bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Mining Influences on a Small Frame Railway Viaduct
Authors: Betkowski Piotr
Published: November 2019

In the article, the example of the rebuilding of the real bridge object shows, how to take into account the impact of mining area deformations on small frame railway viaducts integrated with the embankment. General principles are given, how to determine additional forces induced in the construction, such forces arise as a result of mining deformations on the surface of the area. It is discussed, how to shape the geometry of the bridge structure, so that in the future it will be possible to raise the level of the railway track even by several meters (in order to eliminate the local mining hollow), without rebuilding of the viaduct. Attention is paid to the necessity of shaping the foundations so that the impact on the subsoil tension under the embankment and under the viaduct is the same, so that the viaduct can settle in the same way as the adjacent railway embankment. In addition, technological aspects related to the adjustment of the viaduct to ground conditions (shallow, thin layers of cohesive-plastic soil typical for post-glacial areas in Poland on Silesia Upland) and protection of railway traffic continuity through a bridge type relieving construction are shown. The article is supplemented by the results of 8-years measurements of subsidence and displacements of the viaduct on the deforming mining ground and conclusions from observations. This method of analysis and conclusions may be used in further studies of the interaction between the embankment and the viaduct embedded in the embankment in the situation of active mining deformations of the area.
Methods of Springs Failures Diagnostics in Ore Processing Vibrating Screens
Authors: Krot Pavlo , Zimroz Radoslaw
Published: November 2019

Large-scale vibrating screens are widely used in minerals processing industry. One of main components in any vibrating screen is a set of springs supporting the main body of machine with sieving material inside. These springs are subjected to cyclic loading and fatigue. Changing of their stiffness and subsequent failures have influence on the sieving efficiency and are difficult to predict, hence, online condition monitoring is required. Visual inspection and non-destructive diagnostic methods are not sufficient in this case. Noisy signals from vibration sensors installed on bearings supports of rotating unbalanced exciters are preferably used for diagnostics of spring failures. In this research, vibrating screen motion is represented by multi-DOF (degree-of-freedom) dynamic model, which accounts stochastic disturbances from incoming material and impacts on sieving decks. Specific features of vibration signals are analysed to identify springs deterioration modelled as the bilinear stiffness characteristics. Phase space plots (PSP) are considered as the promising method to recognise nonlinear behaviour of system under the presence of spring damage. Advantages are assessed of spring stiffness change and failures diagnostics as compared with other methods.
Numerical Simulation of Sediments Transport AO a River Sector as Distorted by a Crossing Structure
Authors: Popescu-Busan Ioana - Alina , Lazar Gheorghe I. , Constantin Albert Titus , Nicoara Serban-Vlad
Published: November 2019

The paper presents a 1D numerical modelling of sediments transit on Someș River downstream of its confluence with Agrij tributary, specifically for a 352 m sector affected by a driveway crossing bridge right outside of Jibou Town building area, about 25 km from Zalău Municipality in the North-West of Romania. There was considered a quasi-transitory flow regime as assimilated from a three years data available period of time, i.e. from August 1st, 1985, to July 31st, 1988. As considering the on-site findings and concluding general riverbed restoration suggestions of a technical expertise ordered by the Rivers National Administration, the performed numerical model comes in support of the technical solutions stipulated by a feasibility study conducted by the authors with respect to streambed balance achievement in the range of the mentioned bridge. Specifically, the following main interventions were implied: the accomplishment of a downstream bottom step to break the general scouring phenomenon in the structure vicinity and to produce the re-siltation of the central gaps, and the execution of two upstream river groins designated to lead the flow and carried alluvia towards the bridge central area. Thus, the numerical simulation performed by the help of HEC-RAS 5.0.6 specialized software package looks to establish the optimum location and geometry for the bottom step as correlated with bridge area re-siltation and general scouring on the modelled river sector. Specific structural results and flow parameters outcome – water surface level and velocity development – together with important general sediments transport information (e.g. flexible streambed configuration evolution) was concluded from the reached graphical output.
Coal Mines Risk Modelling Using Energy Spread
Authors: Krysa Zbigniew , Dudek Michal
Published: November 2019

