bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region
Authors: Guthrie J. L. , Strudwick L. , Roberts B. , Allen M. , McFadzen J. , Roth D. , Jorgensen D. , Rodrigues M. , Tang P. , Hanley B. , Johnston J. , Cook V. J. , Gardy J. L. 
Published: May 2019

AbstractFew studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings – regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005–2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.
Demand Satisfaction as a Framework for Understanding Intermittent Water Supply Systems
Authors: Taylor David D. J. , Slocum Alexander H. , Whittle Andrew J. 
Published: May 2019

AbstractNearly one billion people worldwide receive water through piped networks that are not continually pressurized and operate intermittently. The prevalence and persistence of these Intermittent Water Supplies (IWS) is surprising as this mode of operation induces water contamination and customer equity issues. Shortages of source water, customers' water demand, and leaking pipes are frequently cited as necessitating IWS. We propose a framework for understanding the persistence and operation of IWS. The supply system is represented by an average customer and a spatially averaged leakage rate. With this macroscopic hydraulic model, we relate customer demand satisfaction, source water availability, customer demand, and leakage. While this approach ignores the complexities of network topology, we find that the model approximates real systems well (calibrating to four intermittent reference networks achieved R2>0.94). The calibrated model is robust to moderate changes in demand and leakage (maintaining R2>0.83). Using the model, we show that the tipping point between satisfied demand and unsatisfied demand is a local optimum for utilities, which may explain the persistence of IWS. Beyond this point, the volume received by customers does not increase, but utilities must supply more water to the network. The generality of the proposed model enables its use when regulating and upgrading IWS. We demonstrate the latter by critiquing a performance‐based contract that was intended to improve an intermittent supply in India. Demand satisfaction has profound implications for hydraulics and human welfare. We propose the degree of demand satisfaction as a metric for evaluating IWS and for tracking the United Nations Sustainable Development Goal 6.1.
GNER: A Generative Model for Geological Named Entity Recognition Without Labeled Data Using Deep Learning
Authors: Qiu Qinjun , Xie Zhong , Wu Liang , Tao Liufeng 
Published: May 2019

AbstractA variety of detailed data about geological topics and geoscience knowledge are buried in the geoscience literature and rarely used. Named entity recognition (NER) provides both opportunities and challenges to leverage this wealth of data in the geoscience literature for data analysis and further information extraction. Existing NER models and techniques are mainly based on rule‐based and supervised approaches, and developing such systems requires a costly manual effort. In this paper, we first design a generic stepwise framework for domain‐specific NER. Following this framework, domain‐specific entities and domain‐general words are collected and selected as seed terms. Normalization and grouping processes are then applied to these seed terms for further analysis. A random extraction algorithm based on a unigram language model is used to generate a large‐scale training data set consisting of probabilistically labeled pseudosentences. Each generated sentence is then used as input to the self‐training and learning algorithm. Experimental results on two constructed data sets demonstrate that the proposed model effectively recognizes and identifies geological named entities.
The Controlling Factors of Atmospheric Formaldehyde (HCHO) in Amazon as Seen From Satellite
Authors: Zhang Yuxiang , Li Rui , Min Qilong , Bo Haixu , Fu Yuyun , Wang Yipu , Gao Zongting 
Published: May 2019

