bluuebunny/crossref_metadata_2025 huggingface dataset:
Sarcoma Family Kinase-Dependent Pannexin-1 Activation after Cortical Spreading Depression Is Mediated by NR2A-Containing Receptors
Authors: Bu Fan , Nie Lingdi , Quinn John P , Wang Minyan
Published: February 2020

Cortical spreading depression (CSD) is a propagating wave of depolarization followed by depression of cortical activity. CSD triggers neuroinflammation via the pannexin-1 (Panx1) channel opening, which may eventually cause migraine headaches. However, the regulatory mechanism of Panx1 is unknown. This study investigates whether sarcoma family kinases (SFK) are involved in transmitting CSD-induced Panx1 activation, which is mediated by the NR2A-containing N-methyl-D-aspartate receptor. CSD was induced by topical application of K+ to cerebral cortices of rats and mouse brain slices. SFK inhibitor, PP2, or NR2A–receptor antagonist, NVP–AAM077, was perfused into contralateral cerebral ventricles (i.c.v.) of rats prior to CSD induction. Co-immunoprecipitation and Western blot were used for detecting protein interactions, and histofluorescence for addressing Panx1 activation. The results demonstrated that PP2 attenuated CSD-induced Panx1 activation in rat ipsilateral cortices. Cortical susceptibility to CSD was reduced by PP2 in rats and by TAT-Panx308 that disrupts SFK–Panx1 interaction in mouse brain slices. Furthermore, CSD promoted activated SFK coupling with Panx1 in rat ipsilateral cortices. Moreover, inhibition of NR2A by NVP–AAM077 reduced elevation of ipsilateral SFK–Panx1 interaction, Panx1 activation induced by CSD and cortical susceptibility to CSD in rats. These data suggest NR2A-regulated, SFK-dependent Panx1 activity plays an important role in migraine aura pathogenesis.
Blockchain in the Tourism Industry—A Review of the Situation in Croatia and Macedonia
Authors: Erceg Aleksandar , Damoska Sekuloska Jovanka , Kelić Ivan
Published: February 2020

As one of the most interactive economic activities, tourism has improved significantly since the Internet allowed customers (travelers) to look for and create their trips without the need to go to a travel agency. Through the development of Internet marketing, tourists are able to receive information in real-time and view them on the screens of their devices (computers, laptops, mobile phones or tablets), and consequently they can create their own content and share it with others. Due to this development, we are witnessing a new phenomenon, so-called app capitalism, in which companies like Uber and Airbnb make money on services and goods they do not own and finding new business models in the tourism sector which enable customer-to-customer models. To be able to respond to these changes, the tourism industry needs to bring together knowledge, money, and technology for the purpose of creating new business models. The development of technology in all social spheres, including tourism, has provided a strong tool for consumers in terms of both acquiring and disclosing information to others. One of the rapidly growing technologies which is also one of the cutting-edge technologies entering tourism is blockchain. Blockchain technology captured worldwide attention in 2017 and its implementation has been revolutionizing various industries (e.g., retail, healthcare, tourism). The aim of this paper is to analyze the potential of the tourism industry in terms of blockchain implementation. Blockchain technology provides significant benefits to the tourism industry since its implementation can help increase competitive advantage, improve customer satisfaction and enhance performance. In this paper, the authors present the current situation in the Republic of Croatia and the Republic of Macedonia regarding the use of blockchain technology in the tourism industry. The main findings of this paper comprise the detection of key areas regarding why blockchain technology is not implemented in the tourist industry, and what processes should be handled. By presenting a case study of the implementation of blockchain technology in tourism, the authors analyze the potential of using blockchain technology in the tourism industry and discuss topics for further research.
Severe Weather-Induced Exchange Flows through a Narrow Tidal Channel of Calcasieu Lake Estuary
Authors: Wang Jie , Li Chunyan , Xu Fumin , Huang Wei
Published: February 2020

