bluuebunny/crossref_metadata_2025_split huggingface dataset:
The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
Authors: Nicolás César , Martin-Bertelsen Tomas , Floudas Dimitrios , Bentzer Johan , Smits Mark , Johansson Tomas , Troein Carl , Persson Per , Tunlid Anders 
Published: December 2018

AbstractMany trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
Sarm1 induction and accompanying inflammatory response mediates age-dependent susceptibility to rotenone-induced neurotoxicity
Authors: Sur Malinki , Dey Puja , Sarkar Ankita , Bar Sudipta , Banerjee Dipanjana , Bhat Swati , Mukherjee Piyali 
Published: December 2018

AbstractAging is a complex biological process and environmental risk factors like pesticide exposure have been implicated in the increased incidence of age-related neurodegenerative diseases like Parkinson’s disease (PD) but the etiology remains unknown. There is also lack of a proper animal model system to study the progressive effect of these environmental toxins on age-associated neurodegeneration. In this study, we established a drosophila model of aging to study the age-dependent vulnerability to the environmental toxin rotenone that has been implicated in sporadic cases of PD. We demonstrate that age plays a determining role in the increased susceptibility to chronic rotenone exposure that is accompanied by severe locomotor deficits, decreased lifespan and loss of dopaminergic (DA) neurons. Chronic low dose exposure to rotenone results in the rapid induction of the neurodegenerative molecule SARM1/dSarm. Further, the age-dependent dSarm induction is accompanied by a heightened inflammatory response (increased expression ofEigerandRelish) that is independent of reactive oxygen species (ROS) generation in the observed rotenone-induced neurotoxicity. dSarm induction and subsequent locomotor deficits is reversed in the presence of the anti-inflammatory molecule resveratrol. Thus, dSarm and heightened inflammatory responses may play a crucial role in age-dependent vulnerability to the pesticide rotenone thus making it an attractive target to help develop cost-effective therapeutic strategies to prevent ongoing dopaminergic neuronal loss as seen in PD.
Synthesis and Kinetic evaluation of an azido analogue of methylerythritol phosphate: a Novel Inhibitor of E. coli YgbP/IspD
Authors: Baatarkhuu Zoljargal , Chaignon Philippe , Borel Franck , Ferrer Jean-Luc , Wagner Alain , Seemann Myriam 
Published: December 2018

AbstractAs multidrug resistant pathogenic microorganisms are a serious health menace, it is crucial to continuously develop novel medicines in order to overcome the emerging resistance. The methylerythritol phosphate pathway (MEP) is an ideal target for antimicrobial development as it is absent in humans but present in most bacteria and in the parasite Plasmodium falciparum. Here, we report the synthesis and the steady-state kinetics of a novel potent inhibitor (MEPN3) of Escherichia coli YgbP/IspD, the third enzyme of the MEP pathway. MEPN3 inhibits E. coli YgbP/IspD in mixed type mode regarding both substrates. Interestingly, MEPN3 shows the highest inhibitory activity when compared to known inhibitors of E. coli YgbP/IspD. The mechanism of this enzyme was also studied by steady-state kinetic analysis and it was found that the substrates add to the enzyme in sequential manner.
De novo transcriptomic profiling of the clonal Leymus chinensis response to long-term overgrazing-induced memory
Authors: Ren Weibo , Hou Xiangyang , Wu Zinian , Kong Lingqi , Guo Huiqin , Hu Ningning , Wan Dongli , Zhang Jize 
Published: December 2018