The growing importance of the cost of electricity in coal mining, changes in the value chain in recent years and new commodity exchanges cause that mine operators independently or vertically integrated with power plants have possibility to buy and sell coal and electricity and create a specific spread. The study of risk based on the concept of a new indicator: an intrinsic spread. The intrinsic spread is calculated as a difference between the income from the sale of coal and the cost of purchasing the energy required for the coal production. This indicator shows a market risk in the coal mine in a better way, because except for income it includes a part of the cost of exploitation which can be hedged in the exchange market. Spread calculations were made on historical data and simulation modelling. Based on time series of coal and energy prices for various contracts and spot prices obtained from the EEX the impact of the type of contracts on the volatility of the intrinsic spread in subsequent periods measured by the standard deviation of returns has been analysed. It was found that hedge using futures helps to reduce the risk in the mine. Modelling of coal prices and electricity was carried out by conventional financial market econometric models. The best-fitting econometric models are multivariate models and models based on the copulas. The simulation results show that the use of futures contracts contributes little to reducing the intrinsic spread volatility. An econometric model with the technical and economic parameters of the mine typical for hard coal mine has been built. Changes in fixed and variable costs have been simulated based on triangular distributions. Parameters for simulation were estimated based on the economic data from the mines. Additionally, coal and energy prices were dependent on the market volatility. Based on the economic model and Monte Carlo simulation it has been found that the proposed method may be helpful in reducing the coal mine market risk.
Temporal and spatial pattern variation analysis of grassland resources in Huize County, Yunnan, China
Authors: Sun Xiaoli , Li Dongsheng , Cheng Xianfeng , Ma Juan , He Wanrong
Published: November 2019

In order to study the spatial and temporal pattern variations of grassland resources and to promote the sustainable utilization of grassland resources, this paper, taking Huize County as an example, discusses the temporal and spatial pattern variations of grassland resources from the perspective of grassland resources comprehensive dynamic degree, different topographic conditions, geoscience information map and landscape pattern index. Remote sensing images in 2009 and 2016, the second national land survey database and the 2016 land use variation survey database were selected as the basic data source. The results show that: 1) from 2009 to 2016, Xinjie town and Tianba town have great variations in the comprehensive dynamic degree of grassland resources, while Wuxing town and Jinzhong town are the smallest variations. The number of grassland resources in the study area presents a spatial feature of “high in the north and south parts and low in the middle”; 2) topographic conditions have a certain impact on grassland resources. The grassland resources in the study area mostly exist in the areas with the elevation of 1800-2500m, the slope of over 25° and the aspect of sunny and semi-sunny. From 2009 to 2016, grassland resources net increase was 21134.51hm2. 3) From the perspective of geomatics information map and landscape pattern index, grassland resources have both increased and decreased from 2009 to 2016. The land conversion categories that have increased and decreased mainly include cultivated land, garden land, forest land, construction land, water area and other land types, among which the proportion of forest land variations greatly. Although the area of grassland resources increased, the number of grassland resources patches decreased. The average patch area increased, the proximity and aggregation between patches increased, and landscape fragmentation decreased, and the overall landscape pattern developed towards the aggregation direction.
Applications of Linear Systems in Contemporary Urban Design
Authors: Kwiatkowski Krzysztof
Published: November 2019

One of the fundamental disputes in the contemporary urban design is principal of shaping urban systems. The main focus of disputes and research is the clash of urban interior (and its multiplication – residential quarter) systems with freestanding building urbanism. The issue is also discussed from perspective of neighbourly bonds, contact with nature and access to transport. The concept of linear systems was supposed to be an alternative solution to the dispute. The father of the idea of linear cities was Arturo Soria y Mata. The first drafts about the concept appeared in 1882. Its priorities were based on transport accessibility and green zones. In the Polish urban design, the original concepts of linear systems were created by Oskar Hansen (Linear Continuous System) and Włodzimierz Gruszczyński (Ribbon City of Conjugate Transportation) at the turn of 60’s into 70’s. The theory of Hansen predicts creation of four stripes North-South across Poland. The theory was based on demographical and geographical research. To certain extend, Hansen managed to achieve some aspects of the theory. The examples can be seen in the housing estate Przyczółek Grochowski in Warszawa and in the housing estate Lubelska Spółdzielnia Mieszkaniowa in Lublin. The article tackles upon the strengths and weaknesses of linear systems. Their main assets are: transport accessibility, contact with greenery and ability to counteract the urban sprawl. However, the basic weaknesses are schematism and dullness of buildings and the problem of residential cell divided into two parts by long transport belt. Another discussed aspect is comparison between urban interior systems and linear systems. Transforming the structure of linear systems includes three processes – reduction of the scale of systems, naturalisation of the central transport belt and individualisation of the structure of building range. One of the methods opposing the dullness is integration of various types of buildings – “hybridisation.”Besides the enumerated above transformation processes, I think that it is crucial to break the schematism of the linear systems. The parallel belts of residential areas should be replaced by networks. Such networks would leave the enormous fields to untamed and natural space.
Geothermal Waters in Pamukkale as an Hydrogeological Model within the Menderes Massif, Turkey
Authors: Ozgur Nevzat , Kutlu Duygu Sengul
Published: November 2019