AbstractTo understand the relative importance of biogenic emission, biomass burning emission on volatile organic compounds in Amazon, the spatial and temporal correlations between atmospheric column‐integrated formaldehyde (HCHO) and fire count, vegetation hydrological states index, surface solar radiation flux, near‐surface air temperature are studied using synergized satellite products and reanalysis data. A recently developed microwave‐based vegetation index (emissivity difference vegetation index, EDVI) with high temporal resolution is used for the linkages between vegetation and HCHO at daily scale with and without fire contaminations. At large regional scale, EDVI shows highest spatial correlation with HCHO indicating the important controlling effect of biogenic emission. In given subregions with frequent fires, the temporal variations of monthly HCHO show much stronger correlations with fire count. The temporal correlations between monthly HCHO and EDVI are vague and even negative in some subregions. Radiation and temperature show stable positive temporal correlations with HCHO, particularly in areas with few fires. After excluding the samples contaminated by fires, the daily temporal correlation between vegetation (EDVI) and HCHO becomes significant and positive in most areas except the northern rainforest with weak temporal variations of EDVI. We proposed a bilinear model of biogenic‐emission‐induced HCHO (B‐HCHO) using radiation and EDVI as inputs. The bias between modeled long‐term mean B‐HCHO and satellite observation is less than 20%. And the daily time series of modeled B‐HCHO matches observations as well. It is the first time to provide satellite observational evidences of the relative importance of biogenic emission and biomass burning emission on HCHO, the proxy of atmospheric volatile organic compounds concentration.
Satellite‐Based Assessment of Local Environment Change by Wind Farms in China
Authors: Wu Xiao‐lin , Zhang Li‐xiao , Zhao Chuanfeng , Gegen Tana , Zheng Cai‐wang , Shi Xiao‐qin , Geng Jing , Letu Husi 
Published: May 2019

AbstractAs a widely used renewable energy, migrating to wind power can help reduce air pollution and CO2 emissions. However, the construction of wind farms could have certain impacts on the local ecology and meteorology. Based on satellite observations along with the ERA‐Interim reanalysis meteorology, this study examines the difference of vegetation characteristics, local wind speed, and surface temperature between the wind power regions and adjacent comparison areas in XilinGol. It shows that the construction of wind farms results in significant differences (p = 0.01) of normalized difference vegetation index values in the study areas compared to the adjacent areas in summer. The construction of the wind farms in study area has considerable influence on the change of local vegetation growth and related meteorological variables. It reduces the fraction of grassland, disrupts the wind field when speed are less than 4 m/s, and changes the spatial pattern of temperature during daytime and nighttime. However, the influence decreases with time after the installment of wind turbines. This study suggests that it is necessary to assess the impact of renewable energy construction on ecological environment and local climate, particularly for the short‐term period after its installment.
Pore‐Scale Explanation of the Archie's Cementation Exponent: Microstructure, Electrical Anisotropy, and Numerical Experiments
Authors: Yue Wenzheng 
Published: May 2019

AbstractElectrical anisotropy of rock is a key parameter in geophysical research. In this paper, digital rocks were constructed by aligning elliptic grains to create samples with anisotropic pore connectivities. Lattice gas automata are used to research electrical transport properties for revealing the anisotropy and physical meaning of Archie's cementation exponent. Simulated results indicate that the relationship between formation factor and porosity is of anisotropy with the exponent corresponding to the change rate of pore complexity with porosity, instead of pore complexity itself, confirming previous theoretical studies. Besides, the results reveal that anisotropy of pore structure is a main factor leading to the anisotropic relation. Under the effects of fracture, there is a U‐shape transition zone over a range of porosity for anisotropy exponent. Moreover, the simulated data are in good agreement with the laboratory experiments, which can further verify the validity of the results.
miR-340-FHL2 axis inhibits cell growth and metastasis in ovarian cancer
Authors: Huang Zheng , Li Qiuxia , Luo Kaili , Zhang Qinkai , Geng Jingwen , Zhou Xunzhu , Xu Yesha , Qian Mengyao , Zhang Jian-an , Ji Liying , Wu Jianmin 
Published: May 2019

