bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the Analytical Solutions of Heat Transport in Fractured Reservoirs Using a Generalized Multirate Memory Function
Authors: Zhou Quanlin , Oldenburg Curtis M. , Rutqvist Jonny
Published: January 2019

Numerous analytical solutions have been developed for modeling thermal perturbations to underground formations caused by deep‐well injection of fluids. Each solution has been derived for a specific boundary value problem and a simplified flow network with one set of parallel fractures. In this paper, new generalized solutions G*(x, s) are developed using (existing) global transfer functions
and a new memory function g*(s), where x and s are the space and Laplace variable. The memory function represents the solutions of conductive heat exchange between fractures and matrix blocks and between fractured aquifers and unfractured aquitards. The memory function is developed to account for multirate exchange induced by different shapes, sizes, properties, and volumetric fractions of matrix blocks bounded by multiple sets of orthogonal fractures with different spacing. The global transfer functions represent the fundamental solutions to convective, convective‐conductive, and convective‐dispersive heat transport in fractures (or aquifers) without exchange and are available for various (1‐D linear, 1‐D radial, 2‐D dipole, and single‐well injection‐withdrawal) flow fields. The new solutions with exchange are developed using
, thereby greatly simplifying solution development in a novel way, where ϑ and B*(s) are a fracture‐matrix scaling factor and the boundary condition function. The new solutions are applied to several example problems, showing that heat transport in fractured aquifers is significantly impacted by (1) thermal dispersion in fractures that is rarely considered, (2) multirate heat exchange with a wide range of size and anisotropy of rectangular matrix blocks, and (3) heat exchange between aquifers and aquitards.
Mann Receives 2018 Climate Communication Prize
Authors:   AGU
Published: January 2019

Michael E. Mann received the Climate Communication Prize at the 2018 AGU Fall Meeting Honors Ceremony, held 12 December 2018 in Washington, D. C. The prize recognizes an individual “for the communication of climate science.”
Ferrous Iron Under Oxygen‐Rich Conditions in the Deep Mantle
Authors: Boulard E. , Harmand M. , Guyot F. , Lelong G. , Morard G. , Cabaret D. , Boccato S. , Rosa A. D. , Briggs R. , Pascarelli S. , Fiquet G.
Published: January 2019

Recent experiments have demonstrated the existence of previously unknown iron oxides at high pressure and temperature including newly discovered pyrite‐type FeO2 and FeO2Hx phases stable at deep terrestrial lower mantle pressures and temperatures. In the present study, we probed the iron oxidation state in high‐pressure transformation products of Fe3+OOH goethite by in situ X‐ray absorption spectroscopy in laser‐heated diamond‐anvil cell. At pressures and temperatures of ~91 GPa and 1,500–2,350 K, respectively, that is, in the previously reported stability field of FeO2Hx, a measured shift of −3.3 ± 0.1 eV of the Fe K‐edge demonstrates that iron has turned from Fe3+ to Fe2+. We interpret this reductive valence change of iron by a concomitant oxidation of oxygen atoms from O2− to O−, in agreement with previous suggestions based on the structures of pyrite‐type FeO2 and FeO2Hx phases. Such peculiar chemistry could drastically change our view of crystal chemistry in deep planetary interiors.
Cereblon-binding proteins expression levels correlate with hyperdiploidy in newly diagnosed multiple myeloma patients
Authors: Kriegsmann Katharina , Baertsch Marc-Andrea , Awwad Mohamed H. S. , Merz Maximilian , Hose Dirk , Seckinger Anja , Jauch Anna , Becker Natalia , Benner Axel , Raab Marc S. , Hillengass Jens , Bertsch Uta , Dürig Jan , Salwender Hans Jürgen , Hänel Mathias , Fenk Roland , Munder Markus , Weisel Katja , Müller-Tidow Carsten , Goldschmidt Hartmut , Hundemer Michael
Published: January 2019