AbstractSheepgrass (Leymus chinensis) is one of the dominant grass species present on typical steppes of the Inner Mongolia Plateau. However, L. chinensis has developed a dwarfing phenotype in response to the stressful habitat in grasslands that are severely degraded due to heavy grazing. The lack of transcriptomic and genomic information has prohibited the understanding of the transgenerational effect on physiological alterations in clonal L. chinensis at the molecular level in response to livestock grazing. To solve this problem, transcriptomic information from the leaves of clonal L. chinensis obtained from overgrazed (GR) and non-grazed (NG) grasslands was studied using a paired-end Illumina HiSeq 2500 sequencing platform. First, despite the influence of grazing being absent during the growth of clonal offspring in our hydroponic experiment, compared with those from the NG group, clonal L. chinensis from the GR group exhibited significant dwarf-type morphological traits. A total of 116,356 unigenes were subsequently generated and assembled de novo, of which 55,541 could be annotated to homologous matches in the NCBI non-redundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of 3,341 unigenes significantly differed between the GR group and the NG group with an absolute value of Log2 ratio ≥ 1. The altered expression of genes involved in defence and immune responses, pathogenic resistance and cell development indicates that livestock grazing induces a transgenerational effect on the growth inhibition of clonal L. chinensis. The results of the present study will provide important large-scale transcriptomic information on L. chinensis. Furthermore, the results facilitated our investigation of grazing-induced transgenerational effects on both the morphological and physiological characteristics of L. chinensis at the molecular levels.
Shape changes of erythrocytes during blood clot contraction and the structure of polyhedrocytes
Authors: Tutwiler Valerie , Mukhitov Alexander R. , Peshkova Alina D. , Le Minh Giang , Khismatullin R. R. , Vicksman Jacqueline , Nagaswami Chandrasekaran , Litvinov Rustem I. , Weisel John W. 
Published: December 2018

AbstractPolyhedral erythrocytes, named polyhedrocytes, are formed in contracted blood clots and thrombi, as a result of compression by activated contractile platelets pulling on fibrin. This deformation was shown to be mechanical in nature and polyhedrocytes were characterized using light and electron microscopy. Through three-dimensional reconstruction, we quantified the geometry of biconcave, intermediate, and polyhedral erythrocytes within contracting blood clots. During compression, erythrocytes became less oblate and more prolate than the biconcave cells and largely corresponded to convex, irregular polyhedra with a total number of faces ranging from 10 to 16. Faces were polygons with 3 to 6 sides. The majority of the faces were quadrilaterals, though not all sides were straight and not all faces were flat. There were no changes in the surface area or volume. These results describe the gradual natural deformation of erythrocytes as a part of compaction into a tightly packed array that is an important but understudied component of mature blood clots and thrombi.
Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR
Authors: Heinrich Paul , Kohler Christian , Ellmann Lisa , Kuerner Paul , Spang Rainer , Oefner Peter J. , Dettmer Katja 
Published: December 2018

AbstractExperiments with stable isotope tracers such as 13C and 15N are increasingly used to gain insights into metabolism. However, mass spectrometric measurements of stable isotope labeling experiments should be corrected for the presence of naturally occurring stable isotopes and for impurities of the tracer substrate. Here, we analyzed the effect that such correction has on the data: omitting correction or performing invalid correction can result in largely distorted data, potentially leading to misinterpretation. IsoCorrectoR is the first R-based tool to offer said correction capabilities. It is easy-to-use and comprises all correction features that comparable tools can offer in a single solution: correction of MS and MS/MS data for natural stable isotope abundance and tracer impurity, applicability to any tracer isotope and correction of multiple-tracer data from high-resolution measurements. IsoCorrectoR’s correction performance agreed well with manual calculations and other available tools including Python-based IsoCor and Perl-based ICT. IsoCorrectoR can be downloaded as an R-package from: http://bioconductor.org/packages/release/bioc/html/IsoCorrectoR.html.
Neuroticism predicts the impact of serotonin challenges on fear processing in subgenual anterior cingulate cortex
Authors: Hornboll Bettina , Macoveanu Julian , Nejad Ayna , Rowe James , Elliott Rebecca , Knudsen Gitte M. , Siebner Hartwig R. , Paulson Olaf B. 
Published: December 2018

