bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatile Organic Compound Emissions From Soil Following Wetting Events
Authors: Rossabi Sam , Choudoir Mallory , Helmig Detlev , Hueber Jacques , Fierer Noah 
Published: June 2018

AbstractDynamics of carbon dioxide (CO2) emissions following the wetting of dry soil have been widely studied in field and laboratory settings. Nonmethane volatile organic compounds (VOCs) are also emitted from soil following a rain event and are evident from the characteristic smell of wet soil. Few studies have documented VOC emissions before and after soil rewetting. Soil emissions were studied using a dynamic flux chamber system purged with VOC‐free air, with identification and quantification of emissions performed by gas chromatography/mass spectrometry. All soils exhibited a rewetting‐induced pulse of VOC emissions, with VOC emissions 14 times higher (on average) in the few hours after rewetting compared to moist soils 2 days after rewetting. This VOC rewetting pulse mirrored the CO2 rewetting pulse (the so‐called “Birch Effect”) but was shorter in duration. Average VOC emissions were 5.0 ± 2.0% of CO2 emissions (molar C equivalent) and increased with increasing soil organic matter content (ρ = 0.40, ρ = 0.99 with one soil excluded). The amounts and types of VOCs varied with time since rewetting and across the five studied soil types, though acetone and small hydrocarbons were the dominant compounds emitted from all soils. Some of the VOCs emitted are likely important mediators of microbial activities and relevant to atmospheric chemical dynamics. Soil VOC emissions, similar to CO2 emissions, are strongly affected by rewetting events, and it is important to consider these rewetting dynamics when modeling soil and ecosystem VOC emissions and understand their relevance to terrestrial ecosystem functioning and atmospheric processes.
Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives
Authors: Chen Bosheng , Du Kaiqian , Sun Chao , Vimalanathan Arunprasanna , Liang Xili , Li Yong , Wang Baohong , Lu Xingmeng , Li Lanjuan , Shao Yongqi 
Published: June 2018

Abstract
Bombyx mori, the domesticated silkworm, is of great importance as a silk producer and as a powerful experimental model for the basic and applied research. Similar to other animals, abundant microorganisms live inside the silkworm gut; however, surprisingly, the microbiota of this model insect has not been well characterized to date. Here, we comprehensively characterized the gut microbiota of the domesticated silkworm and its wild relatives. Comparative analyses with the mulberry-feeding moths Acronicta major and Diaphania pyloalis revealed a highly diverse but distinctive silkworm gut microbiota despite thousands of years of domestication, and stage-specific signatures in both total (DNA-based) and active (RNA-based) bacterial populations, dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Most fungal sequences were assigned to the phyla Ascomycota and Basidiomycota. Environmental factors, including diet and human manipulation (egg production), likely influence the silkworm gut composition. Despite a lack of spatial variation along the gut, microbial community shifts were apparent between early instars and late instars, in concert with host developmental changes. Our results demonstrate that the gut microbiota of silkworms assembles into increasingly identical community throughout development, which differs greatly from those of other mulberry-feeding lepidopterans from the same niche, highlighting host-specific effects on microbial associations and the potential roles these communities play in host biology.
Integrated DNA/RNA targeted genomic profiling of diffuse large B-cell lymphoma using a clinical assay
Authors: Intlekofer Andrew M. , Joffe Erel , Batlevi Connie L. , Hilden Patrick , He Jie , Seshan Venkatraman E. , Zelenetz Andrew D. , Palomba M. Lia , Moskowitz Craig H. , Portlock Carol , Straus David J. , Noy Ariela , Horwitz Steven M. , Gerecitano John F. , Moskowitz Alison , Hamlin Paul , Matasar Matthew J , Kumar Anita , van den Brink Marcel R. , Knapp Kristina M. , Pichardo Janine D. , Nahas Michelle K. , Trabucco Sally E. , Mughal Tariq , Copeland Amanda R. , Papaemmanuil Elli , Moarii Mathai , Levine Ross L. , Dogan Ahmet , Miller Vincent A. , Younes Anas 
Published: June 2018

