bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sputum Detection of Predisposing Genetic Mutations in Women with Pulmonary Nontuberculous Mycobacterial Disease
Authors: Philley Julie V. , Hertweck Kate L. , Kannan Anbarasu , Brown-Elliott Barbara A. , Wallace Richard J. , Kurdowska Anna , Ndetan Harrison , Singh Karan P. , Miller Edmund J. , Griffith David E. , Dasgupta Santanu 
Published: July 2018

AbstractNontuberculous mycobacterial lung disease (NTM), including Mycobacterium avium complex (MAC), is a growing health problem in North America and worldwide. Little is known about the molecular alterations occurring in the tissue microenvironment during NTM pathogenesis. Utilizing next generation sequencing, we sequenced sputum and matched lymphocyte DNA in 15 MAC patients for a panel of 19 genes known to harbor cancer susceptibility associated mutations. Thirteen of 15 NTM subjects had a diagnosis of breast cancer (BCa) before or after NTM infection. Thirty three percent (4/12) of these NTM-BCa cases exhibited at least 3 somatic mutations in sputa compared to matched lymphocytes. Twenty four somatic mutations were detected with at least one mutation in ATM, ERBB2, BARD1, BRCA1, BRCA2, AR, TP53, PALB2, CASP8, BRIP1, NBN and TGFB1 genes. All four NTM-BCa patients harboring somatic mutations also exhibited 15 germ line BRCA1 and BRCA2 mutations. The two NTM subjects without BCa exhibited twenty somatic mutations spanning BRCA1, BRCA1, BARD1, BRIP1, CHEK2, ERBB2, TP53, ATM, PALB2, TGFB1 and 3 germ line mutations in BRCA1 and BRCA2 genes. A single copy loss of STK11 and AR gene was noted in NTM-BCa subjects. Periodic screening of sputa may aid to develop risk assessment biomarkers for neoplastic diseases in NTM patients.
RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways
Authors: Ahn Richard , Yan Di , Chang Hsin-Wen , Lee Kristina , Bhattarai Shrishti , Huang Zhi-Ming , Nakamura Mio , Singh Rasnik , Afifi Ladan , Taravati Keyon , Munoz-Sandoval Priscila , Pauli Mariela , Rosenblum Michael D. , Liao Wilson 
Published: July 2018

AbstractIt has long been recognized that anatomic location is an important feature for defining distinct subtypes of plaque psoriasis. However, little is known about the molecular differences between scalp, palmoplantar, and conventional plaque psoriasis. To investigate the molecular heterogeneity of these psoriasis subtypes, we performed RNA-seq and flow cytometry on skin samples from individuals with scalp, palmoplantar, and conventional plaque psoriasis, along with samples from healthy control patients. We performed differential expression analysis and network analysis using weighted gene coexpression network analysis (WGCNA). Our analysis revealed a core set of 763 differentially expressed genes common to all sub-types of psoriasis. In contrast, we identified 605, 632, and 262 genes uniquely differentially expressed in conventional, scalp, and palmoplantar psoriasis, respectively. WGCNA and pathway analysis revealed biological processes for the core genes as well as subtype-specific genes. Flow cytometry analysis revealed a shared increase in the percentage of CD4+ T regulatory cells in all psoriasis subtypes relative to controls, whereas distinct psoriasis subtypes displayed differences in IL-17A, IFN-gamma, and IL-22 production. This work reveals the molecular heterogeneity of plaque psoriasis and identifies subtype-specific signaling pathways that will aid in the development of therapy that is appropriate for each subtype of plaque psoriasis.
Comprehensive organic profiling of biological particles derived from blood
Authors: Wu Cheng-Yeu , Martel Jan , Young John D. 
Published: July 2018

