bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies
Authors: Frau Alessandra , Kenny John G. , Lenzi Luca , Campbell Barry J. , Ijaz Umer Z. , Duckworth Carrie A. , Burkitt Michael D. , Hall Neil , Anson Jim , Darby Alistair C. , Probert Christopher S. J. 
Published: June 2019

AbstractMicrobial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.
Untargeted metabolomics unveil alterations of biomembranes permeability in human HaCaT keratinocytes upon 60 GHz millimeter-wave exposure
Authors: Le Pogam Pierre , Le Page Yann , Habauzit Denis , Doué Mickael , Zhadobov Maxim , Sauleau Ronan , Le Dréan Yves , Rondeau David 
Published: June 2019

AbstractA joint metabolomic and lipidomic workflow is used to account for a potential effect of millimeter waves (MMW) around 60 GHz on biological tissues. For this purpose, HaCaT human keratinocytes were exposed at 60.4 GHz with an incident power density of 20 mW/cm², this value corresponding to the upper local exposure limit for general public in the context of a wide scale deployment of MMW technologies and devices. After a 24h-exposure, endo- and extracellular extracts were recovered to be submitted to an integrative UPLC-Q-Exactive metabolomic and lipidomic workflow. R-XCMS data processing and subsequent statistical treatment led to emphasize a limited number of altered features in lipidomic sequences and in intracellular metabolomic analyses, whatever the ionization mode (i.e 0 to 6 dysregulated features). Conversely, important dysregulations could be reported in extracellular metabolomic profiles with 111 and 99 frames being altered upon MMW exposure in positive and negative polarities, respectively. This unexpected extent of modifications can hardly stem from the mild changes that could be reported throughout transcriptomics studies, leading us to hypothesize that MMW might alter the permeability of cell membranes, as reported elsewhere.
Task-dependent functional organizations of the visual ventral stream
Authors: Jo Han-Gue , Ito Junji , Schulte Holthausen Barbara , Baumann Conrad , Grün Sonja , Habel Ute , Kellermann Thilo 
Published: June 2019

AbstractThe visual hierarchy of the ventral stream has been widely studied. However, it remains unclear how the hierarchical system organizes its functional coupling during top-down cognitive process. The present fMRI study investigated task-dependent functional connectivity along the ventral stream, while twenty-eight participants performed object recognition tasks that required different types of visual processing: i) searching or ii) memorizing visual objects embedded in natural scene images or iii) free viewing of the same images. Utilizing a seed-based approach that explicitly compared task-specific BOLD time-series, we identified task-dependent functional connectivity of the visual ventral stream, demonstrating different correlation structures. Searching for a target object manifested both correlated and anti-correlated structures, separating the visual areas V1 and V4 from the posterior part of the inferior temporal cortex (PIT). In contrast, the ventral stream structure remained correlated during memorizing objects, but increased the correlation between the right V4 and PIT. On the other hand, V1 and V4 showed task-dependent activation, whereas PIT was deactivated. These results highlight the context-dependent nature of the visual ventral stream and shed light on how the visual hierarchy is selectively organized to bias object recognition toward features of interest.
Skin Carotenoid Index in a large Japanese population sample
Authors: Obana Akira , Gohto Yuko , Gellermann Werner , Ermakov Igor V. , Sasano Hiroyuki , Seto Takahiko , Bernstein Paul S. 
Published: June 2019