AbstractThe personality trait neuroticism is associated with increased vulnerability to anxiety and mood disorders, conditions linked with abnormal serotonin neurotransmission and emotional processing. The interaction between neuroticism and serotonin during emotional processing is however not understood. Here we investigate how individual neuroticism scores influence the neural response to negative emotional faces and their sensitivity to serotonergic tone. Twenty healthy participants performed an emotional face task under functional MRI on three occasions: increased serotonin tone following infusion of a selective serotonin reuptake inhibitor (SSRI), decreased serotonin tone following acute tryptophan depletion (ATD) protocol, and no serotonin challenge (control). During the task, participants performed a gender-discrimination task of neutral, fearful or angry facial expressions. Individual variations in neuroticism scores were associated with neural response of subgenual anterior cingulate cortex to fearful facial expressions. The association was however opposite under the two serotoninergic challenges. The fear-related response in this region and individual neuroticism scores correlated negatively during citalopram challenge and positively during ATD. Thus, neuroticism scores were associated with the relative impact of serotonin challenges on fear processing in subgenual anterior cingulate cortex. This finding may link to a neural mechanism for the variable therapeutic effect of SSRI treatment observed in clinical populations.
CT Slice Thickness and Convolution Kernel Affect Performance of a Radiomic Model for Predicting EGFR Status in Non-Small Cell Lung Cancer: A Preliminary Study
Authors: Li Yajun , Lu Lin , Xiao Manjun , Dercle Laurent , Huang Yue , Zhang Zishu , Schwartz Lawrence H. , Li Daiqiang , Zhao Binsheng 
Published: December 2018

AbstractWe evaluated whether the optimal selection of CT reconstruction settings enables the construction of a radiomics model to predict epidermal growth factor receptor (EGFR) mutation status in primary lung adenocarcinoma (LAC) using standard of care CT images. Fifty-one patients (EGFR:wildtype = 23:28) with LACs of clinical stage I/II/IIIA were included in the analysis. The LACs were segmented in four conditions, two slice thicknesses (Thin: 1 mm; Thick: 5 mm) and two convolution kernels (Sharp: B70f/B70s; Smooth: B30f/B31f/B31s), which constituted four groups: (1) Thin-Sharp, (2) Thin-Smooth, (3) Thick-Sharp, and (4) Thick-Smooth. Machine learning algorithms selected and combined 1,695 quantitative image features to build prediction models. The performance of prediction models was assessed by calculating the area under the curve (AUC). The best prediction model yielded AUC (95%CI) = 0.83 (0.68, 0.92) using the Thin-Smooth reconstruction setting. The AUC of models using thick slices was significantly lower than that of thin slices (P < 10−3), whereas the impact of reconstruction kernel was not significant. Our study showed that the optimal prediction of EGFR mutational status in early stage LACs was achieved by using thin CT-scan slices, independently of convolution kernels. Results from the prediction model suggest that tumor heterogeneity is associated with EGFR mutation.
Switching excitonic recombination and carrier trapping in cesium lead halide perovskites by air
Authors: Wang Yue , Ren Yinjuan , Zhang Shengli , Wu Jianfeng , Song Jizhong , Li Xiaoming , Xu Jiayue , Sow Chorng Haur , Zeng Haibo , Sun Handong 
Published: December 2018

AbstractAll-inorganic cesium lead halide perovskites have been emerging as the promising semiconductor materials for next-generation optoelectronics. However, the fundamental question of how the environmental atmosphere affects their photophysical properties, which is closely related to the practical applications, remains elusive. Here, we report the dynamic switching between radiative exciton recombination and non-radiative carrier trapping in CsPbBr3 by controlling the atmospheric conditions. Specifically, we show that the photoluminescence (PL) intensity from the CsPbBr3 crystals can be boosted by ~ 60 times by changing the surrounding from vacuum to air. Based on the comprehensive optical characterization, near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) as well as density functional theory (DFT) calculations, we unravel that the physisorption of oxygen molecules, which repairs the trap states by passivating the PL-quenching bromine vacancies, is accountable for the enhanced PL in air. These results are helpful for better understanding the optical properties of all-inorganic perovskites.
Nationwide registry of sepsis patients in Japan focused on disseminated intravascular coagulation 2011–2013
Authors: Hayakawa Mineji , Yamakawa Kazuma , Saito Shinjiro , Uchino Shigehiko , Kudo Daisuke , Iizuka Yusuke , Sanui Masamitsu , Takimoto Kohei , Mayumi Toshihiko 
Published: December 2018