The area is located in the northern shoulder of the eastern part of the E-W trending continental rift zone of the Büyük Menderes and consists of Paleozoic rocks, Mesozoic limestones and sedimentary rocks in age of Eocene, Pliocene and Quaternary. The marbles, quartzites and carbonate rocks, limestones, sedimentary rocks, alluvium and travertine deposits are of passable rocks for geothermal waters. Geothermal waters of Pamukkale show outlet temperatures ranging from 35 to 48 °C and reservoir temperatures of between 150 and 180 °C and are of Mg-Ca-SO4-HCO3 type waters. Geothermal waters in Pamukkale are distinguished by Mg>Ca>Na+K as dominant cations and HCO3>SO4> Cl as dominant anions. The diagram of Na1/1000-K1/100-√Mg shows that the samples of Pamukkale are of immature waters. Finally, the geothermal waters in Pamukkale were represented as a hydrogeological model.
Compressive strength of basalt fiber reinforced concrete (BFRC) comparing on expanded clay and gravel as BFRC aggregate
Authors: Chiadighikaobi P C , Galishnikova V V , Kharun M , Koroteev D D , Dkhar P
Published: November 2019

It is of great important that the compression strength of concrete is known in construction. The types of aggregate used in the concrete have great effect on the compression strength of the concrete. This paper looked into the compression strength of basalt fiber reinforced concrete when it bears expanded clay as aggregate and when it bears the usual gravel as aggregate. One thing to note is that the weight of both BFRC specimens vary as, the BFRC with expanded clay showed much lighter weight than that of BFRC with gravel. This weight difference was explained in the properties of the materials. The main aim of this research paper is to express the comparison differences between the two types basalt fiber reinforced concrete researched in this paper. This paper showed some literature reviews from the papers written from other authors on close and similar topics then, an experimental analysis was conducted to investigate and compare the compression strength of the two concrete mix which the results showed visible differences in the compression strength and crack resistance. From the experiment, it is seen that the concrete with expanded clay (lightweight expanded clay concrete and lightweight expanded clay basalt fiber reinforced concrete) has a rapid strength growth after the 14th day when compared to the usual (gravel) concrete or usual basalt fiber reinforced concrete. The compatibility of basalt fiber with expanded clay is excellent and can be seen from the result analysis.
The interaction between mathematics and architecture
Authors: Sergeeva E V , Moskvina E A , Torshina O A
Published: November 2019

Mathematics and architecture have always been closely interrelated, the main methods of design in architecture has always belonged to mathematics. At the present stage in connection with the development of computer technology and the Internet began a new round in the relationship between mathematics and architecture. A competent architect should have excellent skills in painting and sculpture, as well as a good knowledge of mathematics. We came to the conclusion that the purpose of mathematical training in the University of students of construction specialties is the development of their mathematical competence. This requires: 1) students should be able to solve applied mathematical problems; 2) students should carry out projects related to their future professional activities; 3) students should be able to create mathematical models. We have developed criteria, indicators and levels of development of mathematical competence of students of the University, which allows you to organize control and measuring materials to assess the level of mathematical training of students.
The study of fuel mixtures with palm oil
Authors: Oshchepkov P P , Smirnov S V , Zaev I A , Vorobyev A A
Published: November 2019

The search for alternative fuels for heat engines is an urgent task for scientists around the world. For diesel engines, vegetable oils seem to be the most promising. The use of a partial addition of vegetable oils to diesel fuel allows us to reduce the consumption of hydrocarbons and not cause significant changes in the design of the engine, as well as affect the composition of the exhaust gases. For countries producing palm oil, including Nigeria, this method is economically viable. This article presents the results of computational studies of the features of the combustion process of biodiesel fuel with additives of palm oil and hydrogen peroxide and the effect of additives on the ignition delay period and the combustion process. The calculations have shown the effectiveness of using hydrogen peroxide as an additive to the biofuel under consideration to reduce the ignition delay period and, consequently, improve the power and economic indicators.
Bulk properties of single crystals of the valence-unstable compound SmRh2Si2
Authors: Kliemt K , Banda J , Geibel C , Brando M , Krellner C
Published: November 2019

We present the crystal growth as well as the structural, chemical and physical chracterization of SmRh2Si2 single crystals. Their ground state is antiferromagnetic, as indicated by the behaviour of the magnetic susceptibility and the specific heat at the second order phase transition observed at T
N = 64 K. The Sommerfeld coefficient is small and similar to that of LuRh2Si2 with

γ

0

≈
7

mJ/(molK2). Susceptibility measurements show no Curie-Weiss behaviour at high temperatures which is a consequence of the large Van-Vleck contribution of the excited multiplets of Sm3+. Previous angle-resolved photoemission studies showed that at 10 K, the valence of the Sm ions is smaller than three at the surface as well as in the bulk, suggesting a possible Kondo screening of the Sm3+ ions. This could not be observed in our thermodynamic and transport measurements.
A closer look at the genotoxicity of graphene based materials
Authors: Gurcan Cansu , Taheri Hadiseh , Bianco Alberto , Delogu Lucia Gemma , Yilmazer Acelya
Published: November 2019

