cases are TP53 wild-type; therefore, we hypothesized that targeting the p53 regulator Murine double minute 4 (MDM4) to reactivate p53 signaling may show efficacy. MDM4 expression was elevated in HB patient samples, and increased expression was strongly correlated with decreased expression of p53 target genes. Treatment with NSC207895 (XI-006), which inhibits MDM4 expression, or ATSP-7041, a stapled peptide dual inhibitor of MDM2 and MDM4, showed significant cytotoxic and antiproliferative effects in HB cells. Similar phenotypes were seen with short hairpin RNA (shRNA)-mediated inhibition of MDM4. Both NSC207895 and ATSP-7041 caused significant upregulation of p53 targets in HB cells. Knocking-down TP53 with shRNA or overexpressing MDM4 led to resistance to NSC207895-mediated cytotoxicity, suggesting that this phenotype is dependent on the MDM4-p53 axis. MDM4 inhibition also showed efficacy in a murine model of HB with significantly decreased tumor weight and increased apoptosis observed in the treatment group. This study demonstrates that inhibition of MDM4 is efficacious in HB by upregulating p53 tumor suppressor signaling.
The acidified drinking water-induced changes in the behavior and gut microbiota of wild-type mice depend on the acidification mode
Authors: Whipple Brandon , Agar Jennifer , Zhao Jing , Pearce David A. , Kovács Attila D. 
Published: February 2021

AbstractAcidification of drinking water to a pH between 2.5 and 3.0 is widely used to prevent the spread of bacterial diseases in animal colonies. Besides hydrochloric acid (HCl), sulfuric acid (H2SO4) is also used to acidify drinking water. Here we examined the effects of H2SO4-acidified drinking water (pH = 2.8) received from weaning (postnatal day 21) on the behavior and gut microflora of 129S6/SvEv mice, a mouse strain commonly used in transgenic studies. In contrast to HCl-acidified water, H2SO4-acidified water only temporarily impaired the pole-descending ability of mice (at 3 months of age), and did not change the performance in an accelerating rotarod test. As compared to 129S6/SvEv mice receiving non-acidified or HCl-acidified drinking water, the gut microbiota of 129S6/SvEv mice on H2SO4-acidified water displayed significant alterations at every taxonomic level especially at 6 months of age. Our results demonstrate that the effects of acidified drinking water on the behavior and gut microbiota of 129S6/SvEv mice depends on the acid used for acidification. To shed some light on how acidified drinking water affects the physiology of 129S6/SvEv mice, we analyzed the serum and fecal metabolomes and found remarkable, acidified water-induced alterations.
Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells
Authors: Eagle Gina L. , Herbert John M. J. , Zhuang Jianguo , Oates Melanie , Khan Umair T. , Kitteringham Neil R. , Clarke Kim , Park B. Kevin , Pettitt Andrew R. , Jenkins Rosalind E. , Falciani Francesco 
Published: February 2021

AbstractChronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.
Bsep expression in hilar cholangiocarcinoma of rat model
Authors: Zhang Meng-yu , Wang Jie-ping , He Kai , Xia Xian-ming 
Published: February 2021

AbstractDevelop a rat model of hilar cholangiocarcinoma for detecting bile salt export pump (Bsep) expression in hilar cholangiocarcinoma tissues, in order to provide a new therapeutic target for the gene therapy of hilar cholangiocarcinoma. Sixty male Wistar rats (body weight, 190 ± 8 g) were randomly divided into three groups (the experimental group, the control group and the sham operation group, n = 20 each) as follows: The three groups were fed a standard diet, the experimental group was injected by cholangiocarcinoma QBC939 cell suspension along the hilar bile duct into the bile duct bifurcation with microsyringe, the control group was injected by normal saline, the sham operation group did not inject anything. Every day assess the rats’ mental state, diet, and motion by using Basso–Beattie–Bresnahan and combined behavioral score. At 4 weeks, one rat of the experimental group was sacrificed after it was administered anesthesia, and we recorded changes in hilar bile duct size, texture, and form. This procedure was repeated at 6 weeks. After 6 weeks, hilar cholangiocarcinoma developed only in the experimental group, thereby establishing an experimental model for studying QBC939-induced hilar cholangiocarcinoma. Tumor formation was confirmed by pathological examination, and hilar bile duct tissues were harvested from both the groups. A real-time polymerase chain reaction assay and an immunohistochemical assay were used to analyze the expression of Bsep in hilar bile duct tissues of each group. From the second week, the rats in experimental group began to eat less, and their body mass decreased compared with control group and sham operation group. After 6 weeks, we detected hilar cholangiocarcinoma in the hilar bile duct tissues of 18 rats (90%) in the experimental group. In the experimental group with hilar cholangiocarcinoma, we found that the levels of total cholesterol, total bilirubin, and direct bilirubin were higher compared with those in the control group and sham operation group. Simultaneously, muddy stones emerged from the bile ducts of rats in the experimental group. The Bsep/Gapdh mRNA ratio in hilar cholangiocarcinoma, control group and sham operation group differed markedly. Light microscopy revealed a granular pattern of Bsep protein expression which reacted with the anti-Bsep antibody. Each section was randomly divided into six regions, with 80 cells were observed in every region. Sections with > 10% positive cells were designated positive, Sections with < 10% positive cells were designated negative. Each group included 4800 cells. In the experimental group, 1200 cells (25%) were positive, in the control group, 3648 cells (76%) were positive and in the sham operation group 3598 cells (75%) were positive, and this difference was statistically significant. Bsep expression significantly decreased in hilar cholangiocarcinoma of rats than those in control group and sham operation group, suggesting that drugs targeting Bsep are a new strategy for hilar cholangiocarcinoma.