AbstractSepsis is a syndrome with physiologic, pathologic, and biochemical abnormalities induced by infection. Sepsis can induce the dysregulation of systemic coagulation and fibrinolytic systems, resulting in disseminated intravascular coagulation (DIC), which is associated with a high mortality rate. Although there is no international consensus on available treatments for sepsis-induced DIC, DIC diagnosis and treatment are commonly performed in Japanese clinical settings. Therefore, clinical data related to sepsis-induced DIC diagnosis and treatment can be obtained from Japanese clinical settings. We performed a retrospective nationwide observational study (Japan Septic Disseminated Intravascular Coagulation [J-SEPTIC DIC] study) to collect data regarding characteristics of sepsis patients in Japan, with a focus on coagulofibrinolytic dysregulation and DIC treatment received by each patient. The J-SEPTIC DIC study collected information for a total of 3,195 patients with severe sepsis and septic shock and is the largest data set in Japan on DIC diagnosis and treatment in clinical settings.
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales
Authors: He Yang , Peng Fu , Deng Cao , Xiong Liang , Huang Zi-yan , Zhang Ruo-qi , Liu Meng-jia , Peng Cheng 
Published: December 2018

AbstractThe Lamiales order presents highly varied genome sizes and highly specialized life strategies. Patchouli, Pogostemon cablin (Blanco) Benth. from the Lamiales, has been widely cultivated in tropical and subtropical areas of Asia owing to high demand for its essential oil. Here, we generated ~681 Gb genomic sequences (~355X coverage) for the patchouli, and the assembled genome is ~1.91 Gb and with 110,850 predicted protein-coding genes. Analyses showed clear evidence of whole-genome octuplication (WGO) since the pan-eudicots γ triplication, which is a recent and exclusive polyploidization event and occurred at ~6.31 million years ago. Analyses of TPS gene family showed the expansion of type-a, which is responsible for the synthesis of sesquiterpenes and maybe highly specialization in patchouli. Our datasets provide valuable resources for plant genome evolution, and for identifying of genes related to secondary metabolites and their gene expression regulation.
miR-221/222 promote tumor growth and suppress apoptosis by targeting lncRNA GAS5 in breast cancer
Authors: Zong Yuanyuan , Zhang Yazhou , Sun Xichao , Xu Tao , Cheng Xiankui , Qin Yejun 
Published: December 2018

Abstract
MicroRNAs (miRNAs) are 21–23-nucleotide, short, non-coding RNAs that play important roles in virtually all biological pathways in mammals and other multicellular organisms. The association of miR-221 and miR-222 (miR-221/222) for breast cancer is critical, but their detailed roles in its development and progression remain unclear. In the present study, we found that miR-221/222 were consistently up-regulated in breast cancer tissues. We then investigated the molecular mechanisms by which miR-221/222 contributed to breast cancer and identified growth arrest–specific transcript 5 (GAS5) as a direct target gene of miR-221/222. In contrast with the up-regulated expression levels of miR-221/222, GAS5 levels were significantly down-regulated and negatively correlated with miR-221/222 in breast cancer tissues. In addition, we showed that miR-221/222 inhibitors increased cellular apoptosis, miR-221/222 mimics decreased the cell apoptosis in breast cancer cells, and restoration of GAS5 expression attenuated the anti-apoptotic effects of miR-221/222 in breast cancer cells, indicating that GAS5 was a direct mediator of miR-221/222 function. Finally, we showed that miR-221/222 suppressed GAS5 expression significantly and enhanced tumor growth in a mouse model of breast cancer xenografts. The present study highlighted the important role of miR-221/222 as oncomiRs in breast cancer, which inhibited GAS5 translation. These findings may provide a new perspective for the molecular mechanism of breast carcinogenesis and provide a novel approach to the treatment of breast cancer.
Models of irradiated molecular shocks
Authors: Godard B. , Pineau des Forêts G. , Lesaffre P. , Lehmann A. , Gusdorf A. , Falgarone E. 
Published: December 2018