AbstractCarotenoids are anti-oxidative agents. Human skin and eyes contain specific carotenoid species known to prevent various pathologies caused by oxidative stress. We quantified skin and eye carotenoid levels and investigated their potential correlation in a population including 985 Japanese patients and staff members of an ophthalmology clinic (577 men, 408 women, mean age of 69.7 ± 13.6 [SD]). Skin carotenoid (SC) and macular pigment (MP) levels were measured with reflection spectroscopy and autofluorescence imaging methods, respectively. The mean SC index was 343.1 ± 142.1 (SD). SC indices for women were higher than for men (382 vs 315, p < 0.001). Smokers and overweight subjects (BMI ≥ 25) had lower SC indices. Subjects taking lutein supplements had higher SC indices than non-supplementing subjects (415 vs 325, p < 0.001). SC and MP indices were significantly correlated. The obtained data set can be used for reference purposes by Japanese subjects and researchers interested in tissue responses to diets high in carotenoids and lutein supplementation.
A novel host-adapted strain of Salmonella Typhimurium causes renal disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific
Authors: Work Thierry M. , Dagenais Julie , Stacy Brian A. , Ladner Jason T. , Lorch Jeffrey M. , Balazs George H. , Barquero-Calvo Elías , Berlowski-Zier Brenda M. , Breeden Renee , Corrales-Gómez Natalia , Gonzalez-Barrientos Rocio , Harris Heather S. , Hernández-Mora Gabriela , Herrera-Ulloa Ángel , Hesami Shoreh , Jones T. Todd , Morales Juan Alberto , Norton Terry M. , Rameyer Robert A. , Taylor Daniel R. , Waltzek Thomas B. 
Published: June 2019

AbstractSalmonella spp. are frequently shed by wildlife including turtles, but S. enterica subsp. enterica serovar Typhimurium or lesions associated with Salmonella are rare in turtles. Between 1996 and 2016, we necropsied 127 apparently healthy pelagic olive ridley turtles (Lepidochelys olivacea) that died from drowning bycatch in fisheries and 44 live or freshly dead stranded turtles from the west coast of North and Central America and Hawaii. Seven percent (9/127) of pelagic and 47% (21/44) of stranded turtles had renal granulomas associated with S. Typhimurium. Stranded animals were 12 times more likely than pelagic animals to have Salmonella-induced nephritis suggesting that Salmonella may have been a contributing cause of stranding. S. Typhimurium was the only Salmonella serovar detected in L. olivacea, and phylogenetic analysis from whole genome sequencing showed that the isolates from L. olivacea formed a single clade distinct from other S. Typhimurium. Molecular clock analysis revealed that this novel clade may have originated as recently as a few decades ago. The phylogenetic lineage leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella pathogenicity island 1 suggesting that these genes are important for host adaptation.
Carbon cycle instability and orbital forcing during the Middle Eocene Climatic Optimum
Authors: Giorgioni Martino , Jovane Luigi , Rego Eric S. , Rodelli Daniel , Frontalini Fabrizio , Coccioni Rodolfo , Catanzariti Rita , Özcan Ercan 
Published: June 2019

AbstractThe Middle Eocene Climatic Optimum (MECO) is a global warming event that occurred at about 40 Ma. In comparison to the most known global warming events of the Paleogene, the MECO has some peculiar features that make its interpretation controversial. The main peculiarities of the MECO are a duration of ~500 kyr and a carbon isotope signature that varies from site to site. Here we present new carbon and oxygen stable isotopes records (δ13C and δ18O) from three foraminiferal genera dwelling at different depths throughout the water column and the sea bottom during the middle Eocene, from eastern Turkey. We document that the MECO is related to major oceanographic and climatic changes in the Neo-Tethys and also in other oceanic basins. The carbon isotope signature of the MECO is difficult to interpret because it is highly variable from site to site. We hypothesize that such δ13C signature indicates highly unstable oceanographic and carbon cycle conditions, which may have been forced by the coincidence between a 400 kyr and a 2.4 Myr orbital eccentricity minimum. Such forcing has been also suggested for the Cretaceous Oceanic Anoxic Events, which resemble the MECO event more than the Cenozoic hyperthermals.
Multiple hollow-core anti-resonant fiber as a supermodal fiber interferometer
Authors: Huang Xiaosheng , Zang Jichao , Yoo Seongwoo 
Published: June 2019

