bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic profiling for the molecular classification of metastatic brain tumors
Authors: Orozco Javier I. J. , Knijnenburg Theo A. , Manughian-Peter Ayla O. , Salomon Matthew P. , Barkhoudarian Garni , Jalas John R. , Wilmott James S. , Hothi Parvinder , Wang Xiaowen , Takasumi Yuki , Buckland Michael E. , Thompson John F. , Long Georgina V. , Cobbs Charles S. , Shmulevich Ilya , Kelly Daniel F. , Scolyer Richard A. , Hoon Dave S. B. , Marzese Diego M. 
Published: October 2018

AbstractOptimal treatment of brain metastases is often hindered by limitations in diagnostic capabilities. To meet this challenge, here we profile DNA methylomes of the three most frequent types of brain metastases: melanoma, breast, and lung cancers (n = 96). Using supervised machine learning and integration of DNA methylomes from normal, primary, and metastatic tumor specimens (n = 1860), we unravel epigenetic signatures specific to each type of metastatic brain tumor and constructed a three-step DNA methylation-based classifier (BrainMETH) that categorizes brain metastases according to the tissue of origin and therapeutically relevant subtypes. BrainMETH predictions are supported by routine histopathologic evaluation. We further characterize and validate the most predictive genomic regions in a large cohort of brain tumors (n = 165) using quantitative-methylation-specific PCR. Our study highlights the importance of brain tumor-defining epigenetic alterations, which can be utilized to further develop DNA methylation profiling as a critical tool in the histomolecular stratification of patients with brain metastases.
Chromium-catalyzed para-selective formation of quaternary carbon centers by alkylation of benzamide derivatives
Authors: Liu Pei , Chen Changpeng , Cong Xuefeng , Tang Jinghua , Zeng Xiaoming 
Published: October 2018

AbstractSelective creation of quaternary carbon centers has been a long-standing challenge in synthetic chemistry. We report here the chromium-catalyzed, para-selective formation of arylated quaternary carbon centers by alkylative reactions of benzamide derivatives with tertiary alkylmagnesium bromides at room temperature. The reaction, which was enabled by a low-cost chromium(III) salt combined with trimethylsilyl bromide, introduces a sterically bulky tertiary alkyl scaffold on the para-position of benzamide derivatives in a highly selective fashion without either isomerization of the tertiary alkyl group or formation of ortho-alkylated byproducts. Forming low-valent Cr species in situ by reaction of CrCl3 with t-BuMgBr accompanied by evolution of hydrogen can be considered, which serves as reactive species to promote the reaction. The para-alkylation likely occurs via a radical-type nucleophilic substitution of imino-coordination benzimidate intermediate.
Unveiling a magnetized jet from a low-mass protostar
Authors: Lee Chin-Fei , Hwang Hsiang-Chih , Ching Tao-Chung , Hirano Naomi , Lai Shih-Ping , Rao Ramprasad , Ho Paul. T. P 
Published: October 2018

AbstractProtostellar jets are one of the most intriguing signposts in star formation. Recent detection of a jet rotation indicates that they can carry away angular momenta from the innermost edges of the disks, allowing the disks to feed the central protostars. In current jet-launching models, magnetic fields are required to launch and collimate the jets, however, observationally, it is still uncertain if magnetic fields are really present in the jets. Here we report a clear detection of SiO line polarization in the HH 211 protostellar jet. Since this line polarization has been attributed to the Goldreich-Kylafis effect in the presence of magnetic field, our observations show convincingly the presence of magnetic field in a jet from a low-mass protostar. The implied magnetic field could be mainly toroidal, as suggested in current jet-launching models, in order to collimate the jet at large distances.
Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth
Authors: Kahraman Osman , Langen Ralf , Haselwandter Christoph A. 
Published: October 2018

AbstractMany membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.
Single molecule tracking reveals spatio-temporal dynamics of bacterial DNA repair centres
Authors: Rösch Thomas C. , Altenburger Stephan , Oviedo-Bocanegra Luis , Pediaditakis Miriam , Najjar Nina El , Fritz Georg , Graumann Peter L. 
Published: October 2018

