bluuebunny/crossref_metadata_2025_split huggingface dataset:
The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription
Authors: Katsel Pavel , Roussos Panos , Fam Peter , Khan Sonia , Tan Weilun , Hirose Tetsuro , Nakagawa Shinichi , Pletnikov Mikhail V. , Haroutunian Vahram 
Published: January 2019

AbstractOligodendrocyte (OLG)-related abnormalities have been broadly observed in schizophrenia (SZ); however, the etiology of these abnormalities remains unknown. As SZ is broadly believed to be a developmental disorder, the etiology of the myelin abnormalities in SZ may be related to OLG fate specification during development. Noncoding RNAs (ncRNAs) are an important part of multifaceted transcriptional complexes participating in neurogenic commitment and regulation of postmitotic cell function. The long ncRNA,NEAT1, is a structural component of paraspeckles (subnuclear bodies in interchromatin regions) that may control activity of developmental enhancers of OLG fate specification. Gene expression studies of multiple cortical regions from individuals with SZ showed strong downregulation ofNEAT1levels relative to controls.NEAT1-deficient mice show significant decreases in the numbers of OLG-lineage cells in the frontal cortex. To gain further insight into biological processes affected byNEAT1deficiency, we analyzed RNA-seq data from frontal cortex ofNEAT1-/-mice. Analyses of differentially expressed gene signature fromNEAT1-/-mice revealed a significant impact on processes related to OLG differentiation and RNA posttranscriptional modification with the underlying mechanisms involving Wnt signaling, cell contact interactions, and regulation of cholesterol/lipid metabolism. Additional studies revealed evidence of co-expression ofSOX10, an OLG transcription factor, andNEAT1, and showed enrichment of OLG-specific transcripts inNEAT1purified chromatin isolates from human frontal cortex. Reduced nuclear retention of quaking isoform 5 inNEAT1-/-mice shed light on possible mechanism(s) responsible for reduced expression of OLG/myelin proteins and supported the involvement ofNEAT1in oligodendrocyte function.
Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition
Authors: Tarca Adi L. , Romero Roberto , Xu Zhonghui , Gomez-Lopez Nardhy , Erez Offer , Hsu Chaur-Dong , Hassan Sonia S. , Carey Vincent J. 
Published: January 2019

AbstractDevelopment of maternal blood transcriptomic markers to monitor placental function and risk of obstetrical complications throughout pregnancy requires accurate quantification of gene expression. Herein, we benchmark three state-of-the-art expression profiling techniques to assess in maternal circulation the expression of cell type-specific gene sets previously discovered by single-cell genomics studies of the placenta. We compared Affymetrix Human Transcriptome Arrays, Illumina RNA-Seq, and sequencing-based targeted expression profiling (DriverMapTM) to assess transcriptomic changes with gestational age and labor status at term, and tested 86 candidate genes by qRT-PCR. DriverMap identified twice as many significant genes (q < 0.1) than RNA-Seq and five times more than microarrays. The gap in the number of significant genes remained when testing only protein-coding genes detected by all platforms. qRT-PCR validation statistics (PPV and AUC) were high and similar among platforms, yet dynamic ranges were higher for sequencing based platforms than microarrays. DriverMap provided the strongest evidence for the association of B-cell and T-cell gene signatures with gestational age, while the T-cell expression was increased with spontaneous labor at term according to all three platforms. We concluded that sequencing-based techniques are more suitable to quantify whole-blood gene expression compared to microarrays, as they have an expanded dynamic range and identify more true positives. Targeted expression profiling achieved higher coverage of protein-coding genes with fewer total sequenced reads, and it is especially suited to track cell type-specific signatures discovered in the placenta. The T-cell gene expression signature was increased in women who underwent spontaneous labor at term, mimicking immunological processes at the maternal-fetal interface and placenta.
Electronic thermal conductivity in 2D topological insulator in a HgTe quantum well
Authors: Gusev G. M. , Kvon Z. D. , Levin A. D. , Olshanetsky E. B. , Raichev O. E. , Mikhailov N. N. , Dvoretsky S. A. 
Published: January 2019