Graphene-based materials (GBMs) have attracted many scientists because of their optical, thermal, mechanical and electronic properties. Their good dispersibility in different type of solvents including water, the possibility to formulate them according to desired function, and the wide surface area, which can allow various chemical modifications, expanded the use of these materials in biological systems. For these reasons, GBMs have been extensively studied in vitro and in vivo in the biomedical field. However, the toxicity and genotoxicity of GBMs must be thoroughly investigated before they can be translated into clinical settings. The main mechanism of graphene toxicity is thought to be caused by reactive oxygen species produced in cells, which in turn interact with various biomolecules including DNA. In this review we aimed to discuss different genotoxicity studies performed with GBMs with specific focus on the different cell types and conditions. By comparing and discussing such reports, scientists will be able to engineer non toxic GBMs for future preclinical and/or clinical studies. In order to allow a safer and faster transition to clinic, future studies should involve state-of-the-art technologies such as systems biology approaches or three-dimensional microfluidic systems, which can better predict the normal physiological scenario.
Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities
Authors: Zingaretti Laura M , Renand Gilles , Morgavi Diego P , Ramayo-Caldas Yuliaxis
Published: November 2019

Motivation

We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of ‘Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux’, a family of methods designed to integrate information from heterogeneous data. Here, we extend the classical approach to deal with broader datasets (e.g. compositional data), methods for variable selection and taxon-set enrichment analysis.

Results

The methodology is demonstrated by integrating rumen microbial communities from cows for which methane yield (CH4y) was individually measured. Our approach reproduces the significant link between rumen microbiota structure and CH4 emission. When analyzing the TARA’s ocean data, Link-HD replicates published results, highlighting the relevance of temperature with members of phyla Proteobacteria on the structure and functionality of this ecosystem.

Availability and implementation

The source code, examples and a complete manual are freely available in GitHub https://github.com/lauzingaretti/LinkHD and in Bioconductor https://bioconductor.org/packages/release/bioc/html/LinkHD.html.
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
Authors: Zhang Chengxin , Zheng Wei , Mortuza S M , Li Yang , Zhang Yang
Published: November 2019

Motivation

The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins. There are however no standard and efficient pipeline available for sensitive multiple sequence alignment (MSA) collection. This is particularly challenging when large whole-genome and metagenome databases are involved.

Results

We developed DeepMSA, a new open-source method for sensitive MSA construction, which has homologous sequences and alignments created from multi-sources of whole-genome and metagenome databases through complementary hidden Markov model algorithms. The practical usefulness of the pipeline was examined in three large-scale benchmark experiments based on 614 non-redundant proteins. First, DeepMSA was utilized to generate MSAs for residue-level contact prediction by six coevolution and deep learning-based programs, which resulted in an accuracy increase in long-range contacts by up to 24.4% compared to the default programs. Next, multiple threading programs are performed for homologous structure identification, where the average TM-score of the template alignments has over 7.5% increases with the use of the new DeepMSA profiles. Finally, DeepMSA was used for secondary structure prediction and resulted in statistically significant improvements in the Q3 accuracy. It is noted that all these improvements were achieved without re-training the parameters and neural-network models, demonstrating the robustness and general usefulness of the DeepMSA in protein structural bioinformatics applications, especially for targets without homologous templates in the PDB library.

Availability and implementation

https://zhanglab.ccmb.med.umich.edu/DeepMSA/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Robust empirical Bayes small area estimation with density power divergence
Authors: Sugasawa S
Published: November 2019

A two-stage normal hierarchical model called the Fay–Herriot model and the empirical Bayes estimator are widely used to obtain indirect and model-based estimates of means in small areas. However, the performance of the empirical Bayes estimator can be poor when the assumed normal distribution is misspecified. This article presents a simple modification that makes use of density power divergence and proposes a new robust empirical Bayes small area estimator. The mean squared error and estimated mean squared error of the proposed estimator are derived based on the asymptotic properties of the robust estimator of the model parameters. We investigate the numerical performance of the proposed method through simulations and an application to survey data.
Regulation of cell–cell adhesion in prostate cancer cells by microRNA-96 through upregulation of E-Cadherin and EpCAM
Authors: Voss Gjendine , Haflidadóttir Benedikta S , Järemo Helena , Persson Margareta , Catela Ivkovic Tina , Wikström Pernilla , Ceder Yvonne
Published: November 2019

Prostate cancer is one of the most common cancers in men, yet the biology behind lethal disease progression and bone metastasis is poorly understood. In this study, we found elevated levels of microRNA-96 (miR-96) in prostate cancer bone metastasis samples. To determine the molecular mechanisms by which miR-96 deregulation contributes to metastatic progression, we performed an Argonaute2-immunoprecipitation assay, in which mRNAs associated with cell–cell interaction were enriched. The expression of two cell adhesion molecules, E-Cadherin and EpCAM, was upregulated by miR-96, and potential targets sites were identified in the coding sequences of their mRNAs. We further showed that miR-96 enhanced cell–cell adhesion between prostate cancer cells as well as their ability to bind to osteoblasts. Our findings suggest that increased levels of miR-96 give prostate cancer cells an advantage at forming metastases in the bone microenvironment due to increased cell–cell interaction. We propose that miR-96 promotes bone metastasis in prostate cancer patients by facilitating the outgrowth of macroscopic tumours in the bone.
Reporting From the Whites of Their Eyes: How Whiteness as Neoliberalism Promotes Racism in the News Coverage of “All Lives Matter”
Authors: Kil Sang Hea
Published: November 2019