AbstractAlthough increasing evidence indicated that deregulation of microRNAs (miRNAs) contributed to tumor initiation and progression, but little is known about the biological role of miR-340 in ovarian cancer (OC). In this study, we found that miR-340 expression was downregulated in OC tissues compared with its expression in normal ovarian epithelium and endometrium, and treatment with 5-aza-2′-deoxycytidine (5-Aza-dC) or trichostatin A (TSA) increased miR-340 expression in OC cells. In addition, ectopic miR-340 expression inhibited OC cell growth and metastasis in vitro and in vivo. Four and a half LIM domains protein 2 (FHL2) was confirmed as a direct target of miR-340 and silencing FHL2 mimicked the effects of miR-340 in OC cells. Further mechanistic study showed that miR-340 inhibited the Wnt/β-catenin pathway by targeting FHL2, as well as downstream cell cycle and epithelial-to-mesenchymal transition (EMT) signals in OC cells. Moreover, the greatest association between miR-340 and FHL2 was found in 481 ovarian serous cystadenocarcinoma tissues via pan-cancer analysis. Finally, we revealed that lower miR-340 or higher FHL2 was associated with poor OC patient outcomes. Our findings indicate that the miR-340-FHL2 axis regulates Wnt/β-catenin signaling and is involved in tumorigenesis in OC. Therefore, manipulating the expression of miR-340 or its target genes is a potential strategy in OC therapy.
Comparative mode of action of the antimicrobial peptide melimine and its derivative Mel4 against Pseudomonas aeruginosa
Authors: Yasir Muhammad , Dutta Debarun , Willcox Mark D. P. 
Published: May 2019

AbstractMelimine and Mel4 are chimeric cationic peptides with broad-spectrum antimicrobial activity. They have been shown to be highly biocompatible in animal models and human clinical trials. The current study examined the mechanism of action of these two antimicrobial peptides against P. aeruginosa. The effect of the peptides of endotoxin neutralization, and their interactions with cytoplasmic membranes using DiSC(3)-5 and Sytox green, Syto-9 and PI dyes were analysed. Release of ATP and DNA/RNA were determined using ATP luminescence and increase in OD260 nm. The bacteriolytic ability of the peptides was determined by measuring decreases in OD620 nm. Both the peptides neutralized LPS suggesting their interaction with lipid A. Cytoplasmic membrane was disrupted within 30 seconds, which correlated with reductions in cellular viability. At 2 minutes melimine or Mel4, released 75% and 36% cellular ATP respectively (P < 0.001). Membrane permeabilization started 5 minutes with simultaneous release of DNA/RNA. Flow cytometry demonstrated 52% and 18% bacteria were stained with PI after 30 minutes. Overall, melimine showed higher capacity for membrane disruption compared to Mel4 (P < 0.001). The findings of this study have been summarized as a timeline of bactericidal activity, suggesting that the peptides permeabilized P. aeruginosa within 5 minutes, started lysis within 2 hours of exposure.
Investigation on potential associations of oxidatively generated DNA/RNA damage with lung, colorectal, breast, prostate and total cancer incidence
Authors: Gào Xīn , Holleczek Bernd , Cuk Katarina , Zhang Yan , Anusruti Ankita , Xuan Yang , Xu Yiwei , Brenner Hermann , Schöttker Ben 
Published: May 2019

AbstractOxidative stress has been linked to cancer development in previous studies. However, the association between pre-diagnostic oxidatively generated DNA/RNA damage levels and incident cancer has rarely been investigated. Urinary oxidized guanine/guanosine (OxGua) concentrations, including 8-hydroxy-2′-deoxyguanosine, were assessed in 8,793 older adults in a population-based German cohort. 1,540 incident cancer cases, including 207 lung, 196 colorectal, 218 breast and 245 prostate cancer cases were diagnosed during over 14 years of follow-up. Associations of OxGua levels with cancer outcomes were not observed in the total population in multi-variable adjusted Cox regression models. However, in subgroup analyses, colorectal cancer incidence increased by 8%, 9% and 8% with one standard deviation increase in OxGua levels among current non-smokers, female and non-obese participants, respectively. Additionally, among non-smokers, overall and prostate cancer incidences statistically significantly increased by 5% and 13% per 1 standard deviation increase in OxGua levels, respectively. In contrast, OxGua levels were inversely associated with the risk of prostate cancer among current smokers. However, none of the subgroup analyses had p-values below a threshold for statistical significance after correction for multiple testing. Thus, results need to be validated in further studies. There might be a pattern that oxidatively generated DNA/RNA damage is a weak cancer risk factor in the absence of other strong risk factors, such as smoking, obesity and male sex.
Association between IL-37 gene polymorphisms and risk of HBV-related liver disease in a Saudi Arabian population
Authors: Al-Anazi Mashael R. , Matou-Nasri Sabine , Al-Qahtani Arwa A. , Alghamdi Jahad , Abdo Ayman A. , Sanai Faisal M. , Al-Hamoudi Waleed K. , Alswat Khalid A. , Al-Ashgar Hamad I. , Khan Mohammed Q. , Albenmousa Ali , Shamsi Monis B. , Alanazi Salah K. , Dela Cruz Damian , Bohol Marie Fe F. , Al-Ahdal Mohammed N. , Al-Qahtani Ahmed A. 
Published: May 2019