AbstractWe have measured the differential resistance in a two-dimensional topological insulator (2DTI) in a HgTe quantum well, as a function of the applied dc current. The transport near the charge neutrality point is characterized by a pair of counter propagating gapless edge modes. In the presence of an electric field, the energy is transported by counter propagating channels in the opposite direction. We test a hot carrier effect model and demonstrate that the energy transfer complies with the Wiedemann Franz law near the charge neutrality point in the edge transport regime.
Climatic factors control the geospatial distribution of active ingredients in Salvia miltiorrhiza Bunge in China
Authors: Zhang Chenlu , Yang Dongfeng , Liang Zongsuo , Liu Jingling , Yan Kaijing , Zhu Yonghong , Yang Shushen 
Published: January 2019

AbstractClimate change profoundly influences the geospatial distribution of secondary metabolites and causes the geographical migration of plants. We planted seedlings of the same species in eighteen ecological regions along a latitudinal gradient in eastern and western China, in order to explore the regulation of multi-climatic factors on active ingredient accumulation in Salvia miltiorrhiza Bunge. The correlations between six active ingredient contents and ten climatic factors were investigated to clarify their relationships. We found that climatic factors not only regulated active ingredient contents but also markedly influenced their composition and led to a specific geospatial distribution of these active ingredients in China. The main climatic factors include the air temperature, precipitation, atmospheric vapour pressure and sunshine duration. Future warming in high-latitude regions could cause continued northward expansion of planting areas suitable for S. miltiorrhiza. The effect of extreme climatic conditions on active ingredients should not be overlooked. The findings of this study can help farmers scientifically choose suitable cultivation regions in the future. Furthermore, this study provides an innovative idea for the exploration of secondary metabolic responses to changing ecological factors in medicinal plants.
Disruption of Timing: NeuroHIV Progression in the Post-cART Era
Authors: McLaurin Kristen A. , Li Hailong , Booze Rosemarie M. , Mactutus Charles F. 
Published: January 2019

AbstractThe marked increase in life expectancy for HIV-1 seropositive individuals, following the great success of combination antiretroviral therapy (cART), heralds an examination of the progression of HIV-1 associated neurocognitive disorders (HAND). However, since the seminal call for animal models of HIV-1/AIDS in 1988, there has been no extantin vivoanimal model system available to provide a truly longitudinal study of HAND. Here, we demonstrate that the HIV-1 transgenic (Tg) rat, resembling HIV-1 seropositive individuals on lifelong cART, exhibits age-related, progressive neurocognitive impairments (NCI), including alterations in learning, sustained attention, flexibility, and inhibition; deficits commonly observed in HIV-1 seropositive individuals. Pyramidal neurons from layers II-III of the medial prefrontal cortex (mPFC) displayed profound synaptic dysfunction in HIV-1 Tg animals relative to controls; dysfunction that was characterized by alterations in dendritic branching complexity, synaptic connectivity, and dendritic spine morphology. NCI and synaptic dysfunction in pyramidal neurons from layers II-III of the mPFC independently identified the presence of the HIV-1 transgene with at least 78.5% accuracy. Thus, even in the absence of sensory or motor system deficits and comorbidities, HAND is a neurodegenerative disease characterized by age-related disease progression; impairments which may be due, at least partly, to synaptic dysfunction in the mPFC. Further, the progression of HAND with age in the HIV-1 Tg rat and associated synaptic dysfunction affords an instrumental model system for the development of therapeutics and functional cure strategies.
Impaired non-homologous end joining in human primary alveolar type II cells in emphysema
Authors: Kosmider Beata , Lin Chih-Ru , Vlasenko Liudmila , Marchetti Nathaniel , Bolla Sudhir , Criner Gerard J. , Messier Elise , Reisdorph Nichole , Powell Roger L. , Madesh Muniswamy , Kelsen Steven , Xander Nathaniel , Correll Kelly A. , Mason Robert J. , Bahmed Karim 
Published: January 2019

AbstractEmphysema is characterized by alveolar wall destruction induced mainly by cigarette smoke. Oxidative damage of DNA may contribute to the pathophysiology of this disease. We studied the impairment of the non-homologous end joining (NHEJ) repair pathway and DNA damage in alveolar type II (ATII) cells and emphysema development. We isolated primary ATII cells from control smokers, nonsmokers, and patients with emphysema to determine DNA damage and repair. We found higher reactive oxygen species generation and DNA damage in ATII cells obtained from individuals with this disease in comparison with controls. We also observed low phosphorylation of H2AX, which activates DSBs repair signaling, in emphysema. Our results indicate the impairement of NHEJ, as detected by low XLF expression. We also analyzed the role of DJ-1, which has a cytoprotective activity. We detected DJ-1 and XLF interaction in ATII cells in emphysema, which suggests the impairment of their function. Moreover, we found that DJ-1 KO mice are more susceptible to DNA damage induced by cigarette smoke. Our results suggest that oxidative DNA damage and ineffective the DSBs repair via the impaired NHEJ may contribute to ATII cell death in emphysema.
How a ferromagnet drives an antiferromagnet in exchange biased CoO/Fe(110) bilayers
Authors: Ślęzak M. , Ślęzak T. , Dróżdż P. , Matlak B. , Matlak K. , Kozioł-Rachwał A. , Zając M. , Korecki J. 
Published: January 2019