AbstractWe sought to define the genomic landscape of diffuse large B-cell lymphoma (DLBCL) by using formalin-fixed paraffin-embedded (FFPE) biopsy specimens. We used targeted sequencing of genes altered in hematologic malignancies, including DNA coding sequence for 405 genes, noncoding sequence for 31 genes, and RNA coding sequence for 265 genes (FoundationOne-Heme). Short variants, rearrangements, and copy number alterations were determined. We studied 198 samples (114 de novo, 58 previously treated, and 26 large-cell transformation from follicular lymphoma). Median number of GAs per case was 6, with 97% of patients harboring at least one alteration. Recurrent GAs were detected in genes with established roles in DLBCL pathogenesis (e.g. MYD88, CREBBP, CD79B, EZH2), as well as notable differences compared to prior studies such as inactivating mutations in TET2 (5%). Less common GAs identified potential targets for approved or investigational therapies, including BRAF, CD274 (PD-L1), IDH2, and JAK1/2. TP53 mutations were more frequently observed in relapsed/refractory DLBCL, and predicted for lack of response to first-line chemotherapy, identifying a subset of patients that could be prioritized for novel therapies. Overall, 90% (n = 169) of the patients harbored a GA which could be explored for therapeutic intervention, with 54% (n = 107) harboring more than one putative target.
Assembly and activation of the Hippo signalome by FAT1 tumor suppressor
Authors: Martin Daniel , Degese Maria S. , Vitale-Cross Lynn , Iglesias-Bartolome Ramiro , Valera Juan Luis Callejas , Wang Zhiyong , Feng Xiaodong , Yeerna Huwate , Vadmal Vachan , Moroishi Toshiro , Thorne Rick F. , Zaida Moraima , Siegele Bradford , Cheong Sok C. , Molinolo Alfredo A. , Samuels Yardena , Tamayo Pablo , Guan Kun Liang , Lippman Scott M. , Lyons J. Guy , Gutkind J. Silvio 
Published: June 2018

AbstractDysregulation of the Hippo signaling pathway and the consequent YAP1 activation is a frequent event in human malignancies, yet the underlying molecular mechanisms are still poorly understood. A pancancer analysis of core Hippo kinases and their candidate regulating molecules revealed few alterations in the canonical Hippo pathway, but very frequent genetic alterations in the FAT family of atypical cadherins. By focusing on head and neck squamous cell carcinoma (HNSCC), which displays frequent FAT1 alterations (29.8%), we provide evidence that FAT1 functional loss results in YAP1 activation. Mechanistically, we found that FAT1 assembles a multimeric Hippo signaling complex (signalome), resulting in activation of core Hippo kinases by TAOKs and consequent YAP1 inactivation. We also show that unrestrained YAP1 acts as an oncogenic driver in HNSCC, and that targeting YAP1 may represent an attractive precision therapeutic option for cancers harboring genomic alterations in the FAT1 tumor suppressor genes.
The Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow
Authors: Shao Lijian , Chang Jianhui , Feng Wei , Wang Xiaoyan , Williamson Elizabeth A. , Li Ying , Schajnovitz Amir , Scadden David , Mortensen Luke J. , Lin Charles P. , Li Linheng , Paulson Ariel , Downing James , Zhou Daohong , Hromas Robert A. 
Published: June 2018

AbstractThe transition of hematopoiesis from the fetal liver (FL) to the bone marrow (BM) is incompletely characterized. We demonstrate that the Wiskott–Aldrich syndrome verprolin-homologous protein (WAVE) complex 2 is required for this transition, as complex degradation via deletion of its scaffold Hem-1 causes the premature exhaustion of neonatal BM hematopoietic stem cells (HSCs). This exhaustion of BM HSC is due to the failure of BM engraftment of Hem-1−/− FL HSCs, causing early death. The Hem-1−/− FL HSC engraftment defect is not due to the lack of the canonical function of the WAVE2 complex, the regulation of actin polymerization, because FL HSCs from Hem-1−/− mice exhibit no defects in chemotaxis, BM homing, or adhesion. Rather, the failure of Hem-1−/− FL HSC engraftment in the marrow is due to the loss of c-Abl survival signaling from degradation of the WAVE2 complex. However, c-Abl activity is dispensable for the engraftment of adult BM HSCs into the BM. These findings reveal a novel function of the WAVE2 complex and define a mechanism for FL HSC fitness in the embryonic BM niche.
Molecular signature of progenitor cells isolated from young and adult human hearts
Authors: Walravens Ann-Sophie , Vanhaverbeke Maarten , Ottaviani Lara , Gillijns Hilde , Trenson Sander , Driessche Nina Vanden , Luttun Aernout , Meyns Bart , Herijgers Paul , Rega Filip , Heying Ruth , Sampaolesi Maurilio , Janssens Stefan 
Published: June 2018