Context. The recent discovery of excited molecules in starburst galaxies observed with ALMA and the Herschel space telescope has highlighted the necessity to understand the relative contributions of radiative and mechanical energies in the formation of molecular lines and explore the conundrum of turbulent gas bred in the wake of galactic outflows.
Aims. The goal of the paper is to present a detailed study of the propagation of low velocity (5–25 km s−1) stationary molecular shocks in environments illuminated by an external ultraviolet (UV) radiation field. In particular, we intend to show how the structure, dynamics, energetics, and chemical properties of shocks are modified by UV photons and to estimate how efficiently shocks can produce line emission.
Methods. We implemented several key physico-chemical processes in the Paris-Durham shock code to improve the treatment of the radiative transfer and its impact on dust and gas particles. We propose a new integration algorithm to find the steady-state solutions of magnetohydrodynamics equations in a range of parameters in which the fluid evolves from a supersonic to a subsonic regime. We explored the resulting code over a wide range of physical conditions, which encompass diffuse interstellar clouds and hot and dense photon-dominated regions.
Results. We find that C-type shock conditions cease to exist as soon as G0 > 0.2 (nH/cm−3)1/2. Such conditions trigger the emergence of another category of stationary solutions, called C*-type and CJ-type shocks, in which the shocked gas is momentarily subsonic along its trajectory. These solutions are shown to be unique for a given set of physical conditions and correspond to dissipative structures in which the gas is heated up to temperatures comprised between those found in C-type and adiabatic J-type shocks. High temperatures combined with the ambient UV field favour the production or excitation of a few molecular species to the detriment of others, hence leading to specific spectroscopic tracers such as rovibrational lines of H2 and rotational lines of CH+. Unexpectedly, the rotational lines of CH+ may carry as much as several percent of the shock kinetic energy.
Conclusions. Ultraviolet photons are found to strongly modify the way the mechanical energy of interstellar shocks is processed and radiated away. In spite of what intuition dictates, a strong external UV radiation field boosts the efficiency of low velocity interstellar shocks in the production of several molecular lines which become evident tracers of turbulent dissipation.
Psychiatrische Komorbidität beim Ullrich-Turner-Syndrom
Authors: Mavrogiorgou Paraskevi , Kossmann Christian , Irawan Sarah , Lücke Thomas , Juckel Georg 
Published: December 2018

Zusammenfassung
Ziel Das Ullrich-Turner Syndrom (UTS) ist eine X-chromosomale Störung, deren klinische Symptomatik vielfältig und heterogen ist. Neuropsychiatrische Erkrankungen zählen jedoch nicht zu den typischen Komorbiditäten des Turner-Syndrom, allerdin gs liegen mittlerweile mehrere Berichte in Form von Einzellfalldarstellungen vor.
Methodik Anhand der Darstellung des Falls einer Patientin mit einem Turner-Syndrom und einer schizoaffektiven Störung werden mögliche Zusammenhänge und die dazu vorhandene Literatur diskutiert.
Schlussfolgerung Die gehäuften Berichte über das zusätzliche Auftreten einer psychotischen Symptomatik beim UTS legen einen Zusammenhang zwischen der X-chromosomalen Aberration und einer Erkrankungen aus dem schizophrenen Formenkreis nahe. Hinsichtlich der Komorbidität bedarf es jedoch einer allgemeingültigen nosologischen Kategorisierung, die auch eine weitere notwendige Forschungsaktivität erleichtern würde.