AbstractMineral nanoparticles form in physiological and pathological processes occurring in the human body. The calcium phosphate mineral phase of the particles has affinity for proteins and lipids, but the complete profiling of the organic molecules that bind to the particles has not been described in detail. We report here a comprehensive analysis of organic components found in mineralo-organic particles derived from body fluids. Based on biological staining, fluorescent tagging, proteomics and metabolomics, our results indicate that the mineral particles bind to proteins, amino acids, carbohydrates, polysaccharides, phospholipids, fatty acids, DNA and low molecular weight metabolites. These results can be used to study the formation and effects of mineralo-organic particles in biological fluids.
Ocean sprawl facilitates dispersal and connectivity of protected species
Authors: Henry Lea-Anne , Mayorga-Adame Claudia G. , Fox Alan D. , Polton Jeff A. , Ferris Joseph S. , McLellan Faron , McCabe Chris , Kutti Tina , Roberts J. Murray 
Published: July 2018

AbstractHighly connected networks generally improve resilience in complex systems. We present a novel application of this paradigm and investigated the potential for anthropogenic structures in the ocean to enhance connectivity of a protected species threatened by human pressures and climate change. Biophysical dispersal models of a protected coral species simulated potential connectivity between oil and gas installations across the North Sea but also metapopulation outcomes for naturally occurring corals downstream. Network analyses illustrated how just a single generation of virtual larvae released from these installations could create a highly connected anthropogenic system, with larvae becoming competent to settle over a range of natural deep-sea, shelf and fjord coral ecosystems including a marine protected area. These results provide the first study showing that a system of anthropogenic structures can have international conservation significance by creating ecologically connected networks and by acting as stepping stones for cross-border interconnection to natural populations.
Utilization of 3D printing technology to facilitate and standardize soft tissue testing
Authors: Scholze Mario , Singh Aqeeda , Lozano Pamela F. , Ondruschka Benjamin , Ramezani Maziar , Werner Michael , Hammer Niels 
Published: July 2018

AbstractThree-dimensional (3D) printing has become broadly available and can be utilized to customize clamping mechanisms in biomechanical experiments. This report will describe our experience using 3D printed clamps to mount soft tissues from different anatomical regions. The feasibility and potential limitations of the technology will be discussed. Tissues were sourced in a fresh condition, including human skin, ligaments and tendons. Standardized clamps and fixtures were 3D printed and used to mount specimens. Inquasi-statictensile tests combined with digital image correlation andfatiguetrials we characterized the applicability of the clamping technique. Scanning electron microscopy was utilized to evaluate the specimens to assess the integrity of the extracellular matrix following the mechanical tests. 3D printed clamps showed no signs of clamping-related failure during thequasi-statictests, and intact extracellular matrix was found in the clamping area, at the transition clamping area and the central area from where the strain data was obtained. In thefatiguetests, material slippage was low, allowing for cyclic tests beyond 105cycles. Comparison to other clamping techniques yields that 3D printed clamps ease and expedite specimen handling, are highly adaptable to specimen geometries and ideal for high-standardization and high-throughput experiments in soft tissue biomechanics.
Trees represent community composition of other plant life-forms, but not their diversity, abundance or responses to fragmentation
Authors: Pasion Bonifacio O. , Roeder Mareike , Liu Jiajia , Yasuda Mika , Corlett Richard T. , Slik J. W. Ferry , Tomlinson Kyle W. 
Published: July 2018

AbstractOur understanding of the patterns of plant diversity in tropical forests and their responses to fragmentation are mostly based on tree surveys. But are these patterns and responses representative of other plant life-forms? We sampled trees, lianas, herbs, and ferns in a fragmented tropical forest landscape in South-west China. We compared community types generated by clustering presence-absence data for the non-tree life-forms with those generated for trees. We tested how well measures of tree diversity, density and composition, predicted cognate indices in other life-forms. We compared fragmentation responses, with respect to the three measures, of all four life-forms. Presence-absence data from all life-forms generated three community clusters, with only small differences between classifications, suggesting that tree data identified community types representative of all vascular plant life-forms. Tree species diversity and density indices poorly predicted cognate indices of lianas and ferns, but represented herbs well. However, the slopes of these relationships differed substantially between community types. All life-forms responded to fragmentation variables but their responses did not consistently match with responses of trees. Plot-level tree data can identify vegetation community types, but is poorly representative of the richness and density of other life-forms, and poorly represents forest fragmentation responses for the entire plant community.
Composition, structure and tensile biomechanical properties of equine articular cartilage during growth and maturation
Authors: Oinas J. , Ronkainen A. P. , Rieppo L. , Finnilä M. A. J. , Iivarinen J. T. , van Weeren P. R. , Helminen H. J. , Brama P. A. J. , Korhonen R. K. , Saarakkala S. 
Published: July 2018