Exchange flows between estuaries and the coastal ocean are important for land-ocean interactions and ecosystem health. This study is aimed at resolving severe weather-induced exchange flows between the Calcasieu Lake Estuary and Gulf of Mexico. For that purpose, we use data from a long-term deployment of side-looking acoustic Doppler current profilers (ADCPs) and conductivity-temperature-depth sensors (CTDs) as well as flow velocity data from a boat operated survey. Regression between the transport measured from a boat mounted ADCP and the velocity data from a fixed side-looking ADCP is done to calculate a long-term transport along the Calcasieu Pass. Analyses have been done for the hydrodynamic response to 16 cold fronts passing the study area. Effects of six strongest cold fronts are discussed in more detail. Results have confirmed that the hydrodynamics is highly correlated with the frequent cold fronts. The highest correlation coefficient is r ~0.75 between the north wind and along channel transport. In general, winds from the southern quadrants push water into the estuary before each frontal passage; after the passage of the front, a rapid change of wind direction to the northern quadrants produces strong outward flows. A quasi-steady state balance between the wind stress and water level difference proposed in recent studies for different systems is further confirmed and discussed in this system. The quasi-steady state balance leads to a relatively high R2 value of greater than 0.8 between the modeled water level gradient and actual observed gradient. We have also applied a regression model, derived from the momentum balance requirement, for the subtidal exchange flow as a function of wind components and their squares which yield an R2 value greater than 0.7. With a confidence in the regression model, we further implement it for twelve years from 26 February 2007 to 10 April 2019. Four extreme events during this 12-year period of time are discussed–they include the Hurricane Ike (2008), Tropical Storm Lee (2011), a warm front, and a cold front. This hindcast of the exchange flows over multiple years can provide a useful tool for coastal management and research for estuarine channels where continuous observations of velocity are not always available.
Prediction of Unsteady Developed Tip Vortex Cavitation and Its Effect on the Induced Hull Pressures
Authors: Kim Seungnam , Kinnas Spyros A.
Published: February 2020

Reducing the on-board noise and fluctuating pressures on the ship hull has been challenging and represent added value research tasks in the maritime industry. Among the possible sources for the unpalatable vibrations on the hull, propeller-induced pressures have been one of the main causes due to the inherent rotational motion of propeller and its proximity to the hull. In previous work, a boundary element method, which solves for the diffraction potentials on the ship hull due to the propeller, has been used to determine the propeller induced hull pressures. The flow around the propeller was evaluated via a panel method which solves in time for the propeller loading, trailing wake, and the sheet cavities. In this article, the propeller panel method is extended so that it also solves for the shape of developed tip vortex cavities, the effects of which are also included in the evaluation of the hull pressures. The employed unsteady wake alignment scheme is first applied, in the absence of cavitation, to investigate the propeller performance in non-axisymmetric inflow, such as the inclined-shaft flow or the flow behind an upstream body. In the latter case, the propeller panel method is coupled with a Reynolds-Averaged Navier–Stokes (RANS) solver to determine the effective wake at the propeller plane. The results, including the propeller induced hull pressures, are compared with those measured in the experiments as well as with those from RANS, where the propeller is also simulated as a solid boundary. Then the methods are applied in the cases where partial cavities and developed tip vortex cavities coexist. The predicted cavity patterns, the developed tip vortex trajectories, and the propeller-induced hull pressures are compared with those measured in the experiments.
Collision Prevention Algorithm for Fishing Vessels Using mmWAVE Communication
Authors: Lee Myoung-Ki , Park Young-Soo
Published: February 2020

This study leveraged the millimeter wireless access in vehicular environments (mmWAVE) communication technology to reflect the maneuvering characteristics of small fishing vessels and constructed a collision prevention algorithm that can be applied relatively easily. The algorithm was verified through simulation and actual ship experiments. The algorithm had four components: detection of vessels within three miles; identification of dangerous vessels by applying the time to the closest point of approach (TCPA) and distance at the closest point of approach (DCPA) criteria; continuous monitoring of maritime traffic risk; and incremental alarm signaling. The simulations and experiments confirmed that the alarm was generated incrementally in accordance with the distance to a dangerous situation, with no false alarms. Thus, the proposed algorithm offers potential to enhance the safety of small fishing vessels.
Cysteine Dioxygenase Enzyme Activity and Gene Expression in the Dimorphic Pathogenic Fungus Histoplasma capsulatum Is in both the Mold and Yeast Morphotypes and Exhibits Substantial Strain Variation
Authors: Adams Melissa A. , Shearer Glenmore
Published: February 2020