AbstractInterleukin-37 (IL-37) has recently been recognized as a strong anti-inflammatory cytokine having anti-tumor activity against hepatocellular carcinoma (HCC) in hepatitis B virus (HBV)-infected patients. HCC is a typical inflammation-related cancer, and genetic variations within the IL-37 gene may be associated with the risk of HBV infection. Identification of the allelic patterns that genetically have a high disease risk is essential for the development of preventive diagnostics for HBV-mediated liver disease pathogenesis. In this study, we aimed to investigate the association between single nucleotide polymorphisms (SNPs) within the IL-37 gene and disease sequelae associated with HBV infection. We genotyped ten IL-37 SNPs in 1274 patients infected with HBV and 599 healthy controls from a Saudi Arabian population. Among the selected SNPs, two SNPs (rs2723175 and rs2708973) were strongly associated with HBV infection, and six SNPs (rs2723176, rs2723175, rs2723186, rs364030, rs28947200, rs4392270) were associated with HBV clearance, comparing healthy controls and HBV infected-patients respectively. A suggestive association of rs4849133 was identified with active HBV surface antigen (HBsAg) carrier and HBV-related liver disease progression. In conclusion, our findings suggest that variations at the IL-37 gene may be useful as genetic predictive risk factors for HBV infection and HBV-mediated liver disease progression in the Saudi Arabian population.
Behavioural Response to the Environmental Changes of Various Types in Lister-Hooded Male Rats
Authors: Pisula Wojciech , Modlinska Klaudia , Chrzanowska Anna 
Published: May 2019

AbstractThe animal preference for complexity is most clearly demonstrated when the environmental change takes the form of an increase in complexity. Therefore, one of the potential difficulties in interpretation is that the preference for perceptual novelty may be confounded with the change in environmental complexity. In this study, the environmental complexity was controlled by manipulating with tunnels inside the experimental chamber. Adding new tunnels triggered a very profound change in behaviour, which was demonstrated by the animals’ prolonged stay in the proximity of the novel objects, sniffing, touching, and climbing on top of the tunnels. The removal of the tunnels from the test arena turned out to have the least influence on behaviour compared to the other manipulations used in this study. The reduction of complexity of the tunnels had a moderate effect on rat behavior. Tunnels are important elements in the rats’ environment, since they provide various possibilities for hiding, resting or moving inside the tunnel. They may be treated as a good example of affordances in rat-environment interactions. The results of this study may therefore serve as a basis for constructing a modified theory of animal curiosity which could incorporate the concept of ecological psychology.
Lattice Discontinuities of 1T-TaS2 across First Order Charge Density Wave Phase Transitions
Authors: Wang Wen , Dietzel Dirk , Schirmeisen André 
Published: May 2019