This study evaluates how “all lives matter” (ALM) has advanced Whiteness in the news. Critical race theory’s critique of liberalism’s embrace of race-neutral racism is applied to the journalistic practice of objectivity. Racialized reporting is considered “fair” through the race-neutral journalistic practice of objectivity that mystifies the Whiteness of the news industry. Neoliberalism, a project of liberalism, creates structural racism that impacts society and the newsroom, where regulatory changes help to vertically integrate the media market. This media oligarchy threatens democratic principles, distorts racial reality, and advances Whiteness and its supremacy. Critical discourse analysis method was used on select, major, U.S. newspapers to reveal ALM’s three discursive strategies: (a) co-optation of Black social justice work; (b) fear of Black power or “blue”/police power; and (c) equating ALM with White power. Theoretical significance reflects that Whiteness as neoliberalism owns all, is all, and flattens all differences. The recommendation for resistance is color-conscious, intersectional journalism.
STAT3-miR-17/20 signalling axis plays a critical role in attenuating myocardial infarction following rapamycin treatment in diabetic mice
Authors: Samidurai Arun , Roh Sean K , Prakash Meeta , Durrant David , Salloum Fadi N , Kukreja Rakesh C , Das Anindita
Published: November 2019

Aims

Deregulation of mTOR (mammalian target of rapamycin) signalling occurs in diabetes, which exacerbates injury following myocardial infarction (MI). We therefore investigated the infarct-limiting effect of chronic treatment with rapamycin (RAPA, mTOR inhibitor) in diabetic mice following myocardial ischaemia/reperfusion (I/R) injury and delineated the potential protective mechanism.

Methods and results

Adult male diabetic (db/db) or wild-type (WT) (C57) mice were treated with RAPA (0.25 mg/kg/day, intraperitoneal) or vehicle (5% DMSO) for 28 days. The hearts from treated mice were subjected to global I/R in Langendorff mode. Cardiomyocytes, isolated from treated mice, were subjected to simulated ischaemia/reoxygenation (SI/RO) to assess necrosis and apoptosis. Myocardial infarct size was increased in diabetic heart following I/R as compared to WT. Likewise, enhanced necrosis and apoptosis were observed in isolated cardiomyocytes of diabetic mice following SI/RO. Treatment with RAPA reduced infarct size as well as cardiomyocyte necrosis and apoptosis of diabetes and WT mice. RAPA increased STAT3 phosphorylation and miRNA-17/20a expression in diabetic hearts. In addition, RAPA restored AKT phosphorylation (target of mTORC2) but suppressed S6 phosphorylation (target of mTORC1) following I/R injury. RAPA-induced cardioprotection against I/R injury as well as the induction of miR-17/20a and AKT phosphorylation were abolished in cardiac-specific STAT3-deficient diabetic mice, without alteration of S6 phosphorylation. The infarct-limiting effect of RAPA was obliterated in cardiac-specific miRNA-17-92-deficient diabetic mice. The post-I/R restoration of phosphorylation of STAT3 and AKT with RAPA were also abolished in miRNA-17-92-deficient diabetic mice. Additionally, RAPA suppressed the pro-apoptotic prolyl hydroxylase (Egln3/PHD3), a target of miRNA-17/20a in diabetic hearts, which was abrogated in miRNA-17-92-deficient diabetic mice.

Conclusion

Induction of STAT3-miRNA-17-92 signalling axis plays a critical role in attenuating MI in RAPA-treated diabetic mice. Our study indicates that chronic treatment with RAPA might be a promising pharmacological intervention for attenuating MI and improving prognosis in diabetic patients.
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
Authors: Czipa Erik , Schiller Mátyás , Nagy Tibor , Kontra Levente , Steiner László , Koller Júlia , Pálné-Szén Orsolya , Barta Endre
Published: November 2019

ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein–protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.
Role of non-PTS dependent glucose permease (GlcU) in maintaining the fitness cost during acquisition of nisin resistance by Enterococcus faecalis
Authors: Kumar Sandeep , Narayan Kapil Singh , Shandilya Shruti , Sood Shiv Kumar , Kapila Suman
Published: November 2019

