bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nematode-free agricultural system of a fungus-growing termite
Authors: Kanzaki Natsumi , Liang Wei-Ren , Chiu Chun-I , Yang Ching-Ting , Hsueh Yen-Ping , Li Hou-Feng 
Published: June 2019

AbstractFungus-growing termites forage dead plant materials from the field to cultivate symbiotic Termitomyces fungi in the nest. Termite foraging behavior and the entry of symbiotic arthropod inquilines may transfer nematodes into a nest and adversely affect fungus production. To test whether nematodes were transferred to fungus gardens by termites and inquilines, we examined the occurrence of nematodes in fungus gardens, five termite castes, and nine species of inquilines of a fungus-growing termite, Odontotermes formosanus. Our results revealed that nematodes were commonly carried by foraging termites and beetle inquilines. Numerous nematodes were found under the beetle elytra. No nematodes were found on termite larvae, eggs, and wingless inquilines. In addition, nematodes rarely occurred in the fungus garden. By observing the response of nematodes to three species of Termitomyces spp. and the fungus gardens, we confirmed that the fungus and fungus gardens are not actually toxic to nematodes. We suggest that nematodes were suppressed through grooming behavior and gut antimicrobial activity in termites, rather than through the antimicrobial activity of the fungus.
Biofilm formation by multidrug resistant Enterobacteriaceae strains isolated from solid organ transplant recipients
Authors: Ramos-Vivas José , Chapartegui-González Itziar , Fernández-Martínez Marta , González-Rico Claudia , Fortún Jesús , Escudero Rosa , Marco Francesc , Linares Laura , Montejo Miguel , Aranzamendi Maitane , Muñoz Patricia , Valerio Maricela , Aguado Jose María , Resino Elena , Ahufinger Irene Gracia , Vega Aurora Paz , Martínez-Martínez Luis , Fariñas María Carmen ,   The ENTHERE Study Group, the Group for Study of Infection in Transplantation of the Spanish Society of Infectious Diseases and Clinical Microbiology (GESITRA-SEIMC) and the Spanish Network for Research in Infectious Diseases (REIPI), Ruiz San Millán Juan Carlos , Rodrigo Emilio , Casafont Morencos Fernando , Fabrega Emilio , Cuadrado Antonio , Fariñas-Alvarez Concepción , Gozalo Mónica , Arnaíz de las Revillas Francisco , Martín Dávila Pilar , Martínez Adolfo , Ruíz Garbajosa Patricia , Moreno Asunción , Bodro Marta , Solano María Fernanda , Blanco María José , Nieto Javier , Machado Marina , Olmedo María , Rodríguez Fernández Sara , Rincón Sanz Cristina , Vicente Range Teresa , Agnelli Bento Caroline , Galar Recalde Alicia , Eworo Alia , Fernández-Lomana Fernando Anaya , Rodríguez-Ferrero María Luisa , Sánchez Cámara Luis Alberto , Chaves Fernando , de la Torre Cisneros Julián 
Published: June 2019

AbstractSolid organ transplant (SOT) recipients are especially at risk of developing infections by multidrug resistant bacteria (MDR). In this study, the biofilm-forming capability of 209 MDR strains (Escherichia coli n = 106, Klebsiella pneumoniae n = 78, and Enterobacter spp. n = 25) isolated from rectal swabs in the first 48 hours before or after kidney (93 patients), liver (60 patients) or kidney/pancreas transplants (5 patients) were evaluated by using a microplate assay. Thirty-nine strains were isolated before transplant and 170 strains were isolated post-transplant. Overall, 16% of E. coli strains, 73% of K. pneumoniae strains and 4% Enterobacter strains showed moderate or strong biofilm production. Nine strains isolated from infection sites after transplantation were responsible of infections in the first month. Of these, 4 K. pneumoniae, 1 E. coli and 1 Enterobacter spp. strains isolated pre-transplant or post-transplant as colonizers caused infections in the post-transplant period. Our results suggest that in vitro biofilm formation could be an important factor for adhesion to intestine and colonization in MDR K. pneumoniae strains in SOT recipients, but this factor appears to be less important for MDR E. coli and Enterobacter spp.
Metabolomics reveals novel insight on dormancy of aquatic invertebrate encysted embryos
Authors: Rozema Evelien , Kierszniowska Sylwia , Almog-Gabai Oshri , Wilson Erica G. , Choi Young Hae , Verpoorte Robert , Hamo Reini , Chalifa-Caspi Vered , Assaraf Yehuda G. , Lubzens Esther 
Published: June 2019