AbstractAntiferromagnet/ferromagnet (AFM/FM) bilayers that display the exchange bias (EB) effect have been subjected to intensive material research, being the key elements of novel spintronics systems. In a commonly accepted picture, the antiferromagnet, considered as a rigid material due to its high anisotropy and magnetic hardness, controls the magnetic properties of the ferromagnet, such as a shift of the hysteresis loop or coercivity. We show that this AFM-FM master-slave hierarchy is not generally valid and that the influence of the ferromagnet on the magnetic anisotropy (MA) of the neighbouring antiferromagnet must be considered. Our computer simulation and experimental studies of EB in an epitaxial CoO/Fe(110) bilayer show that the ferromagnetic layer with strong uniaxial magnetic anisotropy determines the interfacial spin orientations of the neighbouring AFM layer and rotates its easy axis. This effect has a strong feedback on the EB effect experienced by the FM layer. Our results show new physics behind the EB effect, providing a route for grafting a desired anisotropy onto the AFM and for precise tailoring of EB in AFM/FM systems.
Isolation and characterization of Lactobacillus-derived membrane vesicles
Authors: Dean Scott N. , Leary Dagmar H. , Sullivan Claretta J. , Oh Eunkeu , Walper Scott A. 
Published: January 2019

AbstractBacterial membrane vesicles have been implicated in a broad range of functions in microbial communities from pathogenesis to gene transfer. Though first thought to be a phenomenon associated with Gram-negative bacteria, vesicle production in Staphylococcus aureus, Lactobacillus plantarum, and other Gram-positives has recently been described. Given that many Lactobacillus species are Generally Regarded as Safe and often employed as probiotics, the engineering of Lactobacillus membrane vesicles presents a new avenue for the development of therapeutics and vaccines. Here we characterize and compare the membrane vesicles (MVs) from three different Lactobacillus species (L. acidophilus ATCC 53544, L. casei ATCC 393, and L. reuteri ATCC 23272), with the aim of developing future strategies for vesicle engineering. We characterize the vesicles from each Lactobacillus species comparing the physiochemical properties and protein composition of each. More than 80 protein components from Lactobacillus-derived MVs were identified, including some that were enriched in the vesicles themselves suggesting vesicles as a vehicle for antimicrobial delivery. Additionally, for each species vesicular proteins were categorized based on biological pathway and examined for subcellular localization signals in an effort to identify possible sorting mechanisms for MV proteins.
Essential roles of C-type lectin Mincle in induction of neuropathic pain in mice
Authors: Ishikawa Asako , Miyake Yasunobu , Kobayashi Kimiko , Murata Yuzo , Iizasa Sayaka , Iizasa Ei’ichi , Yamasaki Sho , Hirakawa Naomi , Hara Hiromitsu , Yoshida Hiroki , Yasaka Toshiharu 
Published: January 2019

AbstractIncreasing evidence indicates that pattern recognition receptors (PRRs) are involved in neuropathic pain after peripheral nerve injury (PNI). While a significant number of studies support an association between neuropathic pain and the innate immune response mediated through Toll-like receptors, a family of PRRs, the roles of other types of PRRs are largely unknown. In this study, we have focused on the macrophage-inducible C-type lectin (Mincle), a PRR allocated to the C-type lectin receptor family. Here, we show that Mincle is involved in neuropathic pain after PNI.Mincle-deficient mice showed impaired PNI-induced mechanical allodynia. After PNI, expression ofMinclemRNA was rapidly increased in the injured spinal nerve. MostMincle-expressing cells were identified as infiltrating leucocytes, although the migration of leucocytes was also observed inMincle-deficient mice. Furthermore,Mincle-deficiency affected the induction of genes, which are reported to contribute to neuropathic pain after PNI in the dorsal root ganglia and spinal dorsal horn. These results suggest that Mincle is involved in triggering sequential processes that lead to the pathogenesis of neuropathic pain.
Effect of Fluoride Doping in Laponite Nanoplatelets on Osteogenic Differentiation of Human Dental Follicle Stem Cells (hDFSCs)
Authors: Veernala Induvahi , Giri Jyotsnendu , Pradhan Arpan , Polley Poulomi , Singh Ruby , Yadava Sunil Kumar 
Published: January 2019