AbstractThe loss of endogenous cardiac regenerative capacity within the first week of postnatal life has intensified clinical trials to induce cardiac regeneration in the adult mammalian heart using different progenitor cell types. We hypothesized that donor age-related phenotypic and functional characteristics of cardiac progenitor cells (CPC) account for mixed results of cell-based cardiac repair. We compared expression profiles and cell turnover rates of human heart-derived c-kitpos progenitors (c-kitpos CPC) and cardiosphere-derived cells (CDC) from young and adult donor origin and studied their in vitro angiogenic and cardiac differentiation potential, which can be relevant for cardiac repair. We report that 3-dimensional CDC expansion recapitulates a conducive environment for growth factor and cytokine release from adult donor cells (aCDC) that optimally supports vascular tube formation and vessel sprouting. Transdifferentiation capacity of c-kitpos CPCs and CDCs towards cardiomyocyte-like cells was modest, however, most notable in young c-kitpos cells and adult CDCs. Progenitors isolated with different methods thus show cell- and donor-specific characteristics that may account for variable contributions in functional myocardial recovery.
Intraflagellar transport 46 (IFT46) is essential for trafficking IFT proteins between cilia and cytoplasm in Paramecium
Authors: Shi Lei , Shi Xuezhen , Shen Yuan 
Published: June 2018

AbstractIntraflagellar transport (IFT) is a bi-directional process by which particles are carried within the cilia or flagella. This process is essential for ciliary growth and functional maintenance. The IFT complex B (IFTB) is linked to a kinesin motor for anterograde transport towards the ciliary tip. The IFT complex A (IFTA) is connected to a dynein motor for retrograde transport towards the ciliary basis. This study focuses on IFT46, an IFTB member that participates in this process. InParamecium, a GFP-labelled IFT46 protein was found in basal bodies and in some cilia, mostly those undergoing biogenesis. RNA interference against IFT46 inParameciumtriggered severe defects in ciliary growth and architecture, including a decreased cilia number and shortened cilia length. This result differed from that obtained from the cells that were depleted of IFT80, another IFTB protein. Moreover, IFT57-GFP fusion protein abnormally accumulated in the cortex and cytoplasm in IFT46-depleted cells compared with the control. Furthermore, transcriptomic analysis showed that IFT46 depletion induced the abnormal expression of several genes that encodeding kinesin and dynein chains. These findings together indicate that IFT46 plays important roles in trafficking IFT proteins between the cytoplasm and cilia ofParamecium.
Preimplantation Genetic Screening with Spent Culture Medium/Blastocoel Fluid for in Vitro Fertilization
Authors: Li Penghao , Song Zhe , Yao Yaxin , Huang Tianhua , Mao Rurong , Huang Jun , Ma Yongyi , Dong Xin , Huang Wenlong , Huang Jihua , Chen Tianjian , Qu Ting , Li Lingxiao , Zhong Ying , Gu Jiang 
Published: June 2018

AbstractPreimplantation genetic screening (PGS) detects chromosomal aneuploidy from DNA extracted from trophectodermal biopsy of the embryos before implantation. Although a controlled study showed no difference in pregnancy rates between this invasive cell biopsy technique and a non-biopsied control group, the potential long-term damage by the current PGS method has not be completely ruled out. We therefore tested a less-invasive protocol which utilizes spent culture medium combining with blastocoel fluid (ECB) to assess chromosomal aneuploidy. We compared the new protocol with the currently employed trophectodermal biopsy method against chromosomal information obtained from the remaining embryo. We found that the new technique generated information about aneuploidy that was not entirely identical to obtained from the biopsied trophectoderm or the remaining embryo. As the origins of the DNA extracted from the three sample types were not the same, the significance and interpretation of each result would have its own meaning. The possible implications derived from the ECB results as well as those from cell biopsy were discussed. The effectiveness of this new approach in selecting the best embryo for uterine implantation awaits further long term evaluation.
Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae
Authors: Li Bin , Zheng Yongqi 
Published: June 2018