Immunomodulatory drugs (IMIDs) are very effective in the treatment of multiple myeloma (MM). The description of their cereblon-mediated mechanism of action was a hallmark in MM research. Although the importance of IMID-induced degradation of cereblon-binding proteins is well described in vitro, the prognostic value of their expression levels in MM cells is less clear. Based on recently published data showing somewhat conflicting RNA levels, we analyzed the association between the levels of the Ikaros family zinc finger protein 1 (IKZF1), IKZF3, and karyopherin subunit alpha 2 (KPNA2) proteins measured by flow cytometry and prognostic parameters in 214 newly diagnosed MM patients who were randomized in the GMMG HD6 trial. No statistically significant associations between the expression levels and age, gender, light chain type, International Staging System (ISS) stage or cytogenetic high- and normal risk groups could be identified. Hyperdiploid MM cells expressed significantly higher levels of IKZF1, IKZF3 and KPNA2 than nonhyperdiploid cells. In contrast, translocation t(11;14) was associated with significantly lower expression levels. In conclusion, the observed overexpression of cereblon-binding proteins in MM cells with gain of chromosomes 5, 9, 11, 15, and 19 is consistent with the previously proposed positive regulation of MYC by IKZF1 and IKZF3, as well as MYC activation in hyperdiploid MM cells.
Inactivating hepatitis C virus in donor lungs using light therapies during normothermic ex vivo lung perfusion
Authors: Galasso Marcos , Feld Jordan J. , Watanabe Yui , Pipkin Mauricio , Summers Cara , Ali Aadil , Qaqish Robert , Chen Manyin , Ribeiro Rafaela V. P. , Ramadan Khaled , Pires Layla , Bagnato Vanderlei S. , Kurachi Cristina , Cherepanov Vera , Moonen Gray , Gazzalle Anajara , Waddell Thomas K. , Liu Mingyao , Keshavjee Shaf , Wilson Brian C. , Humar Atul , Cypel Marcelo
Published: January 2019

Availability of organs is a limiting factor for lung transplantation, leading to substantial mortality rates on the wait list. Use of organs from donors with transmissible viral infections, such as hepatitis C virus (HCV), would increase organ donation, but these organs are generally not offered for transplantation due to a high risk of transmission. Here, we develop a method for treatment of HCV-infected human donor lungs that prevents HCV transmission. Physical viral clearance in combination with germicidal light-based therapies during normothermic ex-vivo Lung Perfusion (EVLP), a method for assessment and treatment of injured donor lungs, inactivates HCV virus in a short period of time. Such treatment is shown to be safe using a large animal EVLP-to-lung transplantation model. This strategy of treating viral infection in a donor organ during preservation could significantly increase the availability of organs for transplantation and encourages further clinical development.
Author Correction: A disinhibitory mechanism biases Drosophila innate light preference
Authors: Zhao Weiqiao , Zhou Peipei , Gong Caixia , Ouyang Zhenhuan , Wang Jie , Zheng Nenggan , Gong Zhefeng
Published: January 2019

Affiliation 2 incorrectly read ‘Department of Neurology of the Second Affiliated Hospital, Department of Neurobiology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310007, China’ and affiliation 3 incorrectly read ‘Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, Zhejiang 310058, China.’
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

Oligodendrocyte (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

Development 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

We 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

Climate 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

The 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

Emphysema 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

Antiferromagnet/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

Bacterial 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

Increasing 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

Bioactive 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

Mycobacterium 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

Springtails (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

Actinobacteria, 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

Supervised 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

In 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.
Factors Associated with Bothersome Lower Urinary Tract Symptoms in Middle-Aged Men Receiving Health Checkup
Authors: Yang Teng-Kai , Chang Chi-Chih , Chang Hong-Chiang , Yang Hung-Ju , Huang Kuo-How
Published: January 2019