AbstractNumerous aquatic invertebrates survive harsh environments by displaying dormancy as encysted embryos. This study aimed at determining whether metabolomics could provide molecular insight to explain the “dormancy syndrome” by highlighting functional pathways and metabolites, hence offering a novel comprehensive molecular view of dormancy. We compared the metabolome of morphologically distinct dormant encysted embryos (resting eggs) and non-dormant embryos (amictic eggs) of a rotifer (Brachionus plicatilis). Metabolome profiling revealed ~5,000 features, 1,079 of which were annotated. Most of the features were represented at significantly higher levels in non-dormant than dormant embryos. A large number of features was assigned to putative functional pathways indicating novel differences between dormant and non-dormant states. These include features associated with glycolysis, the TCA and urea cycles, amino acid, purine and pyrimidine metabolism. Interestingly, ATP, nucleobases, cyclic nucleotides, thymidine and uracil, were not detected in dormant resting eggs, suggesting an impairment of response to environmental and internal cues, cessation of DNA synthesis, transcription and plausibly translation in the dormant embryos. The levels of trehalose or its analogues, with a role in survival under desiccation conditions, were higher in resting eggs. In conclusion, the current study highlights metabolomics as a major analytical tool to functionally compare dormancy across species.
Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector
Authors: Klimešová Eva , Kulyk Olena , Gu Yanjun , Dittrich Laura , Korn Georg , Hajdu Janos , Krikunova Maria , Andreasson Jakob 
Published: June 2019

AbstractAerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 1016 Wcm−2. We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.
Facile One-Pot Synthesis of Bimetallic Co/Mn-MOFs@Rice Husks, and its Carbonization for Supercapacitor Electrodes
Authors: Kim Hyunuk , Sohail Muhammad , Wang Chenbo , Rosillo-Lopez Martin , Baek Kangkyun , Koo Jaehyoung , Seo Myung Won , Kim Seyoung , Foord John S. , Han Seong Ok 
Published: June 2019

AbstractNovel hybrid nanomaterials comprising metal-organic framework compounds carbonised in the presence of biomass material derived from rice husk have been investigated as a new class of sustainable supercapacitor materials for electrochemical energy storage. Specifically, two synthetic routes were employed to grow Co/Mn metal-organic framework compounds in the channels of rice husks, which had been activated previously by heat treatment in air at 400 °C to produce a highly porous network. Pyrolysis of these hybrid materials under nitrogen at 700 °C for 6 h produced metal-containing phases within the nanocarbon, comprising intimate mixtures of Co, MnO and CoMn2O4. The materials thus produced are characterized in detail using a range of physical methods including XRD, electron microscopy and X-ray photoelectron spectroscopy. The synthetic pathway to the metal-organic framework compound is shown to influence significantly the physical properties of the resulting material. Electrochemical evaluation of the materials fabricated revealed that higher specific capacitances were obtained when smaller crystallite sized bimetallic Co/Mn-MOFs were grown inside the rice husks channels compared to larger crystallite sizes. This was in-part due to increased metal oxide loading into the rice husk owing to the smaller crystallite size as well as the increased pseudocapacitance exhibited by the smaller crystallite sizes and increased porosity.
A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation
Authors: Burz Sebastian D. , Abraham Anne-Laure , Fonseca Fernanda , David Olivier , Chapron Audrey , Béguet-Crespel Fabienne , Cénard Stéphanie , Le Roux Karine , Patrascu Orlane , Levenez Florence , Schwintner Carole , Blottière Hervé M. , Béra-Maillet Christel , Lepage Patricia , Doré Joël , Juste Catherine 
Published: June 2019