AbstractBioactive nanosilicates are emerging prominent next generation biomaterials due to their intrinsic functional properties such as advanced biochemical and biophysical cues. Recent studies show interesting dose-dependent effect of fluoride ions on the stem cells. Despite of interesting properties of fluoride ions as well as nanosilicate, there is no reported literature on the effect of fluoride-doped nanosilicates on stem cells. We have systematically evaluated the interaction of fluoride nanosilicate platelets (NS + F) with human dental follicle stem cells (hDFSCs) to probe the cytotoxicity, cellular transport (internalization) and osteogenic differentiation capabilities in comparison with already reported nanosilicate platelets without fluoride (NS − F). To understand the osteoinductive and osteoconductive properties of the nanosilicate system, nanosilicate treated hDFSCs are cultured in three different medium namely normal growth medium, osteoconductive medium, and osteoinductive medium up to 21 d. NS + F treated stem cells show higher ALP activity, osteopontin levels and significant alizarin red staining compared to NS − F treated cells. This study highlights that the particles having fluoride additives (NS + F) aid in enhancing the osteogenic differentiation capabilities of hDFSCs thus potential nanobiomaterial for periodontal bone tissue regeneration.
Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants
Authors: Guo Feng , Zhang Tong , Li Bing , Wang Zhiping , Ju Feng , Liang Yi-ting 
Published: January 2019

AbstractMycobacterium often presents as an abundant bacterial genus in activated sludge in many wastewater treatment plants (WWTPs), but the species-level taxonomy and functions remain poorly understood. In this study, we profiled the mycobacterial communities in eleven WWTPs from five countries by pyrosequencing the rpoB amplicons and searching against a customized database of mycobacterial rpoB sequences. Results indicated that major mycobacterial species were related to M. brumae, M. crocinum, M. sphagni, etc., most of which belong to poorly characterized rapidly-growing group. A few opportunistic pathogenic species were detected, suggesting the potential risk of mycobacteria in WWTPs. Genomic analysis of four isolates from activated sludge indicated these genomes contained genes of degradations of alkane, aromatics, steroids and a variety of cytochrome P450 families. Additionally, a few key genes responsible for cholesterol degradation were detected in a full-scale activated sludge metatranscriptomic dataset reported previously and taxonomically assigned to mycobacteria. Evidence showed that all isolates can degrade cholesterol, a major composition of sewage. Relative abundance of mycobacteria in activated sludge was enriched by 4.7 folds after adding cholesterol into the influent for one week. Our results provided the insights into mycobacterial species and functions in WWTPs.
Structure and functions of the ventral tube of the clover springtail Sminthurus viridis (Collembola: Sminthuridae)
Authors: Chen Chong-Guang , Chen Tong , Hua Bao-Zhen , Wan Tao-Ruan 
Published: January 2019

AbstractSpringtails (Collembola) are unique in Hexapoda for bearing a ventral tube (collophore) on the first abdominal segment. Although numerous studies have been conducted on the functions of the ventral tube, its fine structure has not been thoroughly elucidated to date. In this paper, we observed the jumping behavior of the clover springtailSminthurus viridis(Linnaeus, 1758) and dissected the ventral tube using light microscopy to elucidate the fine structure and the possible function of the ventral tube. The results show that a pair of eversible vesicles can be extended from the apical opening of the ventral tube. The eversible vesicles are furnished with numerous small papillae, and can be divided into a basal part and a distal part. The eversible vesicles have a central lumen connected to the tiny papillae and leading to the body cavity. The eversible vesicles can reach any part of the body, and may serve as following functions: (a) absorbing moisture; (b) uptaking water; (c) cleaning the body surface; and (d) fastening the body on a smooth surface.
Genome-guided and mass spectrometry investigation of natural products produced by a potential new actinobacterial strain isolated from a mangrove ecosystem in Futian, Shenzhen, China
Authors: Hu Dini , Gao Cheng , Sun Chenghang , Jin Tao , Fan Guangyi , Mok Kai Meng , Lee Simon Ming-Yuen 
Published: January 2019