Nisin is used for food preservation due to its antibacterial activity. However, some bacteria survive under the prevailing conditions owing to the acquisition of resistance. This study aimed to characterize nisin-resistant Enterococcus faecalis isolated from raw buffalo milk and investigate their fitness cost. FE-SEM, biofilm and cytochrome c assay were used for characterization. Growth kinetics, HPLC, qPCR and western blotting were performed to confer their fitness cost. Results revealed that nisin-resistant E. faecalis were morphologically different from sensitive strain and internalize more glucose. However, no significant difference was observed in the growth pattern of the resistant strain compared to that of the sensitive strain. A non-phosphotransferase glucose permease (GlcU) was found to be associated with enhanced glucose uptake. Conversely, Mpt, a major phosphotransferase system responsible for glucose uptake, did not play any role, as confirmed by gene expression studies and western blot analysis of HPr protein. The phosphorylation of His-15 residue of HPr phosphoprotein was reduced, while that of the Ser-46 residue increased with progression in nisin resistance, indicating that it may be involved in the regulation of pathogenicity. In conclusion, resistance imposes a significant fitness cost and GlcU plays a key role in maintaining the fitness cost in nisin-resistant variants.
Playing Analog Games Is Associated With Reduced Declines in Cognitive Function: A 68-Year Longitudinal Cohort Study
Authors: Altschul Drew M , Deary Ian J
Published: November 2019

Objectives

Playing analog games may be associated with better cognitive function but, to date, these studies have not had extensive longitudinal follow-up. Our goal was to examine the association between playing games and change in cognitive function from age 11 to age 70, and from age 70 to 79.

Method

Participants were 1,091 nonclinical, independent, community-dwelling individuals all born in 1936 and residing in Scotland. General cognitive function was assessed at ages 11 and 70, and hierarchical domains were assessed at ages 70, 73, 76, and 79 using a comprehensive cognitive battery of 14 tests. Games playing behaviors were assessed at ages 70 and 76. All models controlled for early life cognitive function, education, social class, sex, activity levels, and health issues. All analyses were preregistered.

Results

Higher frequency of playing games was associated with higher cognitive function at age 70, controlling for age 11 cognitive function, and the majority of this association could not be explained by control variables. Playing more games was also associated with less general cognitive decline from age 70 to age 79, and in particularly, less decline in memory ability. Increased games playing between 70 and 76 was associated with less decline in cognitive speed.

Discussion

Playing games were associated with less relative cognitive decline from age 11 to age 70, and less cognitive decline from age 70 to 79. Controlling for age 11 cognitive function and other confounders, these findings suggest that playing more games is linked to reduced lifetime decline in cognitive function.
Joint estimate of the co-seismic 2011 Tohoku earthquake fault slip and post-seismic viscoelastic relaxation by GRACE data inversion
Authors: Cambiotti G
Published: November 2019

Satellite-derived gravity data offer a novel perspective for understanding the physics of megathrust earthquakes at subduction zones. Nonetheless, their temporal resolution and observational errors make it difficult to discern the different phases of the seismic cycle, as the elastostatic deformation (co-seismic) and the stress relaxation by viscous flow (post-seismic). To overcome these difficulties and to take advantage of the physical constraints on the temporal evolution and on the spatial pattern of the earthquake-induced gravity disturbances, we have jointly estimated the fault slip of the 2011 Tohoku earthquake and the rheological stratification by means of a Bayesian inversion of GRACE data time series and within the framework of spherically symmetric self-gravitating compressible viscoelastic Earth models. This approach, in addition to improve the exploitation of satellite-derived gravity data, allows us (i) to constrain the fault slip taking advantage of information from both the co- and post-seismic signatures and (ii) to investigate the trade-off between the fault slip and the shallow rheological stratification. In this respect, it can be used to improve the modelling of crustal displacements from GPS data, even if their higher accuracy and temporal resolution allow to discriminate well the co-seismic signature from the others.
The Incidence and Prevalence of Anxiety, Depression, and Post-traumatic Stress Disorder in a National Cohort of US Veterans With Inflammatory Bowel Disease
Authors: Thakur Elyse R , Sansgiry Shubhada , Kramer Jennifer R , Waljee Akbar K , Gaidos Jill K , Feagins Linda A , Govani Shail M , Dindo Lilian , El-Serag Hashem B , Hou Jason K
Published: November 2019

Background

Patients with inflammatory bowel disease (IBD) are more susceptible to mental health problems than the general population; however, temporal trends in psychiatric diagnoses’ incidence or prevalence in the United States are lacking. We sought to identify these trends among patients with IBD using national Veterans Heath Administration data.

Methods

We ascertained the presence of anxiety, depression, or posttraumatic stress disorder among veterans with IBD (ulcerative colitis or Crohn’s disease) during fiscal years 2000–2015. Patients with prior anxiety, depression, or posttraumatic stress disorder before their first Veterans Health Administration IBD encounter were excluded to form the study cohort. We calculated annual prevalence, incidence rates, and age standardized and stratified by gender using a direct standardization method.

Results

We identified 60,086 IBD patients (93.9% male). The prevalence of anxiety, depression, and/or posttraumatic stress disorder increased from 10.8 per 100 with IBD in 2001 to 38 per 100 with IBD in 2015; 19,595 (32.6%) patients had a new anxiety, depression, and/or posttraumatic stress disorder diagnosis during the study period. The annual incidence rates of these mental health problems went from 6.1 per 100 with IBD in 2001 to 3.6 per 100 in 2015. This trend was largely driven by decline in depression.