In the dimorphism (mold/yeast) Histoplasma capsulatum (Hc) literature are reports that yeast (the so-called pathogenic form) uniquely expresses a cysteine dioxygenase (CDO, approx. 10,500 dal) activity which the mold morphotype (the so-called saprophytic soil form) does not express (C.F., Kumar et al., Biochem 22, 762, 1983). This yeast-specific CDO activity is postulated to play a critical role in the mold-to-yeast shift. A number of years ago, our lab isolated the gene encoding the Hc cysteine dioxygenase (CDO1, Genbank accession AY804144) and noted significant expression in the mold morphotype of several Histoplasma strains and also determined that the predicted protein would be over double the 10,500 dal reported by Kumar et al. Our report demonstrates (in the class 1 Downs strain, the class 2 G271B strain and two Panamanian strains, 184AS and 186AS) that the CDO1 gene is expressed in both the mold and yeast morphotypes and both morphotypes show significant CDO activity. Furthermore, we show via a FLAG-tag analysis that the expressed protein is approximately 24.7 ± 2.4 kd, in agreement with the putative protein sequence (determined from cDNA sequence) which yields 23.8 kd and is consistent with most other eukaryotic CDO enzymes. Additionally, we demonstrate that intracellular cysteine levels are actually significantly higher in the mold form of the two Panamanian strains, 184AS and 186AS, equal in both mold and yeast in the class 1 Downs strain and significantly higher in yeast of the more pathogenic class 2 G217B strain.
A Principal Component-Guided Sparse Regression Approach for the Determination of Bitcoin Returns
Authors: Panagiotidis Theodore , Stengos Thanasis , Vravosinos Orestis
Published: February 2020

We examine the significance of fourty-one potential covariates of bitcoin returns for the period 2010–2018 (2872 daily observations). The recently introduced principal component-guided sparse regression is employed. We reveal that economic policy uncertainty and stock market volatility are among the most important variables for bitcoin. We also trace strong evidence of bubbly bitcoin behavior in the 2017–2018 period.
Crop Boom as a Trigger of Smallholder Livelihood and Land Use Transformations: The Case of Coffee Production in the Northern Mountain Region of Vietnam
Authors: Nghiem Tuyen , Kono Yasuyuki , Leisz Stephen J.
Published: February 2020

Coffee is considered a boom crop in Southeast Asia. However, while it bears typical boom crop characteristics in many places where it has been grown, in other places it has contributed to agrarian transformation. This paper examines the context of coffee development in the Northwestern Mountain Region of Vietnam and describes how smallholder coffee growing has triggered an agricultural transition process, and corresponding land use changes, from subsistence-based to commercialized agriculture production. The research was conducted in a commune located in Son La province. Interviews with 46 selected households and three focus group discussions (10–15 people each) were conducted to understand changes in crop systems, corresponding land use, and labor use, due to the adoption of coffee (the boom crop). The research found that coffee has replaced swidden crops and enables a multicrop system, with less land devoted to swidden land use. The income from coffee is used to hire labor and to pay for the inputs needed to mechanize rice farming. The research findings show that the coffee boom has brought about livelihood transformation, changed land use, and transformed local livelihoods from subsistence to production for the market.
On the Zeros of the Big q-Bessel Functions and Applications
Authors: Bouzeffour Fethi , Ben Mansour Hanene , Garayev Mubariz
Published: February 2020

This paper deals with the study of the zeros of the big q-Bessel functions. In particular, we prove new orthogonality relations for functions which are similar to the one for the classical Bessel functions. Also we give some applications related to the sampling theory.
A Machine Learning Approach to Forecast Economic Recessions—An Italian Case Study
Authors: Cicceri Giovanni , Inserra Giuseppe , Limosani Michele
Published: February 2020