AbstractActinobacteria, a group of gram-positive bacteria, can produce plenty of valuable bioactive secondary metabolites, especially antibiotics. Hence, in order to search for new actinobacteria, actinobacterial isolates were obtained from rhizosphere soil collected from the Futian mangrove ecosystem in Shenzhen, China. According to 16S rRNA sequences, 14 actinobacterial strains of the genus Streptomyces, Rhodococcus, Microbacterium, Micromonospora, Actinoplanes and Mycobacterium were isolated and identified. Among these, strain Mycobacterium sp.13 was described as a potential new species belonging to the genus Mycobacterium within the class of actinobacteria according to the genomic analysis. The genome-based 16S rRNA sequences had 98.48% sequence similarity with Mycobacterium moriokaense DSM 44221T. Meanwhile, the genome sequences of Mycobacterium sp.13 showed an average nucleotide identity (ANI) with the Mycobacterium mageritense DSM 44476, Mycobacterium smegmatis MKD8 and Mycobacterium goodii strain X7B of only 74.79%, 76.12% and 76.42%, respectively. Furthermore, genome-mining results showed that Mycobacterium sp.13 contained 105 gene clusters encoding to the secondary metabolite biosynthesis, where many kinds of terpene, bacteriocin, T1pks, Nrps, saccharide, fatty acid, butyrolactone, ectoine and resorcinol were included. Finally, through LC-MS and HR-MS, analyzing the small molecules from ethyl acetate extract of this strain, asukamycin C and apramycin were for the first time found present to be in Mycobacterium moriokaense strain. Our study provides evidence in support of the potential new Mycobacterium sp.13 isolated from the mangrove environment as a possible novel source of natural products.
A Fast and Refined Cancer Regions Segmentation Framework in Whole-slide Breast Pathological Images
Authors: Guo Zichao , Liu Hong , Ni Haomiao , Wang Xiangdong , Su Mingming , Guo Wei , Wang Kuansong , Jiang Taijiao , Qian Yueliang 
Published: January 2019

AbstractSupervised learning methods are commonly applied in medical image analysis. However, the success of these approaches is highly dependent on the availability of large manually detailed annotated dataset. Thus an automatic refined segmentation of whole-slide image (WSI) is significant to alleviate the annotation workload of pathologists. But most of the current ways can only output a rough prediction of lesion areas and consume much time in each slide. In this paper, we propose a fast and refined cancer regions segmentation framework v3_DCNN, which first preselects tumor regions using a classification model Inception-v3 and then employs a semantic segmentation model DCNN for refined segmentation. Our framework can generate a dense likelihood heatmap with the 1/8 side of original WSI in 11.5 minutes on the Camelyon16 dataset, which saves more than one hour for each WSI compared with the initial DCNN model. Experimental results show that our approach achieves a higher FROC score 83.5% with the champion’s method of Camelyon16 challenge 80.7%. Based on v3 DCNN model, we further automatically produce heatmap of WSI and extract polygons of lesion regions for doctors, which is very helpful for their pathological diagnosis, detailed annotation and thus contributes to developing a more powerful deep learning model.
Metrics for evaluating the stability and reproducibility of mass spectra
Authors: Zhvansky E. S. , Pekov S. I. , Sorokin A. A. , Shurkhay V. A. , Eliferov V. A. , Potapov A. A. , Nikolaev E. N. , Popov I. A. 
Published: January 2019

AbstractIn this work, we demonstrate a new approach for assessing the stability and reproducibility of mass spectra obtained via ambient ionization methods. This method is suitable for both comparing experiments during which only one mass spectrum is measured and for evaluating the internal homogeneity of mass spectra collected over a period of time. The approach uses Pearson’s r coefficient and the cosine measure to compare the spectra. It is based on the visualization of dissimilarities between measurements, thus leading to the analysis of dissimilarity patterns. The cosine measure and correlations are compared to obtain better metrics for spectra homogeneity. The method filters out unreliable scans to prevent the analyzed sample from being wrongly characterized. The applicability of the method is demonstrated on a set of brain tumor samples. The developed method could be employed in neurosurgical applications, where mass spectrometry is used to monitor the intraoperative tumor border.