The prospective study is to investigate the associations between serum testosterone levels and LUTS among middle-aged men ≥40 years receiving health check-up. Lower urinary tract symptoms were evaluated by the self-administered International Prostate Symptom Score questionnaire. Serum prostate specific antigen and total testosterone level were checked in all subjects. A total of 1752 men were enrolled into the study. The mean age was 55.6 ± 9.7 years. All study subjects were stratified into low, medium and high testosterone levels by two cut-off, 3.0 and 4.11 ng/mL. We found that testosterone levels were significantly associated with metabolic syndrome and body fat components. Compared to those with low testosterone levels, subjects with high and medium testosterone had a significantly higher IPSS (5.84 ± 5.55 vs 6.71 ± 5.68 and 6.34 ± 5.66, p = 0.032) and storage score (2.76 ± 2.29 vs 3.20 ± 2.49 and 2.90 ± 2.49; p = 0.009), and a more moderate/severe LUTS (IPSS ≧ 8) (26.5% vs 35.7% and 29.9%; p = 0.002). Multivariate analyses showed that high vs low testosterone levels (OR, 1.76; 95% CI, 1.26–2.45) and prostate volume ≧25 vs <25 mL (OR, 1.38; 95% CI, 1.04–1.82) significantly associated with the presence of moderate/severe LUTS. Pearson correlation analyses showed significantly positive correlations between testosterone level and IPSS in whole study sample (Pearson correlation coefficient, 0.066; p < 0.01) and in the subgroup of moderate/severe LUTS (Pearson correlation coefficient, 0.038; p < 0.05). In conclusion, high testosterone and prostate volume adversely impacted LUTS in our target population.
Manually-parcellated gyral data accounting for all known anatomical variability
Authors: Mikhael Shadia S. , Mair Grant , Valdes-Hernandez Maria , Hoogendoorn Corné , Wardlaw Joanna M. , Bastin Mark E. , Pernet Cyril
Published: January 2019

Morphometric brain changes occur throughout the lifetime and are often investigated to understand healthy ageing and disease, to identify novel biomarkers, and to classify patient groups. Yet, to accurately characterise such changes, an accurate parcellation of the brain must be achieved. Here, we present a manually-parcellated dataset of the superior frontal, the supramarginal, and the cingulate gyri of 10 healthy middle-aged subjects along with a fully detailed protocol based on two anatomical atlases. Gyral parcels were hand-drawn then reviewed by specialists blinded from the protocol to ensure consistency. Importantly, we follow a procedure that allows accounting for anatomical variability beyond what is usually achieved by standard analysis packages and avoids mutually referring to neighbouring gyri when defining gyral edges. We also provide grey matter thickness, grey matter volume, and white matter surface area information for each parcel. This dataset and corresponding measurements are useful in assessing the accuracy of equivalent parcels and metrics generated by image analysis tools and their impact on morphometric studies.
An X-ray computed micro-tomography dataset for oil removal from carbonate porous media
Authors: Pak Tannaz , Archilha Nathaly Lopes , Mantovani Iara Frangiotti , Moreira Anderson Camargo , Butler Ian B.
Published: January 2019

This study reveals the pore-scale details of oil mobilisation and recovery from a carbonate rock upon injection of aqueous nanoparticle (NP) suspensions. X-ray computed micro-tomography (μCT), which is a non-destructive imaging technique, was used to acquire a dataset which includes: (i) 3D images of the sample collected at the end of fluid injection steps, and (ii) 2D radiogram series collected during fluid injections. The latter allows monitoring fluid flow dynamics at time resolutions down to a few seconds using a laboratory-based μCT scanner. By making this dataset publicly available we enable (i) new image reconstruction algorithms to be tested on large images, (ii) further development of image segmentation algorithms based on machine learning, and (iii) new models for multi-phase fluid displacements in porous media to be evaluated using images of a dynamic process in a naturally occurring and complex material. This dataset is comprehensive in that it offers a series of images that were captured before/during/and after the immiscible fluid injections.
Three-dimensional depth profiling of prostate tissue by micro ATR-FTIR spectroscopic imaging with variable angles of incidence
Authors: Song Cai Li , Kazarian Sergei G.
Published: January 2019

Variable angle micro ATR-FTIR, via the insertion of circular apertures, was used to measure tissue samples at various penetration depths.
Responsive surface bioaffinity binding to construct flexible and sensitive electrochemical aptasensors
Authors: Liu Ying , Zhu Zhencai , Wang Chao , Gao Rui , Yang Xiaoyan , Liu Shufeng
Published: January 2019

A responsive surface bioaffinity binding strategy was developed for the fabrication of simple, flexible and amplified electrochemical aptasensors.
Molecular evidence of a toxic effect on a biofilm and its matrix
Authors: Ding Yuanzhao , Zhou Yufan , Yao Juan , Xiong Yijia , Zhu Zihua , Yu Xiao-Ying
Published: January 2019