AbstractOwing to the growing recognition of the gut microbiota as a main partner of human health, we are expecting that the number of indications for fecal microbiota transplantation (FMT) will increase. Thus, there is an urgent need for standardization of the entire process of fecal transplant production. This study provides a complete standardized procedure to prepare and store live and ready-to-use transplants that meet the standard requirements of good practices to applied use in pharmaceutical industry. We show that, if time before transformation to transplants would exceed 24 hours, fresh samples should not be exposed to temperatures above 20 °C, and refrigeration at 4 °C can be a safe solution. Oxygen-free atmosphere was not necessary and simply removing air above collected samples was sufficient to preserve viability. Transplants prepared in maltodextrin-trehalose solutions, stored in a -80 °C standard freezer and then rapidly thawed at 37 °C, retained the best revivification potential as proven by 16S rRNA profiles, metabolomic fingerprints, and flow cytometry assays over a 3-month observation period. Maltodextrin-trehalose containing cryoprotectants were also efficient in preserving viability of lyophilized transplants, either in their crude or purified form, an option that can be attractive for fecal transplant biobanking and oral formulation.
High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material
Authors: Filia Anastasia , Droop Alastair , Harland Mark , Thygesen Helene , Randerson-Moor Juliette , Snowden Helen , Taylor Claire , Diaz Joey Mark S. , Pozniak Joanna , Nsengimana Jérémie , Laye Jon , Newton-Bishop Julia A. , Bishop D. Timothy 
Published: June 2019

AbstractSystematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.
Simultaneous observation of higher-order non-classicalities based on experimental photocount moments and probabilities
Authors: Peřina Jan , Haderka Ondřej , Michálek Václav 
Published: June 2019

AbstractUsing a sub-Poissonian optical field generated from a weak twin beam by photon-number resolving post-selection we have simultaneously observed higher-order non-classicalities in photocount moments (sub-Poissonian statistics) and probabilities (witnessed by the Klyshko inequalities). Up to the seventh-order non-classicalities in photocount moments simultaneously with up to the eleventh-order non-classicalities in photocount probabilities have been experimentally observed. Non-classicality counting parameters of different orders as experimental counterparts of the theoretical Lee non-classicality depth have been suggested to quantify and also mutually compare the robustness of these non-classicalities against the noise.
Microevolution of antimicrobial resistance and biofilm formation of Salmonella Typhimurium during persistence on pig farms
Authors: Tassinari Eleonora , Duffy Geraldine , Bawn Matt , Burgess Catherine M. , McCabe Evonne M. , Lawlor Peadar G. , Gardiner Gillian , Kingsley Robert A. 
Published: June 2019

AbstractSalmonella Typhimurium and its monophasic variant S. 4,[5],12:i:- are the dominant serotypes associated with pigs in many countries. We investigated their population structure on nine farms using whole genome sequencing, and their genotypic and phenotypic variation. The population structure revealed the presence of phylogenetically distinct clades consisting of closely related clones of S. Typhimurium or S. 4,[5],12:i:- on each pig farm, that persisted between production cycles. All the S. 4,[5],12:i:- strains carried the Salmonella genomic island-4 (SGI-4), which confers resistance to heavy metals, and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene. Most clonal groups were highly drug resistant due to the presence of multiple antimicrobial resistance (AMR) genes, and two clades exhibited evidence of recent on-farm plasmid-mediated acquisition of additional AMR genes, including an IncHI2 plasmid. Biofilm formation was highly variable but had a strong phylogenetic signature. Strains capable of forming biofilm with the greatest biomass were from the S. 4,[5],12:i:- and S. Typhimurium DT104 clades, the two dominant pandemic clones found over the last 25 years. On-farm microevolution resulted in enhanced biofilm formation in subsequent production cycle.
Multi-Method Molecular Characterisation of Human Dust-Mite-associated Allergic Asthma
Authors: Whittle E. , Leonard M. O. , Gant T. W. , Tonge D. P 
Published: June 2019