AbstractArticular cartilage undergoes structural and biochemical changes during maturation, but the knowledge on how these changes relate to articular cartilage function at different stages of maturation is lacking. Equine articular cartilage samples of four different maturation levels (newborn, 5-month-old, 11-month-old and adult) were collected (N = 25). Biomechanical tensile testing, Fourier transform infrared microspectroscopy (FTIR-MS) and polarized light microscopy were used to study the tensile, biochemical and structural properties of articular cartilage, respectively. The tensile modulus was highest and the breaking energy lowest in the newborn group. The collagen and the proteoglycan contents increased with age. The collagen orientation developed with age into an arcade-like orientation. The collagen content, proteoglycan content, and collagen orientation were important predictors of the tensile modulus (p < 0.05 in multivariable regression) and correlated significantly also with the breaking energy (p < 0.05 in multivariable regression). Partial least squares regression analysis of FTIR-MS data provided accurate predictions for the tensile modulus (r = 0.79) and the breaking energy (r = 0.65). To conclude, the composition and structure of equine articular cartilage undergoes changes with depth that alter functional properties during maturation, with the typical properties of mature tissue reached at the age of 5–11 months.
Jug r 6 is the allergenic vicilin present in walnut responsible for IgE cross-reactivities to other tree nuts and seeds
Authors: Dubiela Pawel , Kabasser Stefan , Smargiasso Nicolas , Geiselhart Sabine , Bublin Merima , Hafner Christine , Mazzucchelli Gabriel , Hoffmann-Sommergruber Karin 
Published: July 2018

AbstractWalnuts are ranked high in the list of the culprit foods inducing severe allergic reactions. Jug r 2 has been identified as a major allergen in common walnut by cDNA cloning from a somatic cell line. So far, studies were performed on the allergenic activity of recombinant Jug r 2, yet there is still no evidence about the physicochemical characteristics of the natural allergen. Therefore, we aimed to purify and deeply characterize natural Jug r 2 and to assess IgE cross-reactivity among vicilins from different tree nuts. Extensive mass spectrometry analysis of the obtained purified vicilin allowed identification of the protein sequence that displayed only 44% identity to Jug r 2. The newly identified vicilin (Jug r 6) was recognized by IgE of 26% in walnut allergic patients’ sera tested. In contrast to Jug r 2, Jug r 6 displayed a remarkable level of cross-reactivity when tested with homologues from hazelnut, sesame and pistachio. It is the first report showing the necessity of proteomic studies to improve allergy component resolved diagnosis.
Automatic microscopic detection of mycobacteria in sputum: a proof-of-concept
Authors: Zingue D. , Weber P. , Soltani F. , Raoult D. , Drancourt M. 
Published: July 2018

AbstractThe laboratory diagnosis of lung mycobacterioses including tuberculosis comprises the microscopic examination of sputum smear after appropriate staining such as Ziehl-Neelsen staining to observe acid-fast bacilli. This standard procedure is operator-dependant and its sensitivity depends on the duration of observation. We developed and evaluated an operator-independent microscopic examination of sputum smears for the automated detection and enumeration of acid-fast bacilli using a ZEISS Axio Scan.Z1 microscope. The sensitivity, specificity, positive predictive value, negative predictive values and accuracy were calculated using standard formulations by comparison with standard microscopic examination. After in-house parameterization of the automatic microscope and counting software, the limit of detection evaluated by seeding negative sputa with Mycobacterium bovis BCG or Mycobacterium tuberculosis H37Rv (100–105 bacilli/mL) was of 102 bacilli/mL of sputum with a 100% positivity rate. Then, the evaluation of 93 sputum specimens including 34 smear-positive and 59 smear-negative specimens yielded a sensitivity of 97.06% [84.67–99.93%], a specificity of 86.44% [73.01–92.78%]. Up to 100 smear slides could be stocked for reading in the microscope magazine and results are exportable into the laboratory information system. Based on these preliminary results, we are implanting this automatic protocol in the routine workflow so that only smears detected positive by automatic microscopy are confirmed by standard microscopic examination.
The Inverse Poisson Functional for forecasting response time to environmental events and global climate change
Authors: Zachary Daniel S. 
Published: July 2018