AbstractSingle-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living bacterial cells at high spatial and temporal resolution. We have performed single-molecule imaging of early DNA double-strand break (DSB) repair events during homologous recombination in the model bacterium Bacillus subtilis. Our findings reveal that DNA repair centres arise at all sites on the chromosome and that RecN, RecO and RecJ perform fast, enzyme-like functions during detection and procession of DNA double strand breaks, respectively. Interestingly, RecN changes its diffusion behavior upon induction of DNA damage, from a largely diffusive to a DNA-scanning mode, which increases efficiency of finding all sites of DNA breaks within a frame of few seconds. RecJ continues being bound to replication forks, but also assembles at many sites on the nucleoid upon DNA damage induction. RecO shows a similar change in its mobility as RecN, and also remains bound to sites of damage for few hundred milliseconds. Like RecN, it enters the nucleoid in damaged cells. Our data show that presynaptic preparation of DSBs including loading of RecA onto ssDNA is highly rapid and dynamic, and occurs throughout the chromosome, and not only at replication forks or only at distinct sites where many breaks are processes in analogy to eukaryotic DNA repair centres.
Experimental evidence characterizing pressure fluctuations at the seafloor-water interface induced by an earthquake
Authors: Matsumoto Hiroyuki , Kimura Toshinori , Nishida Shuhei , Machida Yuya , Araki Eiichiro 
Published: October 2018

AbstractAn unusual combination of a laboratory experiment and in situ measurement of pressure fluctuations during an earthquake allows us to resolve some uncertainties in bottom pressure recorders (BPRs). In situ BPRs are usually contaminated by seismic waves during earthquakes; thus uncertainty still remains in the data obtained from BPRs. We examine in situ BPR data together with pressure variations produced by a dead weight (a pressure standard) in a laboratory experiment during an earthquake. The features recorded by the in situ BPRs are analysed as part of the overall experiment. We demonstrated that a 10-kg dead weight on a piston-cylinder across an area of 10 mm2 is capable of reproducing pressure fluctuations at a depth of 1000 m in the water column. The experiment also indicates that the internal mechanics of BPRs are isolated from incident seismic waves, suggesting that BPRs measure true in situ pressures without instrumentally induced disturbances. This constitutes the first instance in which pressure fluctuations recorded by in situ BPRs during an earthquake were reproduced using a pressure standard in the laboratory.
Design the magnetic microencapsulated phase change materials with poly(MMA-MAA) @ n-octadecane modified by Fe3O4
Authors: Zhuang Xueheng , Zhang Ying , Cai Chang , Zhang Jing , Zhu Yuejin 
Published: October 2018

AbstractMagnetic microencapsulated phase change materials (magnetic MicroPCMs) are hotly researched for their dual-functions with phase change and magnetic properties, which provided the new applications in fields of maneuverable phase change materials and infrared electromagnetic dual shield. A series of magnetic MicroPCMs samples are synthesized by polymerization and coprecipitation method and the chemical composition contained poly(MMA-MAA) @ n-octadecane modified by Fe3O4. In addition, the characterizations exhibit the excellent magnetic and phase change properties. The magnetic MicroPCMs samples present 20 emu·g−1 saturation magnetization with still high enthalpy of 132 J·g−1, which fully illustrates that the magnetic MicroPCMs fulfill both application on thermal energy storage and magnetic control.
Droplet digital PCR quantification of miR-1290 as a circulating biomarker for pancreatic cancer
Authors: Tavano Francesca , Gioffreda Domenica , Valvano Maria R. , Palmieri Orazio , Tardio Matteo , Latiano Tiziana P. , Piepoli Ada , Maiello Evaristo , Pirozzi Felice , Andriulli Angelo 
Published: October 2018

AbstractDroplet digital PCR was used to validate miR-1290 as circulating biomarker for pancreatic cancer (PC). The diagnostic performance of miR-1290 was evaluate in 167 PC patients and 267 healthy subjects at clinical risk of developing the disease (HS). MiR-1290 plasma levels were compared to CA 19-9 determinations, and the combination of the two biomarkers was also taken into account. Plasma levels of miR-1290 were higher in PC patients compared to HS (p = 2.55 × 10−16). A similar trend was observed for CA 19-9 determinations (p = 1.03 × 10−47). ROC curve analysis revealed that miR-1290 in combination with CA 19-9 was effective for discriminating between PC patients and HS (AUC = 0.956, 95% CI = 0.933–0.979) than the two biomarkers tested alone (miR-1290: AUC = 0.734, 0.678–0.789; CA 19-9: AUC = 0.914, 0.877–0.951). The discriminating ability was higher when only PC patients with low or slightly increased CA 19-9 levels were compared with HS. MiR-1290 concentrations were not able to differentiate between PC patients with single or multiple risk factors for developing PC. Our data suggest that the absolute quantification of circulating miR-1290 levels does not allow to select patients at clinical risk of PC for entry into a surveillance program, and underline the methodological challenges still existing in utilizing circulating miRNAs as new promising biomarkers for PC.
Transcriptome analysis for phosphorus starvation-induced lipid accumulation in Scenedesmus sp
Authors: Yang Fangfang , Xiang Wenzhou , Li Tao , Long Lijuan 
Published: October 2018