Conclusions

The prevalence of anxiety, depression, and posttraumatic stress disorder is high among US veterans with IBD and increasing, given the chronicity of IBD and psychological diagnoses. Incidence, particularly depression, appears to be declining. Confirmation and reasons for this encouraging trend are needed.
Hatching Asynchrony in Oviraptorid Dinosaurs Sheds Light on Their Unique Nesting Biology
Authors: Yang T -R , Engler T , Lallensack J N , Samathi A , Makowska M , Schillinger B
Published: November 2019

Synopsis

Dinosaur nesting biology has been an intriguing research topic, though dinosaur behaviors were relatively less illuminated because of the constraints of the fossil record. For instance, hatching asynchrony, where eggs in a single clutch hatch at different times, is unique to modern neoavian birds but was also suggested to be present in oviraptorid dinosaurs based on a possible partial clutch of four embryo-containing eggs from Mongolia. Unfortunately, unequivocal evidence for the origination of these eggs from a single clutch is lacking. Here we report a new, better preserved partial oviraptorid clutch with three embryo-containing eggs—a single egg (Egg I) and a pair (Egg II/III)—from the Late Cretaceous Nanxiong Group of Jiangxi Province, China. Geopetal features indicate that the pair of eggs was laid prior to the single egg. Neutron tomographic images in combination with osteological features indicate that the embryo of the single egg is less developed than those of the paired eggs. Eggshell histology suggests that the embryo-induced erosion in the paired eggs is markedly more pronounced than in the single egg, providing a new line of evidence for hatching asynchrony. The inferred hatching asynchrony in combination with previously surmised thermoregulatory incubation and communal nesting behaviors very likely suggests that oviraptorid dinosaurs presented a unique reproductive biology lacking modern analogs, which is contrary to the predominant view that their reproductive biology was intermediate between that of modern crocodiles and birds.
Clinical Management of the Microbiome in Irritable Bowel Syndrome
Authors: Andrews Christopher N , Sidani Sacha , Marshall John K
Published: November 2019

Background

A growing body of evidence suggests that dysbiosis contributes to the onset and symptomatology of irritable bowel syndrome (IBS) and other functional bowel disorders. Changes to the gastrointestinal microbiome may contribute to the underlying pathophysiology of IBS.

Methods

The present review summarizes the potential effects of microbiome changes on GI transit, intestinal barrier function, immune dysregulation and inflammation, gut–brain interactions and neuropsychiatric function.

Results

A multimodal approach to IBS management is recommended in accordance with current Canadian guidelines. Pharmacologic treatments are advised to target the presumed underlying pathophysiological mechanism, such as dysregulation of GI transit, peristalsis, intestinal barrier function and pain signalling. The management plan for IBS may also include treatments directed at dysbiosis, including dietary modification and use of probiotics, which may promote the growth of beneficial bacteria, affect intestinal gas production and modulate the immune response; and the administration of periodic short courses of a nonsystemic antibiotic such as rifaximin, which may re-establish microbiota diversity and improve IBS symptoms.

Conclusion

Dysregulated host–microbiome interactions are complex and the use of microbiome-directed therapies will necessarily be empiric in individual patients. A management algorithm comprising microbiome- and nonmicrobiome-directed therapies is proposed.
Experimental validation of a 2D–3D conversion method for estimation of multiple 3D characteristics of discrete elements
Authors: Ueda Takao
Published: November 2019