AbstractA series of Poisson distributions are fit to sets of global cost-of-impact data representing large-scale accidents and anthropogenic catastrophes. The fits are used to build a function representing data means and are designated the Inverse Poisson Functional. Climate and environmental data have been used to develop a cost-frequency population distribution and to estimate the expected time between events. On a global scale, we show that expected wait- or reaction- times can be estimated using the Poisson density function. The functional is generated, representing the locus of means (peaks) from the individual Poisson distributions from different impact costs. Past (ex-post) forecasts relate to a range of natural and anthropogenic disasters; future (ex-ante) forecast presents global CO2emissions. This paper shows that a substantial reaction to global climate change (CO2emissions extremum) will occur in 55 to 120 years (95% CI) with a model prediction of 80 years.
Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization
Authors: de la Cuesta-Zuluaga Jacobo , Corrales-Agudelo Vanessa , Velásquez-Mejía Eliana P. , Carmona Jenny A. , Abad José M. , Escobar Juan S. 
Published: July 2018

AbstractWesternization and its accompanying epidemiological transitions are associated with changes in gut microbiota. While the extremes of this lifestyle spectrum have been compared (hunter-gatherers, industrialized countries), populations undergoing such shifts have received little attention. To fill the gap of knowledge about the microbiome evolution following broad lifestyle changes and the emergence of disease-associated dysbiosis, we performed a cross-sectional study in which we characterized the microbiota of 441 Colombian adults through 16S rRNA gene sequencing and determined its relationship with demographic, health-related and dietary parameters. We showed that in the gut microbiota of this cohort thrive taxa proper of both hunter-gatherers (Prevotella, Treponema) and citizens of industrialized countries (Bacteroides, Bifidobacterium, Barnesiella); the relative abundances of these taxa differed from those in Western and non-Western populations. We also showed that the Colombian gut microbiota is composed of five consortia of co-abundant microorganisms that are differentially associated with lifestyle, obesity and cardiometabolic disease, and highlighted metabolic pathways that might explain associations between microbiota and host health. Our results give insights into the evolution of the gut microbiota, and underscore the importance of this community to human health. Promoting the growth of specific microbial consortia could help ameliorating physiological conditions associated with Western lifestyles.
Inflammatory response of microglia to prions is controlled by sialylation of PrPSc
Authors: Srivastava Saurabh , Katorcha Elizaveta , Makarava Natallia , Barrett James P. , Loane David J. , Baskakov Ilia V. 
Published: July 2018