AbstractTransition metal dichalcogenides are lamellar materials which can exhibit unique and remarkable electronic behavior due to effects of electron-electron and electron-phonon coupling. Among these materials, 1T-tantalum disulfide (1T-TaS2) has spurred considerable interest, due to its multiple first order phase transitions between different charge density wave (CDW) states. In general, the basic effects of charge density wave formation in 1T-TaS2 can be attributed to in plane re-orientation of Ta-atoms during the phase transitions. Only in recent years, an increasing number of studies has also emphasized the role of interlayer interaction and stacking order as a crucial aspect to understand the specific electronic behavior of 1T-TaS2, especially for technological systems with a finite number of layers. Obviously, continuously monitoring the out of plane expansion of the sample can provide direct inside into the rearrangement of the layer structure during the phase transition. In this letter, we therefore investigate the c-axis lattice discontinuities of 1T-TaS2 by atomic force microscopy (AFM) method under ultra-high vacuum conditions. We find that the c-axis lattice experiences a sudden contraction across the nearly-commensurate CDW (NC-CDW) phase to commensurate CDW (C-CDW) phase transition during cooling, while an expansion is found during the transition from the C-CDW phase to a triclinic CDW phase during heating. Thereby our measurements reveal, how higher order C-CDW phase can favor a more dense stacking. Additionally, our measurements also show subtler effects like e.g. two expansion peaks at the start of the transitions, which can provide further insight into the mechanisms at the onset of CDW phase transitions.
Exploring the mechanism of “Rare Earth” texture evolution in a lean Mg–Zn–Ca alloy
Authors: Guan Dikai , Liu Xingguang , Gao Junheng , Ma Le , Wynne Bradley P. , Rainforth W. Mark 
Published: May 2019

AbstractThe entire recrystallisation sequence and associated crystallographic texture evolution of Mg-0.8Zn-0.2Ca (wt.%) alloy was tracked using a quasi-in-situ electron backscatter diffraction (EBSD) method. Characteristic “Rare Earth” (RE) texture was formed, originating mainly from double twins and twinning-related shear bands consisting of compression and double twins. The RE textures appeared during the nucleation stage and were preserved during the relative uniform grain growth period because of solute segregation and concurrent precipitation although the alloying element content was very low. Ca and Zn co-segregated along grain boundaries with no evidence that segregation was preferred along special types of grain boundaries. The interactions between deformation microstructures, concurrent precipitation, solute drag, grain growth and texture evolution are discussed in detail. All the results indicate that Ca performs a similar role to that of RE elements in forming RE texture.
Multi-context blind source separation by error-gated Hebbian rule
Authors: Isomura Takuya , Toyoizumi Taro 
Published: May 2019

AbstractAnimals need to adjust their inferences according to the context they are in. This is required for the multi-context blind source separation (BSS) task, where an agent needs to infer hidden sources from their context-dependent mixtures. The agent is expected to invert this mixing process for all contexts. Here, we show that a neural network that implements the error-gated Hebbian rule (EGHR) with sufficiently redundant sensory inputs can successfully learn this task. After training, the network can perform the multi-context BSS without further updating synapses, by retaining memories of all experienced contexts. This demonstrates an attractive use of the EGHR for dimensionality reduction by extracting low-dimensional sources across contexts. Finally, if there is a common feature shared across contexts, the EGHR can extract it and generalize the task to even inexperienced contexts. The results highlight the utility of the EGHR as a model for perceptual adaptation in animals.
Mechanical and electrical properties of MCMB/Chopped carbon fiber composite with different bead size
Authors: Im Ui-Su , Kim Jiyoung , Lee Byung-Rok , Peck Dong-Hyun , Jung Doo-Hwan 
Published: May 2019

AbstractThe carbonization and graphitization of carbon/carbon (C/C) composites prepared from mesocarbon microbeads (MCMB) and chopped carbon fiber (CCF) have been studied with a wide range of temperatures, CCF contents and MCMB sizes. Three different sizes of MCMB were prepared with coal tar pitch at three temperatures, 420, 430 and 440 °C, and identified as about 12.8, 16.0 and 20.1 µm, respectively. Each size of MCMB was mixed with CCFs at ratios of 2, 4, 6 and 8 wt. % and formed into block shape. After carbonization at 1200 °C, carbonized C/C blocks (CCBs) were graphitized at 2000, 2400 and 2800 °C. The CCB prepared with CCF content of 2 wt. % and an MCMB size of 16.0 µm exhibited the highest flexural strength of about 151 MPa. The graphitized C/C block (GCB) with CCF content of 2 wt. %, which was graphitized at 2000 °C showed the highest flexural strength of about 159 MPa.