Shewanella oneidensisMR-1 wild-type and a hyper-adhesive mutant CP2-1-S1 model organisms and Cr(vi) are used to study biofilm and toxic chemical interactions.
Polycyclic N-oxides: high performing, low sensitivity energetic materials
Authors: Snyder Christopher J. , Wells Lucille A. , Chavez David E. , Imler Gregory H. , Parrish Damon A.
Published: January 2019

Polycyclic N-oxides were developed based on the heterocycles 1,2,4,5-tetrazine and 4H,8H-difurazano[3,4-b:3′,4′-e]pyrazine.
Lewis acid-catalyzed annulative partial dimerization of 3-aryloxyacrylates to 4-arylchroman-2-ones: synthesis of analogues of tolterodine, RORγ inhibitors and a GPR40 agonist
Authors: Kunkalkar Rupesh A. , Fernandes Rodney A.
Published: January 2019

A captivating and beguiling annulative partial dimerization of 3-aryloxyacrylates to 4-arylchroman-2-ones catalyzed by Lewis acid (BF3·OEt2) has been developed.
Cryptand-imidazolium supported total synthesis of the lasso peptide BI-32169 and itsd-enantiomer
Authors: Chen Ming , Wang Shuanglong , Yu Xihan
Published: January 2019

The first total synthesis of natural lasso peptide is reported, in which cryptand-imidazolium complex support manipulates the peptide chain to achieve a lasso peptide configuration of BI-32169. Moreover, the synthesis ofd-enantiomeric lasso peptideviathis new method opens up new horizons in the study of lasso peptides.
Solvent controlled self-assembly of π-stacked/H-bonded supramolecular organic frameworks from a C3-symmetric monomer for iodine adsorption
Authors: Li Yangxue , Yu Haiyang , Xu Feifan , Guo Qiaoyuan , Xie Zhigang , Sun Zhiyong
Published: January 2019

Three π-stacked/H-bonded supramolecular organic frameworks (SOFs) with different architectures based on a C3-symmetric monomer were achieved through tuning the solvent systems.
Syntheses of two-dimensional propylammonium lead halide perovskite microstructures by a solution route
Authors: Ma Dewei , Xu Zhousu , Wang Fangjie , Deng Xujun
Published: January 2019

Syntheses of 2D propylammonium lead halide perovskite microstructures are reported. The I-containing perovskite exhibits a flower-like hierarchical morphology and possesses the chemical formula (C3H7NH3)6Pb4I14. The hydrogen-bonding interactions between organic group C3H7NH3+ and bilateral nearest-neighboring perovskite sheets are deemed to be responsible for this structure.
Investigation of the pyramid–prism boundary of a rapidly grown KDP crystal
Authors: Chen Duanyang , Wang Bin , Wang Hu , Bai Yunbo , Xu Nuo , Li Baizhong , Qi Hongji , Shao Jianda
Published: January 2019

To investigate the pyramid–prism (PY–PR) boundary of a rapidly grown KDP crystal, the exact position of the PY–PR boundary of an X-cut rapidly grown KDP sample is determined by measuring the refractive-index non-uniformity.
Digestive ripening mechanism investigation in a classical Lee–Meisel method based on in situ UV-vis spectra
Authors: Yu Liang , You Hongjun , Zhang Qifan , Zhang Lingling , Fang Jixiang
Published: January 2019

Digestive ripening is introduced into the classical Lee–Meisel synthesis to obtain uniform and size-controllable Ag nanoparticles.
Vibrational circular dichroism under the quantum magnifying glass: from the electronic flow to the spectroscopic observable
Authors: Fusè Marco , Egidi Franco , Bloino Julien
Published: January 2019

A chemically intuitive method to analyse and interpret vibrational circular dichroism spectra based on the vibrational transition current density.
From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica
Authors: Oliver Daniel , Michaelis Monika , Heinz Hendrik , Volkov Victor V. , Perry Carole C.
Published: January 2019

Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications.
An ab initio study of sensing applications of MoB2 monolayer: a potential gas sensor
Authors: Bano Amreen , Krishna Jyoti , Pandey Devendra K. , Gaur N. K.
Published: January 2019