AbstractNeuroinflammation is recognized as one of the obligatory pathogenic features of neurodegenerative diseases including Alzheimer’s, Parkinson’s or prion diseases. In prion diseases, space and time correlations between deposition of disease-associated, pathogenic form of the prion protein or PrPScand microglial-mediated neuroinflammation has been established. Yet, it remains unclear whether activation of microglia is triggered directly by a contact with PrPSc, and what molecular features of PrPScmicroglia sense and respond to that drive microglia to inflammatory states. The current study asked the questions whether PrPSccan directly trigger activation of microglia and whether the degree of microglia response depends on the nature of terminal carbohydrate groups on the surface of PrPScparticles. PrPScwas purified from brains of mice infected with mouse-adapted prion strain 22L or neuroblastoma N2a cells stably infected with 22L. BV2 microglial cells or primary microglia were cultured in the presence of purified 22L. We found that exposure of BV2 cells or primary microglia to purified PrPSctriggered proinflammatory responses characterized by an increase in the levels of TNFα, IL6, nitric oxide (NO) and expression of inducible Nitric Oxide Synthase (iNOS). Very similar patterns of inflammatory response were induced by PrPScpurified from mouse brains and neuroblastoma cells arguing that microglia response is independent of the source of PrPSc. To test whether the microglial response is mediated by carbohydrate epitopes on PrPScsurface, the levels of sialylation of PrPScN-linked glycans was altered by treatment of purified PrPScwith neuraminidase. Partial cleavage of sialic acid residues was found to boost the inflammatory response of microglia to PrPSc. Moreover, transient degradation of Iκβα observed upon treatment with partially desialylated PrPScsuggests that canonical NFκB activation pathway is involved in inflammatory response. The current study is the first to demonstrate that PrPSccan directly trigger inflammatory response in microglia. In addition, this work provides direct evidence that the chemical nature of the carbohydrate groups on PrPScsurface is important for microglial activation.
Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study
Authors: Vallès Yvonne , Inman Claire K. , Peters Brandilyn A. , Ali Raghib , Wareth Laila Abdel , Abdulle Abdishakur , Alsafar Habiba , Anouti Fatme Al , Dhaheri Ayesha Al , Galani Divya , Haji Muna , Hamiz Aisha Al , Hosani Ayesha Al , Houqani Mohammed Al , Junaibi Abdulla Al , Kazim Marina , Kirchhoff Tomas , Mahmeed Wael Al , Maskari Fatma Al , Alnaeemi Abdullah , Oumeziane Naima , Ramasamy Ravichandran , Schmidt Ann Marie , Weitzman Michael , Zaabi Eiman Al , Sherman Scott , Hayes Richard B. , Ahn Jiyoung 
Published: July 2018

AbstractCigarette smoking alters the oral microbiome; however, the effect of alternative tobacco products remains unclear. Middle Eastern tobacco products like dokha and shisha, are becoming globally widespread. We tested for the first time in a Middle Eastern population the hypothesis that different tobacco products impact the oral microbiome. The oral microbiome of 330 subjects from the United Arab Emirates Healthy Future Study was assessed by amplifying the bacterial16S rRNAgene from mouthwash samples. Tobacco consumption was assessed using a structured questionnaire and further validated by urine cotinine levels. Oral microbiome overall structure and specific taxon abundances were compared, using PERMANOVA and DESeq analyses respectively. Our results show that overall microbial composition differs between smokers and nonsmokers (p = 0.0001). Use of cigarettes (p = 0.001) and dokha (p = 0.042) were associated with overall microbiome structure, while shisha use was not (p = 0.62). The abundance of multiple genera were significantly altered (enriched/depleted) in cigarette smokers; however, onlyActinobacillus,Porphyromonas,LautropiaandBifidobacteriumabundances were significantly changed in dokha users whereas no genera were significantly altered in shisha smokers. For the first time, we show that smoking dokha is associated to oral microbiome dysbiosis, suggesting that it could have similar effects as smoking cigarettes on oral health.
Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins
Authors: Marques Cláudia , Fernandes Iva , Meireles Manuela , Faria Ana , Spencer Jeremy P. E. , Mateus Nuno , Calhau Conceição 
Published: July 2018

AbstractHigh-fat (HF) diets are thought to disrupt the profile of the gut microbiota in a manner that may contribute to the neuroinflammation and neurobehavioral changes observed in obesity. Accordingly, we hypothesize that by preventing HF-diet induced dysbiosis it is possible to prevent neuroinflammation and the consequent neurological disorders. Anthocyanins are flavonoids found in berries that exhibit anti-neuroinflammatory properties in the context of obesity. Here, we demonstrate that the blackberry anthocyanin-rich extract (BE) can modulate gut microbiota composition and counteract some of the features of HF-diet induced dysbiosis. In addition, we show that the modifications in gut microbial environment are partially linked with the anti-neuroinflammatory properties of BE. Through fecal metabolome analysis, we unravel the mechanism by which BE participates in the bilateral communication between the gut and the brain. BE alters host tryptophan metabolism, increasing the production of the neuroprotective metabolite kynurenic acid. These findings strongly suggest that dietary manipulation of the gut microbiota with anthocyanins can attenuate the neurologic complications of obesity, thus expanding the classification of psychobiotics to anthocyanins.