AbstractChloroplast genomes of plants are highly conserved in both gene order and gene content, are maternally inherited, and have a lower rate of evolution. Chloroplast genomes are considered to be good models for testing lineage-specific molecular evolution. In this study, we use Schisandraceae as an example to generate insights into the overall evolutionary dynamics in chloroplast genomes and to establish the phylogenetic relationship of Schisandraceae based on chloroplast genome data using phylogenomic analysis. By comparing three Schisandraceae chloroplast genomes, we demonstrate that the gene order, gene content, and length of chloroplast genomes in Schisandraceae are highly conserved but experience dynamic evolution among species. The number of repeat variations were detected, and the Schisandraceae chloroplast genome was revealed as unusual in having a 10 kb contraction of the IR due to the genome size variations compared with other angiosperms. Phylogenomic analysis based on 82 protein-coding genes from 66 plant taxa clearly elucidated that Schisandraceae is a sister to a clade that includes magnoliids, monocots, and eudicots within angiosperms. As to genus relationships within Schisandraceae, Kadsura and Schisandra formed a monophyletic clade which was sister to Illicium.
Influence of oxygen on generation of reactive chemicals from nitrogen plasma jet
Authors: Uhm Han Sup , Ki Se Hoon , Baik Ku Youn , Choi Eun Ha 
Published: June 2018

AbstractA nonthermal plasma jet is operated at atmospheric pressure inside a vacuum chamber filled with nitrogen gas. Various chemical compounds are fabricated from nitrogen and water molecules in plasma jet with varying oxygen content. Detailed theoretical investigation of these chemical compounds is carried out in terms of different oxygen ratio ξ. Experimental measurements are also carried out for comparison with theoretical results. Hydroxyl molecules are mostly generated at surface of water, and some of them can penetrate into water. The density of hydroxyl molecules has its maximum without oxygen, and decreases to zero as ξ increases to 0.25. The density of the ammonia of NH3 also deceases as ξ increases to 0.25. On the other hand, theory and experiment show that the density of the NO3 increases drastically as ξ increases to 0.25. The hydrogen peroxide density in plasma activated water deceases, reaches its minimum value at ξ = 0.05, and then increases again, as ξ increases from a small value to a large value. The pH value of the plasma activated water, which is slightly changed to alkali without oxygen, decreases as ξ increases.
Numerical emulation of Thru-Reflection-Line calibration for the de-embedding of Surface Acoustic Wave devices
Authors: Mencarelli D. , Djafari-Rouhani B. , Pennec Y. , Pitanti A. , Zanotto S. , Stocchi M. , Pierantoni L. 
Published: June 2018

AbstractIn this contribution, a rigorous numerical calibration is proposed to characterize the excitation of propagating mechanical waves by interdigitated transducers (IDTs). The transition from IDT terminals to phonon waveguides is modeled by means of a general circuit representation that makes use of Scattering Matrix (SM) formalism. In particular, the three-step calibration approach called the Thru-Reflection-Line (TRL), that is a well-established technique in microwave engineering, has been successfully applied to emulate typical experimental conditions. The proposed procedure is suitable for the synthesis/optimization of surface-acoustic-wave (SAW) based devices: the TRL calibration allows to extract/de-embed the acoustic component, namely resonator or filter, from the outer IDT structure, regardless of complexity and size of the letter. We report, as a result, the hybrid scattering parameters of the IDT transition to a mechanical waveguide formed by a phononic crystal patterned on a piezoelectric AlN membrane, where the effect of a discontinuity from periodic to uniform mechanical waveguide is also characterized. In addition, to ensure the correctness of our numerical calculations, the proposed method has been validated by independent calculations.
Direct current stimulation of endothelial monolayers induces a transient and reversible increase in transport due to the electroosmotic effect
Authors: Cancel Limary M. , Arias Katherin , Bikson Marom , Tarbell John M. 
Published: June 2018