Theoretically studied MoB2 monolayer detects NO2 gas with fast recovery time.
Rotational (de)-excitation of linear C3O by collision with He
Authors: Khadri Fehmi , Hammami Kamel
Published: January 2019

Calculation of the rate coefficients of C3O(1Σ+) induced by collision with He is performed for thermal temperatures below 25 K.
Stabilizing amorphous Sb by adding alien seeds for durable memory materials
Authors: Xu Meng , Li Bowen , Xu Kailang , Tong Hao , Cheng Xiaomin , Xu Ming , Miao Xiangshui
Published: January 2019

We developed a doping strategy to improve the thermal stability of phase-change memory by adding alien tetrahedral seeds.
Acetate as a model for aspartate-based CXCR4 chemokine receptor binding of cobalt and nickel complexes of cross-bridged tetraazamacrocycles
Authors: Cain Amy N. , Carder Freeman TaRynn N. , Roewe Kimberly D. , Cockriel David L. , Hasley Travis R. , Maples Randall D. , Allbritton Elisabeth M. A. , D'Huys Thomas , van Loy Tom , Burke Benjamin P. , Prior Timothy J. , Schols Dominique , Archibald Stephen J. , Hubin Timothy J.
Published: January 2019

Ni and Co complexes of cross-bridged vs. unbridged tetraazamacrocycle acetate complexes reveal preferences likely to impact CXCR4 antagonist interactions.
Tuning a robust system: N,O zinc guanidine catalysts for the ROP of lactide
Authors: Schäfer Pascal M. , McKeown Paul , Fuchs Martin , Rittinghaus Ruth D. , Hermann Alina , Henkel Johanna , Seidel Sebastian , Roitzheim Christoph , Ksiazkiewicz Agnieszka N. , Hoffmann Alexander , Pich Andrij , Jones Matthew D. , Herres-Pawlis Sonja
Published: January 2019

Four non-toxic, highly active and robust complexes have been used in the ring opening polymerisation of non-purifed lactide to substitute Sn(Oct)2.
Real-time monitoring of electrochemical reactions on single nanoparticles by dark-field and Raman microscopy
Authors: Qiu Kaipei , Fato Tano Patrice , Wang Pei-Yao , Long Yi-Tao
Published: January 2019

Dark-field and Raman microscopy to probe the single NP electrochemistry in real time.
Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
Authors: Rogers Simon , Ong Cher Wei , Wandy Joe , Ernst Madeleine , Ridder Lars , van der Hooft Justin J. J.
Published: January 2019

Integration of MS2LDA substructure discovery with MAGMa spectral annotations and ClassyFire term predictions complemented with MotifDB significantly advances metabolite annotation.
A review on the sustainable routes for the synthesis and applications of cuprous oxide nanoparticles and their nanocomposites
Authors: Yadav Sushma , Jain Arti , Malhotra Priti
Published: January 2019

Nature acts as a “Bio-Laboratory”, consisting of plants, algae, fungi, yeast,etc., which are composed of bio-molecules.
Sustainable hydrothermal self-assembly of hafnium–lignosulfonate nanohybrids for highly efficient reductive upgrading of 5-hydroxymethylfurfural
Authors: Zhou Shenghui , Dai Fanglin , Chen Yian , Dang Chao , Zhang Cunzhi , Liu Detao , Qi Haisong
Published: January 2019

Lignosulfonate, a waste by-product from the paper industry, was simply assembled with HfCl4 to construct sustainable catalysts (Hf–LigS) for highly efficient reductive upgrading of 5-hydroxymethylfurfural.
Enhancement of therapeutic effect in breast cancer with a steroid-conjugated ruthenium complex
Authors: Lv Gaochao , Qiu Ling , Li Ke , Liu Qingzhu , Li Xi , Peng Ying , Wang Shijie , Lin Jianguo
Published: January 2019

A hybrid metallic prodrug for targeting PR-positive breast cancer therapy was prepared, which revealed significantly in vivo antitumor effect.
Electrical and room temperature multiferroic properties of polyvinylidene fluoride nanocomposites doped with nickel ferrite nanoparticles
Authors: Rana Dhiraj Kumar , Singh Suresh Kumar , Kundu Shovan Kumar , Roy Subir , Angappane S. , Basu Soumen
Published: January 2019