AbstractAsthma is a chronic inflammatory disorder of the airways. Disease presentation varies greatly in terms of cause, development, severity, and response to medication, and thus the condition has been subdivided into a number of asthma phenotypes. There is still an unmet need for the identification of phenotype-specific markers and accompanying molecular tools that facilitate the classification of asthma phenotype. To this end, we utilised a range of molecular tools to characterise a well-defined group of female adults with poorly controlled atopic asthma associated with house dust mite (HDM) allergy, relative to non-asthmatic control subjects. Circulating messenger RNA (mRNA) and microRNA (miRNA) were sequenced and quantified, and a differential expression analysis of the two RNA populations performed to determine how gene expression and regulation varied in the disease state. Further, a number of circulating proteins (IL-4, 5, 10, 13, 17 A, Eotaxin, GM-CSF, IFNy, MCP-1, TARC, TNFα, Total IgE, and Endotoxin) were quantified to determine whether the protein profiles differed significantly dependent on disease state. Finally, we utilised a previously published assessment of the circulating “blood microbiome” performed using 16S rRNA amplification and sequencing. Asthmatic subjects displayed a range of significant alterations to circulating gene expression and regulation, relative to healthy control subjects, that may influence systemic immune activity. Notably, several circulating mRNAs were detected in just the asthma group or just in the control group, and many more were observed to be expressed at significantly different levels in the asthma group compared to the control group. Proteomic analysis revealed increased levels of inflammatory proteins within the serum, and decreased levels of the bacterial endotoxin protein in the asthmatic state. Comparison of blood microbiome composition revealed a significant increase in the Firmicutes phylum with asthma that was associated with a concomitant reduction in the Proteobacteria phylum. This study provides a valuable insight into the systemic changes evident in the HDM-associated asthma, identifies a range of molecules that are present in the circulation in a condition-specific manner (with clear biomarker potential), and highlights a range of hypotheses for further study.
Impact of body mass index on robotic transaxillary thyroidectomy
Authors: Yap Zeng , Kim Won Woong , Kang Sang-Wook , Lee Cho Rok , Lee Jandee , Jeong Jong Ju , Nam Kee-Hyun , Chung Woong Youn 
Published: June 2019

AbstractObesity is associated with increased operating times and higher complication rates in many types of surgery. Its impact on robotic thyroidectomy however, is not well documented. The aim of this study was to investigate the relationship between body mass index (BMI) and robotic transaxillary thyroidectomy (RTAT). A retrospective review of prospectively collected data of all patients who underwent RTAT at Yonsei University Health System from October 2007 to December 2014 was performed. Patients were divided into three groups based on BMI (Group 1: BMI < 25, Group 2: BMI 25–29.99, Group 3: BMI ≥ 30), and compared. A total of 3697 patients were analyzed. No differences between the three groups were observed in clinicopathological factors, extent of surgery or length of stay. After multivariate analysis, only seroma and transient voice hoarseness were related to increasing BMI. Total operative time was significantly longer for Group 3 patients with less-than-bilateral total thyroidectomy (BTT), but was not significantly different for patients with BTT. Although obese patients undergoing RTAT have a slightly higher risk of seroma, transient voice hoarseness, and longer operative times, BMI did not influence the other important surgical outcomes of thyroidectomy. Therefore, obesity should not be a contraindication for performing RTAT.
A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity
Authors: Sheppard Emily C. , Rogers Sally , Harmer Nicholas J. , Chahwan Richard 
Published: June 2019