AbstractWe investigated the effects of direct current stimulation (DCS) on fluid and solute transport across endothelial cell (EC) monolayersin vitro. Our motivation was transcranial direct current stimulation (tDCS) that has been investigated for treatment of neuropsychiatric disorders, to enhance neurorehabilitation, and to change cognition in healthy subjects. The mechanisms underlying this diversity of applications remain under investigation. To address the possible role of blood-brain barrier (BBB) changes during tDCS, we applied direct current to cultured EC monolayers in a specially designed chamber that generated spatially uniform direct current. DCS induced fluid and solute movement across EC layers that persisted only for the duration of the stimulation suggesting an electroosmosis mechanism. The direction of induced transport reversed with DCS polarity – a hallmark of the electroosmotic effect. The magnitude of DCS-induced flow was linearly correlated to the magnitude of the applied current. A mathematical model based on a two-pore description of the endothelial transport barrier and a Helmholtz model of the electrical double layer describes the experimental data accurately and predicts enhanced significance of this mechanism in less permeable monolayers. This study demonstrates that DCS transiently alters the transport function of the BBB suggesting a new adjunct mechanism of tDCS.
Uncovering global metabolic response to cordycepin production in Cordyceps militaris through transcriptome and genome-scale network-driven analysis
Authors: Raethong Nachon , Laoteng Kobkul , Vongsangnak Wanwipa 
Published: June 2018

AbstractThe cellular metabolic adaptations ofCordyceps militarishave been progressively studied. In particular, the cordycepin pathway is of interest in medicinal applications. Even though the metabolic pathways for cordycepin production are known to be related to different carbon sources, the regulatory mechanisms at a systems level are poorly characterized. To explore the regulatory mechanisms, this study therefore aimed to investigate the global metabolic response to cordycepin production inC. militaristhrough transcriptome analysis and genome-scale network-driven analysis. Here, transcriptome analysis of 16,805 expressed genes inC. militarisstrain TBRC6039 grown on different carbon sources was performed. Of these genes, 2,883 were significantly differentially expressed genes, uncovering sucrose- and glucose-mediated changes in the transcriptional regulation of central carbon metabolism inC. militaris, which was shown using the CmSNF1 mechanism as an example. After applying genome-scale metabolic network-driven analysis, reporter metabolites and key metabolic subnetworks involving adenosine, cordycepin and methionine were proposed through the up-regulation of cordycepin biosynthetic genes. Our findings suggest that the transcriptional regulation of these pathways is a ubiquitous feature in response to specific culture conditions during cordycepin overproduction.
Low circulating chemerin levels correlate with hepatic dysfunction and increased mortality in decompensated liver cirrhosis
Authors: Horn Paul , von Loeffelholz Christian , Forkert Franziska , Stengel Sven , Reuken Philipp , Aschenbach René , Stallmach Andreas , Bruns Tony 
Published: June 2018

AbstractNutritional status, infections, inflammation and extrahepatic organ dysfunction are critical factors for the progression of chronic liver disease. Chemerin is an immune-metabolically and chemotactically active adipokine and we hypothesized that it is associated with disease severity and prognosis in patients with advanced decompensated cirrhosis. Therefore, we measured serum concentrations of chemerin in a prospectively characterized cohort of 80 patients with decompensated cirrhosis and ascites and assessed the associations with markers of disease severity and short-term outcome at 28 days. In a subset of patients (n = 40), ascitic fluid chemerin was determined. Advanced liver disease was associated with decreased serum but not ascitic chemerin levels. Serum chemerin correlated with markers of hepatic function (total bilirubin, albumin, INR) and inversely correlated with indicators of portal hypertension (platelet count, gastrointestinal bleeding) but not with extrahepatic organ failure and systemic inflammation. Patients presenting with acute-on-chronic liver failure or infection did not exhibit altered serum or ascitic fluid chemerin concentrations. However, serum chemerin levels below 87 ng/ml predicted an increased risk for mortality or liver transplantation within 28 days independently of MELD and infections. We conclude that low serum chemerin is an independent adverse prognostic factor in patients with advanced decompensated cirrhosis.