AbstractHollow-core anti-resonant fiber technology has made a rapid progress in low loss broadband transmission, enabled by its much reduced light-material overlap. This unique characteristic has driven emerging of new applications spanning from extreme wavelength generation to beam delivery. The successful demonstrations appear to suggest progression of the technology toward device level development and all-fiberized systems. We investigate this opportunity and report an in-fiber interferometer built in a dual hollow-core anti-resonant fiber. By placing multiple air cores in a single fiber, coherently interacting transverse modes are excited, which becomes a basis of an interferometer. We use this hollow core based inherent supermodal interaction to demonstrate highly sensitive in-fiber interferometer. Unique combination of the air guidance and the supermodal interaction offers robust, simple yet highly sensitive interferometer with suppressed temperature cross-talk that has been an enduring problem in fiber strain sensing applications. The in-fiber interferometer is further investigated as a sensing element for pressure measurement based on an interferometric phase change upon external strain. The interferometer features 39.3 nm/MPa of ultrahigh sensitivity with 0.14 KPa/°C of negligible gas pressure temperature crosstalk. The performance, which is much improved from prior fiber sensors, testifies advances of hollow core fiber technology toward a device level.
Evaluation of Candida peritonitis with underlying peritoneal fibrosis and efficacy of micafungin in murine models of intra-abdominal candidiasis
Authors: Ashizawa Nobuyuki , Miyazaki Taiga , Abe Shinichi , Takazono Takahiro , Saijo Tomomi , Obata Yoko , Shimamura Shintaro , Yamamoto Kazuko , Imamura Yoshifumi , Koji Takehiko , Nishino Tomoya , Izumikawa Koichi , Yanagihara Katsunori , Kohno Shigeru , Mukae Hiroshi 
Published: June 2019

AbstractCandida peritonitis is a crucial disease, however the optimal antifungal therapy regimen has not been clearly defined. Peritoneal fibrosis (PF) can be caused by abdominal surgery, intra-abdominal infection, and malignant diseases, and is also widely recognized as a crucial complication of long-term peritoneal dialysis. However, the influence of PF on Candida peritonitis prognosis remains unknown. Here, we evaluated the severity of Candida peritonitis within the context of PF and the efficacy of micafungin using mice. A PF mouse model was generated by intraperitoneally administering chlorhexidine gluconate. Candida peritonitis, induced by intraperitoneal inoculation of Candida albicans, was treated with a 7-day consecutive subcutaneous administration of micafungin. Candida infection caused a higher mortality rate in the PF mice compared with the control mice on day 7. Proliferative Candida invasion into the peritoneum and intra-abdominal organs was confirmed pathologically only in the PF mice. However, all mice in both groups treated with micafungin survived until day 20. Micafungin treatment tends to suppress inflammatory cytokines in the plasma 12 h after infection in both groups. Our results suggest that PF enhances early mortality in Candida peritonitis. Prompt initiation and sufficient doses of micafungin had good efficacy for Candida peritonitis, irrespective of the underlying PF.
Animal Study to Evaluate the Effect of Carbon Dioxide Insufflation on Recurrent Laryngeal Nerve Function in Transoral Endoscopic Thyroidectomy
Authors: Zhang Daqi , Li Shijie , Dionigi Gianlorenzo , Zhang Jiao , Niu Chunbo , Wang Tie , Liang Nan , Sun Hui 
Published: June 2019

AbstractData with regard to potential recurrent laryngeal nerve (RLN) compromise caused by intra-neck CO2 insufflation during transoral endoscopic thyroidectomy vestibular approach (TOETVA) are missing. RLN electromyographic (EMG) profiles, metabolic and hemodynamic parameters (oxygen saturation, heart rate, blood pressure, experimental time, CO2 partial pressure, pH, O2 partial pressure), central venous pressure (CVP), airpocket temperature and pressure were recorded in a TOETVA animal model. Twelve pigs were randomly divided into different groups according to increasing CO2 insufflation pressures. Nerves segments were then collected for histopathology. Significant variation of metabolic and hemodynamic parameters were registered when CO2 insufflation pressures increased x3 and x5 the baseline parameters. Combined EMG amplitude drop and latency increase also were documented. There was no significant change in the intraluminal temperature. RLNs structure were preserved with normal axons, no fibrosis, and no vacuolization and without loss of myelinated fibers during the experiment. RLN EMG profiles (but not histology) were altered when CO2 insufflation pressures increased.
Limited evidence of hierarchical encoding in the cheerleader effect
Authors: Carragher Daniel J. , Thomas Nicole A. , Gwinn O. Scott , Nicholls Mike E. R. 
Published: June 2019