AbstractDNA and RNA nucleases play a critical role in a growing number of cellular processes ranging from DNA repair to immune surveillance. Nevertheless, many nucleases have unknown or poorly characterized activities. Elucidating nuclease substrate specificities and co-factors can support a more definitive understanding of cellular mechanisms in physiology and disease. Using fluorescence-based methods, we present a quick, safe, cost-effective, and real-time versatile nuclease assay, which uniquely studies nuclease enzyme kinetics. In conjunction with a substrate library we can now analyse nuclease catalytic rates, directionality, and substrate preferences. The assay is sensitive enough to detect kinetics of repair enzymes when confronted with DNA mismatches or DNA methylation sites. We have also extended our analysis to study the kinetics of human single-strand DNA nuclease TREX2, DNA polymerases, RNA, and RNA:DNA nucleases. These nucleases are involved in DNA repair, immune regulation, and have been associated with various diseases, including cancer and immune disorders.
Temporal changes in the spatial distribution of carabid beetles around arable field-woodlot boundaries
Authors: Knapp Michal , Seidl Miroslav , Knappová Jana , Macek Martin , Saska Pavel 
Published: June 2019

AbstractCarabids are considered beneficial arthropods in agroecosystems, where they prey on crop pests or consume weed seeds. Therefore, knowledge of the spatial distribution of carabids in agricultural landscapes is crucial to efficiently manage the ecosystem services that they provide. In the present study, we investigated the spatial distribution of carabids around arable field-woodlot boundaries in different seasons: (1) early spring, (2) late spring, (3) summer and (4) late autumn. The spatial distribution of carabid abundance (activity-density) and species richness varied seasonally, and the total abundance was highest within arable fields, except in early spring when it peaked at the boundaries. The observed pattern was mainly driven by the spatial distribution of the open-habitat species, which aggregated near the field boundaries during winter and early spring. The open-habitat species penetrated into woodlots during the summer season but occurred almost exclusively outside woodlots in the other sampling periods. The abundance of the forest species was highest within woodlots with the exception of the early spring season, when their abundance peaked at the boundaries. Carabid species richness was highest within arable fields in close proximity to woodlot boundaries with the exception of the summer season, when the total species richness was similar across habitats.
Complex molecular mechanisms underlying MYMIV-resistance in Vigna mungo revealed by comparative transcriptome profiling
Authors: Kundu Anirban , Singh Pankaj Kumar , Dey Avishek , Ganguli Sayak , Pal Amita 
Published: June 2019

AbstractMungbean Yellow Mosaic India Virus (MYMIV)-infection creates major hindrance in V. mungo cultivation and poses significant threat to other grain legume production. Symptoms associated include severe patho-physiological alterations characterized by chlorotic foliar lesion accompanied by reduced growth. However, dissection of the host’s defense machinery remains a tough challenge due to limited of host’s genomic resources. A comparative RNA-Seq transcriptomes of resistant (VM84) and susceptible (T9) plants was carried out to identify genes potentially involved in V. mungo resistance against MYMIV. Distinct gene expression landscapes were observed in VM84 and T9 with 2158 and 1679 differentially expressed genes (DEGs), respectively. Transcriptomic responses in VM84 reflect a prompt and intense immune reaction demonstrating an efficient pathogen surveillance leading to activation of basal and induced immune responses. Functional analysis of the altered DEGs identified multiple regulatory pathways to be activated or repressed over time. Up-regulation of DEGs including NB-LRR, WRKY33, ankyrin, argonaute and NAC transcription factor revealed an insight on their potential roles in MYMIV-resistance; and qPCR validation shows a propensity of their accumulation in VM84. Analyses of the current RNA-Seq dataset contribute immensely to decipher molecular responses that underlie MYMIV-resistance and will aid in the improvement strategy of V. mungo and other legumes through comparative functional genomics.