Accurate assessment of three-dimensional (3D) characteristics, such as the shape and size distribution, of discrete elements (e.g. particles, granules, grains, voids, crystals, cells and fibers) is required in various fields. But generally, in practice, two-dimensional (2D) instead of 3D assessment is conducted due to limitations in time, cost or measurement technology (as in microscopic observation of discrete elements). In this study, experimental validation was conducted for a 2D–3D conversion method, developed in 2018, which estimates multiple 3D parameters based on 2D counterparts, using an x-ray computed tomography analysis of silica sand. Six 3D parameters (volume, surface area, long-axis length, sphericity and long/middle and long/short axis ratios) were successfully estimated based on five measured 2D parameters (sectional area, perimeter, long-axis length, circularity and long/short axis ratio).
Survey of period variations of superhumps in SU UMa-type dwarf novae. X. The tenth year (2017)
Authors: Kato Taichi , Isogai Keisuke , Wakamatsu Yasuyuki , Hambsch Franz-Josef , Itoh Hiroshi , Tordai Tamás , Vanmunster Tonny , Dubovsky Pavol A , Kudzej Igor , Medulka Tomáš , Kimura Mariko , Ohnishi Ryuhei , Monard Berto , Pavlenko Elena P , Antonyuk Kirill A , Pit Nikolaj V , Antonyuk Oksana I , Babina Julia V , Baklanov Aleksei V , Sosnovskij Aleksei A , Pickard Roger D , Miller Ian , Maeda Yutaka , de Miguel Enrique , Brincat Stephen M , Licchelli Domenico , Cook Lewis M , Shugarov Sergey Yu , Zaostrojnykh Anna M , Chochol Drahomir , Golysheva Polina , Katysheva Natalia , Zubareva Alexandra M , Stone Geoff , Kasai Kiyoshi , Starr Peter , Littlefield Colin , Kiyota Seiichiro , Andreev Maksim V , Sergeev Alexandr V , Ruiz Javier , Myers Gordon , Simon Andrii O , Vasylenko Volodymyr V , Soldán Francisco , Ögmen Yenal , Nakajima Kazuhiro , Nelson Peter , Masi Gianluca , Menzies Kenneth , Sabo Richard , Bolt Greg , Dvorak Shawn , Stanek Krzysztof Z , Shields Joseph V , Kochanek Christopher S , Holoien Thomas W-S , Shappee Benjamin , Prieto José L , Kojima Tadashi , Nishimura Hideo , Kaneko Shizuo , Fujikawa Shigehisa , Stubbings Rod , Muyllaert Eddy , Poyner Gary , Moriyama Masayuki , Maehara Hiroyuki , Schmeer Patrick , Denisenko Denis
Published: November 2019

Continuing the project described by Kato et al. (2009, PASJ, 61, S395), we collected times of superhump maxima for 102 SU UMa-type dwarf novae observed mainly during the 2017 season, and characterized these objects. WZ Sge-type stars identified in this study are PT And, ASASSN-17ei, ASASSN-17el, ASASSN-17es, ASASSN-17fn, ASASSN-17fz, ASASSN-17hw, ASASSN-17kd, ASASSN-17la, PNV J20205397$+$2508145, and TCP J00332502$-$3518565. We obtained new mass ratios for seven objects using growing superhumps (stage A). ASASSN-17gf is an EI Psc-type object below the period minimum. CRTS J080941.3$+$171528 and DDE 51 are objects in the period gap, and both showed a long-lasting phase of stage A superhumps. We also summarize the recent advances in understanding of SU UMa-type and WZ Sge-type dwarf novae.
Understanding Majority Attitudes toward Minority Nations in Multinational Federations: The Case of Canada
Authors: Ferland Benjamin , Turgeon Luc
Published: November 2019

While a relatively large body of literature has explored the conditions that might promote either reform or the status quo in multinational federations, few studies have explored majority attitudes toward minority nations in the context of multinational federations. In this article, we ask what factors account for majority attitudes toward minority nations in multinational federations. In making use of data from the 2011 Canadian election study (CES), we explore both attitudes toward Quebec in general and the willingness to do more for Quebec, which we refer to respectively as “affective attitudes” and “policy attitudes.” Our findings demonstrate the key role played by generalized prejudice and perceptions of how one’s province is treated in the Canadian federation in structuring both sets of attitudes. The impact of Canadian identity, on the other hand, is more limited. Meanwhile, conservative ideological predispositions are a predictor of policy attitudes but not affective attitudes.
THE REAL GRADED BRAUER GROUP
Authors: Karoubi Max , Weibel Charles
Published: November 2019

We introduce a version of the Brauer–Wall group for Real vector bundles of algebras (in the sense of Atiyah) and compare it to the topological analogue of the Witt group. For varieties over the reals, these invariants capture the topological parts of the Brauer–Wall and Witt groups.
Neurological Soft Signs and Brain Network Abnormalities in Schizophrenia
Authors: Kong Li , Herold Christina J , Cheung Eric F C , Chan Raymond C K , Schröder Johannes
Published: November 2019

Neurological soft signs (NSS) are often found in patients with schizophrenia. A wealth of neuroimaging studies have reported that NSS are related to disturbed cortical-subcortical-cerebellar circuitry in schizophrenia. However, the association between NSS and brain network abnormalities in patients with schizophrenia remains unclear. In this study, the graph theoretical approach was used to analyze brain network characteristics based on structural magnetic resonance imaging (MRI) data. NSS were assessed using the Heidelberg scale. We found that there was no significant difference in global network properties between individuals with high and low levels of NSS. Regional network analysis showed that NSS were associated with betweenness centrality involving the inferior orbital frontal cortex, the middle temporal cortex, the hippocampus, the supramarginal cortex, the amygdala, and the cerebellum. Global network analysis also demonstrated that NSS were associated with the distribution of network hubs involving the superior medial frontal cortex, the superior and middle temporal cortices, the postcentral cortex, the amygdala, and the cerebellum. Our findings suggest that NSS are associated with alterations in topological attributes of brain networks corresponding to the cortical-subcortical-cerebellum circuit in patients with schizophrenia, which may provide a new perspective for elucidating the neural basis of NSS in schizophrenia.