Abstract“The cheerleader effect” refers to the increase in attractiveness that an individual face experiences when seen in a group of other faces. It has been proposed that the cheerleader effect occurs because (a) the visual system rapidly summarises a group of faces into an ensemble representation, (b) which is hypothesised to be highly attractive because of its average facial characteristics, and (c) observers remember individual faces to be more alike the ensemble representation than they were, due to hierarchical structure of visual working memory. Across three experiments, we investigated whether the cheerleader effect is consistent with hierarchical encoding, by asking observers to give attractiveness ratings to the same target faces shown in groups and alone. Consistent with hierarchical encoding, the largest attractiveness increases of 1.5–2.0% occurred when target faces were presented in groups of faces that could be mentally summarised to create an ensemble representation with average facial characteristics. Surprisingly, smaller cheerleader effects still occurred in conditions that were incompatible with hierarchical encoding (i.e., groups with non-human images). Together, these results offer only limited evidence for the role of hierarchical encoding in the cheerleader effect, suggesting that alternative mechanisms must be explored in future research.
The two faces of titanium dioxide nanoparticles bio-camouflage in 3D bone spheroids
Authors: Souza W. , Piperni S. G. , Laviola P. , Rossi A. L. , Rossi Maria Isabel D. , Archanjo Bráulio S. , Leite P. E. , Fernandes M. H. , Rocha L. A. , Granjeiro J. M. , Ribeiro A. R. 
Published: June 2019

AbstractTitanium (Ti) and its alloys are widely used in dental implants and hip-prostheses due to their excellent biocompatibility. Growing evidence support that surface degradation due to corrosion and wear processes, contribute to implant failure, since the release of metallic ions and wear particles generate local tissue reactions (peri-implant inflammatory reactions). The generated ions and wear debris (particles at the micron and nanoscale) stay, in a first moment, at the interface implant-bone. However, depending on their size, they can enter blood circulation possibly contributing to systemic reactions and toxicities. Most of the nanotoxicological studies with titanium dioxide nanoparticles (TiO2NPs) use conventional two-dimensional cell culture monolayers to explore macrophage and monocyte activation, where limited information regarding bone cells is available. Recently three-dimensional models have been gaining prominence since they present a greater anatomical and physiological relevance. Taking this into consideration, in this work we developed a human osteoblast-like spheroid model, which closely mimics bone cell-cell interactions, providing a more realistic scenario for nanotoxicological studies. The treatment of spheroids with different concentrations of TiO2NPs during 72 h did not change their viability significantly. Though, higher concentrations of TiO2NPs influenced osteoblast cell cycle without interfering in their ability to differentiate and mineralize. For higher concentration of TiO2NPs, collagen deposition and pro-inflammatory cytokine, chemokine and growth factor secretion (involved in osteolysis and bone homeostasis) increased. These results raise the possible use of this model in nanotoxicological studies of osseointegrated devices and demonstrate a possible therapeutic potential of this TiO2NPs to prevent or reverse bone resorption.
Biosynthesis and Extracellular Concentrations of N,N-dimethyltryptamine (DMT) in Mammalian Brain
Authors: Dean Jon G. , Liu Tiecheng , Huff Sean , Sheler Ben , Barker Steven A. , Strassman Rick J. , Wang Michael M. , Borjigin Jimo 
Published: June 2019