AbstractPhosphorus stress was applied to enhance the lipid production in Scenedesmus sp. The highest lipid production (350 mg L−1) and lipid content (approximately 41.0% of dry weight) were obtained by addition of 2 mg L−1 NaH2PO4·2H2O every 2 days, which were higher than those in replete phosphorus. Correspondingly, carbohydrate content decreased significantly. We speculated that phosphorus limitation could block starch biosynthesis, and photosynthate flow tended to fatty acid biosynthesis to cope with stress. To investigate the mechanism that phosphorus stress triggers the carbon fixation to lipid biosynthesis, the transcriptome analysis was carried out by the Illumina RNA-seq platform. A total of 2897 genes were identified as differentially expressed genes. The observed overexpression of lipid production under phosphorus stress was bolstered by up-regulation of genes encoding for DGAT and pyruvate kinase, activation of carbohydrate metabolism pathway and fatty acid biosynthesis, and repression of carbohydrate synthesis-presumably to shunt the carbon flux toward TAG biosynthesis. The transcriptome will be useful to understand the lipid metabolism pathway and obtain the engineering economic algae species aimed at biodiesel production.
Estimating the risk of Dengue, Chikungunya and Zika outbreaks in a large European city
Authors: Solimini Angelo G. , Manica Mattia , Rosà Roberto , della Torre Alessandra , Caputo Beniamino 
Published: October 2018

AbstractOutbreaks of arbovirus infections vectored by invasive Aedes albopictus have already occurred and are predicted to become increasingly frequent in Southern Europe. We present a probabilistic model to assess risk of arbovirus outbreaks based on incident cases worldwide, on the probability of arrival of infected travelers, and on the abundance of the vector species. Our results show a significant risk of Chikungunya outbreak in Rome from mid June to October in simulations with high human biting rates (i.e. when ≥50% of the population is bitten every day). The outbreak risk is predicted to be highest for Chikungunya and null for Zika. Simulated increase of incident cases in selected endemic countries has no major impact on the outbreak risk. The model correctly estimated the number of imported cases and can be easily adapted to other urban areas where Ae. albopictus is the only potential vector present.
A genome-scale metabolic network alignment method within a hypergraph-based framework using a rotational tensor-vector product
Authors: Shen Tie , Zhang Zhengdong , Chen Zhen , Gu Dagang , Liang Shen , Xu Yang , Li Ruiyuan , Wei Yimin , Liu Zhijie , Yi Yin , Xie Xiaoyao 
Published: October 2018

AbstractBiological network alignment aims to discover important similarities and differences and thus find a mapping between topological and/or functional components of different biological molecular networks. Then, the mapped components can be considered to correspond to both their places in the network topology and their biological attributes. Development and evolution of biological network alignment methods has been accelerated by the rapidly increasing availability of such biological networks, yielding a repertoire of tens of methods based upon graph theory. However, most biological processes, especially the metabolic reactions, are more sophisticated than simple pairwise interactions and contain three or more participating components. Such multi-lateral relations are not captured by graphs, and computational methods to overcome this limitation are currently lacking. This paper introduces hypergraphs and association hypergraphs to describe metabolic networks and their potential alignments, respectively. Within this framework, metabolic networks are aligned by identifying the maximal Z-eigenvalue of a symmetric tensor. A shifted higher-order power method was utilized to identify a solution. A rotational strategy has been introduced to accelerate the tensor-vector product by 250-fold on average and reduce the storage cost by up to 1,000-fold. The algorithm was implemented on a spark-based distributed computation cluster to significantly increase the convergence rate further by 50- to 80-fold. The parameters have been explored to understand their impact on alignment accuracy and speed. In particular, the influence of initial value selection on the stationary point has been simulated to ensure an accurate approximation of the global optimum. This framework was demonstrated by alignments among the genome-wide metabolic networks of Escherichia coli MG-1655 and Halophilic archaeon DL31. To our knowledge, this is the first genome-wide metabolic network alignment at both the metabolite level and the enzyme level. These results demonstrate that it can supply quite a few valuable insights into metabolic networks. First, this method can access the driving force of organic reactions through the chemical evolution of metabolic network. Second, this method can incorporate the chemical information of enzymes and structural changes of compounds to offer new way defining reaction class and module, such as those in KEGG. Third, as a vertex-focused treatment, this method can supply novel structural and functional annotation for ill-defined molecules. The related source code is available on request.
Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features
Authors: Gudenas Brian L. , Wang Liangjiang 
Published: October 2018