The higher values of magneto-dielectric coupling is observed in flexible multiferroic polyvinylidene fluoride (PVDF) nanocomposites doped with nickel ferrite (NFO) nanoparticles.
Boron selective thin film composite nanofiltration membrane fabricated via a self-assembled trimesic acid layer at a liquid–liquid interface on an ultrafiltration support
Authors: Kumar Rajesha , Ahmed Mansour , Ok Salim , B. Garudachari , Thomas Jibu P.
Published: January 2019

A negatively charged nanofiltration membrane was prepared with a high selectivity for the rejection of both multivalent and monovalent ions during seawater pre-treatment.
Enhanced catalytic and SERS performance of shape/size controlled anisotropic gold nanostructures
Authors: Nehra Kamalesh , Pandian Senthil Kumar , Bharati Moram Sree Satya , Soma Venugopal Rao
Published: January 2019

Au nanostars of different sizes and shapes prepared using a simple method and their applications.
Cu2+-BTC based metal–organic framework: a redox accessible and redox stable MOF for selective and sensitive electrochemical sensing of acetaminophen and dopamine
Authors: Sofi Feroz Ahmad , Bhat Mohsin Ahmad , Majid Kowsar
Published: January 2019

A Cu2+ plus benzenetricarboxylate (BTC) based ‘3D’ metal–organic framework HKUST-1 was synthesized via a facile microwave assisted route.
Metal-cation substitutions induced the enhancement of second harmonic generation in A8BS6 (A = Cu, and Ag; B = Si, Ge, and Sn)
Authors: Gao Le , Lee Ming-Hsien , Zhang Jun
Published: January 2019

The substitution from Ag to Cu with isostructural compounds induces the apparent enhancement of the SHG responses, which is mainly attributed to the different intensity of dp hybridization between the metal cation and S.
Single particle ICP-MS and GC-MS provide a new insight into the formation mechanisms during the green synthesis of AgNPs
Authors: Zhang Huiling , Huang Yuxiong , Gu Jianqiang , Keller Arturo , Qin Yuwei , Bian Yue , Tang Kun , Qu Xiaolei , Ji Rong , Zhao Lijuan
Published: January 2019

For the first time, the formation kinetics and responsible metabolites during the green synthesis of AgNPs were elucidated by sp-ICP-MS and GC-MS.
Fluorescence sensing and intracellular imaging of Pd2+ ions by a novel coumarinyl-rhodamine Schiff base
Authors: Adak Arup Kumar , Purkait Rakesh , Manna Saikat Kumar , Ghosh Bankim Chandra , Pathak Sudipta , Sinha Chittaranjan
Published: January 2019

Coumarinyl-rhodamine, HCR, served as an extremely selective sensor for Pd2+ ions in ethanol/H2O (8 : 2, v/v, HEPES buffer, pH 7.2) solution and the limit of detection (LOD) was 18.8 nM (3σ method).
Metal-free synthesis of 2,2-disubstituted indolin-3-ones
Authors: Jiang Xinpeng , Zhu Bingbin , Lin Kai , Wang Guan , Su Wei-Ke , Yu Chuanming
Published: January 2019

A straightforward method for the synthesis of indolin-3-ones bearing a C2-quaternary functionality is reported. This cross-coupling reaction allows the facile synthesis of a series of 2,2-disubstituted indolin-3-ones in the absence of a metal catalyst in up to 94% yields.
MoS2-modified graphite felt as a high performance electrode material for zinc–polyiodide redox flow batteries
Authors: Liu Jian , Ma Ting , Zhou Meng , Liu Shuang , Xiao Jin , Tao Zhanliang , Chen Jun
Published: January 2019

MoS2 nanoplates were in situ grafted onto graphite felt to enable high performance zinc–polyiodine redox flow batteries.
Correction: All-solution-processed, flexible thin-film transistor based on PANI/PETA as gate/gate insulator
Authors: Hong Jin-Yong , Shin Kyoung-Hwan , Yoon Dai Gun , Chin Byung Doo , Kim Sung Hyun
Published: January 2019

Correction for ‘All-solution-processed, flexible thin-film transistor based on PANI/PETA as gate/gate insulator’ by Jin-Yong Hong et al., RSC Adv., 2015, 5, 105785–105788.