In economic activity, recessions represent a period of failure in Gross Domestic Product (GDP) and usually are presented as episodic and non-linear. For this reason, they are difficult to predict and appear as one of the main problems in macroeconomics forecasts. A classic example turns out to be the great recession that occurred between 2008 and 2009 that was not predicted. In this paper, the goal is to give a different, although complementary, approach concerning the classical econometric techniques, and to show how Machine Learning (ML) techniques may improve short-term forecasting accuracy. As a case study, we use Italian data on GDP and a few related variables. In particular, we evaluate the goodness of fit of the forecasting proposed model in a case study of the Italian GDP. The algorithm is trained on Italian macroeconomic variables over the period 1995:Q1-2019:Q2. We also compare the results using the same dataset through Classic Linear Regression Model. As a result, both statistical and ML approaches are able to predict economic downturns but higher accuracy is obtained using Nonlinear Autoregressive with exogenous variables (NARX) model.
COSMO-RS Based Prediction for Alpha-Linolenic Acid (ALA) Extraction from Microalgae Biomass Using Room Temperature Ionic Liquids (RTILs)
Authors: Rezaei Motlagh Shiva , Harun Razif , Awang Biak Dayang Radiah , Hussain Siti Aslina , Omar Rozita , Elgharbawy Amal A.
Published: February 2020

One of the essential fatty acids with therapeutic impacts on human health is known to be omega-3 polyunsaturated fatty acids (PUFA). More lately, ionic liquids (ILs) have received significant attention among scientists in overcoming the disadvantages of traditional solvents in biomass lipid extraction. However, the large pool of cations and anions possibly accessible will lead to a growing number of innovatively synthesized ILs. Nevertheless, the exhaustive measurement of all these systems is economically impractical. The conductive screening model for real solvents (COSMO-RS) is considered a precious approach with the availability of a few models to predict the characteristics of ILs. This work introduces the estimate of capacity values at infinite dilution for a range of ILs using COSMO-RS software as part of solid-liquid extraction. This favorable outcome presented that the capacity values of the IL molecules are extremely dependent on both anions and cations. Among the 352 combinations of cation/anion tested, short alkyl chain cations coupled with inorganic anions were found to be most efficient and therefore superior in the extraction method. Sulphate-, chloride-, and bromide-based ILs were found to have higher extraction capacities in contrast with the remainders, while propanoate revealed an extraordinary capacity when combined with ethyl-based cations. Eventually, the predicted results from COSMO-RS were validated through the experimentally calculated extraction yield of alpha-linolenic acid (ALA) compound from Nannochloropsis sp. microalgae. Three selected ILs namely [EMIM][Cl], [TMAm][Cl], and [EMPyrro][Br] were selected from COSMO-RS for empirical extraction purpose and the validation results pinpointed the good prediction capability of COSMO-RS.
Identification of Prostaglandin Pathway in Dinoflagellates by Transcriptome Data Mining
Authors: Di Dato Valeria , Ianora Adrianna , Romano Giovanna
Published: February 2020

Dinoflagellates, a major class of marine eukaryote microalgae composing the phytoplankton, are widely recognised as producers of a large variety of toxic molecules, particularly neurotoxins, which can also act as potent bioactive pharmacological mediators. In addition, similarly to other microalgae, they are also good producers of polyunsaturated fatty acids (PUFAs), important precursors of key molecules involved in cell physiology. Among PUFA derivatives are the prostaglandins (Pgs), important physiological mediators in several physiological and pathological processes in humans, also used as “biological” drugs. Their synthesis is very expensive because of the elevated number of reaction steps required, thus the search for new Pgs production methods is of great relevance. One possibility is their extraction from microorganisms (e.g., diatoms), which have been proved to produce the same Pgs as humans. In the present study, we took advantage of the available transcriptomes for dinoflagellates in the iMicrobe database to search for the Pgs biosynthetic pathway using a bioinformatic approach. Here we show that dinoflagellates express nine Pg-metabolism related enzymes involved in both Pgs synthesis and reduction. Not all of the enzymes were expressed simultaneously in all the species analysed and their expression was influenced by culturing conditions, especially salinity of the growth medium. These results confirm the existence of a biosynthetic pathway for these important molecules in unicellular microalgae other than diatoms, suggesting a broad diffusion and conservation of the Pgs pathway, which further strengthen their importance in living organisms.
25th International Symposium on Infections in the Critically Ill Patient
Authors: Artigas Antonio , Carlet Jean , Ferrer Ricard , Niederman Michael , Torres Antoni
Published: February 2020