AbstractLong non-coding RNAs are involved in biological processes throughout the cell including the nucleus, chromatin and cytosol. However, most lncRNAs remain unannotated and functional annotation of lncRNAs is difficult due to their low conservation and their tissue and developmentally specific expression. LncRNA subcellular localization is highly informative regarding its biological function, although it is difficult to discover because few prediction methods currently exist. While protein subcellular localization prediction is a well-established research field, lncRNA localization prediction is a novel research problem. We developed DeepLncRNA, a deep learning algorithm which predicts lncRNA subcellular localization directly from lncRNA transcript sequences. We analyzed 93 strand-specific RNA-seq samples of nuclear and cytosolic fractions from multiple cell types to identify differentially localized lncRNAs. We then extracted sequence-based features from the lncRNAs to construct our DeepLncRNA model, which achieved an accuracy of 72.4%, sensitivity of 83%, specificity of 62.4% and area under the receiver operating characteristic curve of 0.787. Our results suggest that primary sequence motifs are a major driving force in the subcellular localization of lncRNAs.
Advanced high resolution x-ray diagnostic for HEDP experiments
Authors: Faenov A. Y. , Pikuz T. A. , Mabey P. , Albertazzi B. , Michel Th. , Rigon G. , Pikuz S. A. , Buzmakov A. , Makarov S. , Ozaki N. , Matsuoka T. , Katagiri K. , Miyanishi K. , Takahashi K. , Tanaka K. A. , Inubushi Y. , Togashi T. , Yabuuchi T. , Yabashi M. , Casner A. , Kodama R. , Koenig M. 
Published: October 2018

AbstractHigh resolution X-ray imaging is crucial for many high energy density physics (HEDP) experiments. Recently developed techniques to improve resolution have, however, come at the cost of a decreased field of view. In this paper, an innovative experimental detector for X-ray imaging in the context of HEDP experiments with high spatial resolution, as well as a large field of view, is presented. The platform is based on coupling an X-ray backligther source with a Lithium Fluoride detector, characterized by its large dynamic range. A spatial resolution of 2 µm over a field of view greater than 2 mm2 is reported. The platform was benchmarked with both an X-ray free electron laser (XFEL) and an X-ray source produced by a short pulse laser. First, using a non-coherent short pulse laser-produced backlighter, reduced penumbra blurring, as a result of the large size of the X-ray source, is shown. Secondly, we demonstrate phase contrast imaging with a fully coherent monochromatic XFEL beam. Modeling of the absorption and phase contrast transmission of X-ray radiation passing through various targets is presented.
A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals
Authors: Rugen Michael D. , Vernet Mathieu M. J. L. , Hantouti Laila , Soenens Amalia , Andriotis Vasilios M. E. , Rejzek Martin , Brett Paul , van den Berg Richard J. B. H. N. , Aerts Johannes M. F. G. , Overkleeft Hermen S. , Field Robert A. 
Published: October 2018

AbstractIminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- l-ido-deoxynojirimycin (l-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of l-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. l-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.
Aggregated SOD1 causes selective death of cultured human motor neurons
Authors: Benkler Chen , O’Neil Alison L. , Slepian Susannah , Qian Fang , Weinreb Paul H. , Rubin Lee L. 
Published: October 2018

AbstractMost human neurodegenerative diseases share a phenotype of neuronal protein aggregation. In Amyotrophic Lateral Sclerosis (ALS), the abundant protein superoxide dismutase (SOD1) or the TAR-DNA binding protein TDP-43 can aggregate in motor neurons. Recently, numerous studies have highlighted the ability of aggregates to spread from neuron to neuron in a prion-like fashion. These studies have typically focused on the use of neuron-like cell lines or neurons that are not normally affected by the specific aggregated protein being studied. Here, we have investigated the uptake of pre-formed SOD1 aggregates by cultures containing pluripotent stem cell-derived human motor neurons. We found that all cells take up aggregates by a process resembling fluid-phase endocytosis, just as found in earlier studies. However, motor neurons, despite taking up smaller amounts of SOD1, were much more vulnerable to the accumulating aggregates. Thus, the propagation of disease pathology depends less on selective uptake than on selective response to intracellular aggregates. We further demonstrate that anti-SOD1 antibodies, being considered as ALS therapeutics, can act by blocking the uptake of SOD1, but also by blocking the toxic effects of intracellular SOD1. This work demonstrates the importance of using disease relevant cells even in studying phenomena such as aggregate propagation.