AbstractN,N-dimethyltryptamine (DMT), a psychedelic compound identified endogenously in mammals, is biosynthesized by aromatic-L-amino acid decarboxylase (AADC) and indolethylamine-N-methyltransferase (INMT). Whether DMT is biosynthesized in the mammalian brain is unknown. We investigated brain expression of INMT transcript in rats and humans, co-expression of INMT and AADC mRNA in rat brain and periphery, and brain concentrations of DMT in rats. INMT transcripts were identified in the cerebral cortex, pineal gland, and choroid plexus of both rats and humans viain situhybridization. Notably, INMT mRNA was colocalized with AADC transcript in rat brain tissues, in contrast to rat peripheral tissues where there existed little overlapping expression of INMT with AADC transcripts. Additionally, extracellular concentrations of DMT in the cerebral cortex of normal behaving rats, with or without the pineal gland, were similar to those of canonical monoamine neurotransmitters including serotonin. A significant increase of DMT levels in the rat visual cortex was observed following induction of experimental cardiac arrest, a finding independent of an intact pineal gland. These results show for the first time that the rat brain is capable of synthesizing and releasing DMT at concentrations comparable to known monoamine neurotransmitters and raise the possibility that this phenomenon may occur similarly in human brains.
Trader as a new optimization algorithm predicts drug-target interactions efficiently
Authors: Masoudi-Sobhanzadeh Yosef , Omidi Yadollah , Amanlou Massoud , Masoudi-Nejad Ali 
Published: June 2019

AbstractSeveral machine learning approaches have been proposed for predicting new benefits of the existing drugs. Although these methods have introduced new usage(s) of some medications, efficient methods can lead to more accurate predictions. To this end, we proposed a novel machine learning method which is based on a new optimization algorithm, named Trader. To show the capabilities of the proposed algorithm which can be applied to the different scope of science, it was compared with ten other state-of-the-art optimization algorithms based on the standard and advanced benchmark functions. Next, a multi-layer artificial neural network was designed and trained by Trader to predict drug-target interactions (DTIs). Finally, the functionality of the proposed method was investigated on some DTIs datasets and compared with other methods. The data obtained by Trader showed that it eliminates the disadvantages of different optimization algorithms, resulting in a better outcome. Further, the proposed machine learning method was found to achieve a significant level of performance compared to the other popular and efficient approaches in predicting unknown DTIs. All the implemented source codes are freely available at https://github.com/LBBSoft/Trader.
The ENCODE Blacklist: Identification of Problematic Regions of the Genome
Authors: Amemiya Haley M. , Kundaje Anshul , Boyle Alan P. 
Published: June 2019

AbstractFunctional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. The removal of the ENCODE blacklist is an essential quality measure when analyzing functional genomics data.
IL-10 producing B cells rescue mouse fetuses from inflammation-driven fetal death and are able to modulate T cell immune responses
Authors: Busse Mandy , Campe Kim-Norina Jutta , Nowak Desiree , Schumacher Anne , Plenagl Susanne , Langwisch Stefanie , Tiegs Gisa , Reinhold Annegret , Zenclussen Ana Claudia 
Published: June 2019

AbstractUnderstanding the mechanisms leading to fetal death following maternal subclinical infections is crucial to develop new therapeutic strategies. Here we addressed the relevance of IL-10 secreting B cells (B10) in the maintenance of the immune balance during gestation. µMT females lacking mature B cells presented normal pregnancies, although their fetuses were smaller and their Treg pool did not expand as in B cell sufficient controls. Pregnant µMT females were more susceptible to LPS despite having less Treg; their fetuses died at doses compatible with pregnancy in WT animals. Adoptive transfer of IL-10 negative B effector cells or B cells from IL-10 deficient mice did not modify this outcome. The transfer of B10 cells or application of recombinant murine IL-10 reduced the fetal loss, associated with a normalization of Treg numbers and cytokine modulation at the feto-maternal interface. B cell-derived IL-10 suppressed the production of IL-17A and IL-6 by T cells and promoted the conversion of naïve cells into Treg. B10 cells are required to restore the immune balance at the feto-maternal interface when perturbed by inflammatory signals. Our data position B cells in a central role in the maintenance of the balance between immunity and tolerance during pregnancy.