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Characteristics and Formation Tendency of Freckle Segregation in Electroslag Remelted Bearing Steel
Authors: Yan Wei , Zhang Yang , Chen Weiqing , Li Jing
Published: February 2020

Undesirable macro segregation defects, freckles, restrict the commercial production of large-sized electroslag remelting (ESR) bearing steel ingots through degradation of the mechanical properties and service lifetime. In order to clarify the freckle characteristics and formation tendency as well as the formation mechanism, freckles from an industrial large-sized GCr15SiMn ESR ingot were investigated through structural and compositional analysis, along with simulation calculation. The results show that freckles consist of (Si, Mn, Cr)-enriched equiaxed grains and occur in about the 1/2 radius region at the middle-upper part of the ESR ingot, where the secondary dendritic arm spacing (SDAS) and solidification front angle are large but cooling rate is small. The absolute value of relative Rayleigh number, Ra, also reaches its maximum in the 1/2 radius region, with a liquid fraction of 0.3–0.5, corresponding to the region where freckles form. Based on the experimental and simulation results, to evaluate the freckle formation in industrial-scale GCr15SiMn ESR ingots, the threshold value of relative Ra, a freckle criterion considering the compositional and thermal effects, was determined to be about −0.023.
High-Temperature Nano-Indentation Creep Behavior of Multi-Principal Element Alloys under Static and Dynamic Loads
Authors: Sadeghilaridjani Maryam , Mukherjee Sundeep
Published: February 2020

Creep is a serious concern reducing the efficiency and service life of components in various structural applications. Multi-principal element alloys are attractive as a new generation of structural materials due to their desirable elevated temperature mechanical properties. Here, time-dependent plastic deformation behavior of two multi-principal element alloys, CoCrNi and CoCrFeMnNi, was investigated using nano-indentation technique over the temperature range of 298 K to 573 K under static and dynamic loads with applied load up to 1000 mN. The stress exponent was determined to be in the range of 15 to 135 indicating dislocation creep as the dominant mechanism. The activation volume was ~25b3 for both CoCrNi and CoCrFeMnNi alloys, which is in the range indicating dislocation glide. The stress exponent increased with increasing indentation depth due to higher density and entanglement of dislocations, and decreased with increasing temperature owing to thermally activated dislocations. The results for the two multi-principal element alloys were compared with pure Ni. CoCrNi showed the smallest creep displacement and the highest activation energy among the three systems studied indicating its superior creep resistance.
Light Gradient-Based Screening of Arabidopsis thaliana on a 384-Well Type Plant Array Chip
Authors: Park Youn-Hee , Park Je-Kyun
Published: February 2020

Arabidopsis thaliana (Arabidopsis), as a model for plant research, is widely used for various aspects of plant science. To provide a more sophisticated and microscopic environment for the germination and growth of Arabidopsis, we report a 384-well type plant array chip in which each Arabidopsis seed is independently seeded in a solid medium. The plant array chip is made of a poly(methyl methacrylate) (PMMA) acrylic material and is assembled with a home-made light gradient module to investigate the light effects that significantly affect the germination and growth of Arabidopsis. The light gradient module was used to observe the growth pattern of seedlings according to the intensity of the white light and to efficiently screen for the influence of the white light. To investigate the response to red light (600 nm), which stimulates seed germination, the light gradient module was also applied to the germination test. As a result, the germination results showed that the plant array chip can be used to simultaneously screen wild type seeds and phytochrome B mutant seeds on a single array chip according to the eight red light intensities.
Reply to Comment on “Enumeration of Escherichia coli in Probiotic Products. Microorganisms 2019, 7, 437”
Authors: Zimmer Camille , Dorea Caetano C.
Published: February 2020

We thank Wassenaar and colleagues for their Comment on our recent paper [...]
Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
Authors: Costa Ohana Y.A. , Zerillo Marcelo M. , Zühlke Daniela , Kielak Anna M. , Pijl Agata , Riedel Katharina , Kuramae Eiko E.
Published: February 2020

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin–antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
Detection Methods for Aflatoxin M1 in Dairy Products
Authors: Vaz Andreia , Cabral Silva Ana C. , Rodrigues Paula , Venâncio Armando
Published: February 2020

Mycotoxins are toxic compounds produced mainly by fungi of the genera Aspergillus, Fusarium and Penicillium. In the food chain, the original mycotoxin may be transformed in other toxic compounds, reaching the consumer. A good example is the occurrence of aflatoxin M1 (AFM1) in dairy products, which is due to the presence of aflatoxin B1 (AFB1) in the animal feed. Thus, milk-based foods, such as cheese and yogurts, may be contaminated with this toxin, which, although less toxic than AFB1, also exhibits hepatotoxic and carcinogenic effects and is relatively stable during pasteurization, storage and processing. For this reason, the establishment of allowed maximum limits in dairy products and the development of methodologies for its detection and quantification are of extreme importance. There are several methods for the detection of AFM1 in dairy products. Usually, the analytical procedures go through the following stages: sampling, extraction, clean-up, determination and quantification. For the extraction stage, the use of organic solvents (as acetonitrile and methanol) is still the most common, but recent advances include the use of the Quick, Easy, Cheap, Effective, Rugged, and Safe method (QuEChERS) and proteolytic enzymes, which have been demonstrated to be good alternatives. For the clean-up stage, the high selectivity of immunoaffinity columns is still a good option, but alternative and cheaper techniques are becoming more competitive. Regarding quantification of the toxin, screening strategies include the use of the enzyme-linked immunosorbent assay (ELISA) to select presumptive positive samples from a wider range of samples, and more reliable methods—high performance liquid chromatography with fluorescence detection or mass spectroscopy—for the separation, identification and quantification of the toxin.
Interactions between Magnaporthiopsis maydis and Macrophomina phaseolina, the Causes of Wilt Diseases in Maize and Cotton
Authors: Degani Ofir , Dor Shlomit , Abraham Dekel , Cohen Roni
Published: February 2020

Fungal pathogens are a significant threat to crops worldwide. The soil fungus, Magnaporthiopsis maydis, severely affects sensitive maize hybrids by causing the rapid wilting of plants at the maturity stage. Similarly, the soil fungus, Macrophomina phaseolina, develops in a variety of host plants, which leads to rot and plant mortality. The presence of both pathogens together in diseased cotton plants in Israel suggests possible interactions between them. Here, these relationships were tested in a series of experiments accompanied by real-time PCR tracking in maize and cotton. Despite the fact that neither of the pathogens was superior in a growth plate confrontation assay, their co-inoculum had a significant influence under field conditions. In maize sprouts and fully matured plants, infection by both pathogens (compared to inoculation with each of them alone) led to lesser amounts of M. maydis DNA but to increased amounts of M. phaseolina DNA levels. These results were obtained under a restricted water regime, while optimal water irrigation led to less pronounced differences. In water-stressed cotton sprouts, infection with both pathogens led to an increase in DNA amounts of each of the pathogens. Whereas the M. maydis DNA levels in the double infection remain high at the end of the season, a reduction in the amount of M. phaseolina DNA was observed. The double infection caused an increase in growth parameters in maize and cotton and decreased levels of dehydration in maize plants accompanied by an increase in yield production. Dehydration symptoms were minor in cotton under an optimal water supply. However, under a restricted water regime, the double infection abolished the harmful effect of M. phaseolina on the plants’ development and yield. These findings are the first report of interactions between these two pathogens in maize and cotton, and they encourage expanding the study to additional plant hosts and examining the potential involvement of other pathogens.
The Helicobacter pylori HspR-Modulator CbpA Is a Multifunctional Heat-Shock Protein
Authors: Pepe Simona , Scarlato Vincenzo , Roncarati Davide
Published: February 2020

The medically important human pathogen Helicobacter pylori relies on a collection of highly conserved heat-shock and chaperone proteins to preserve the integrity of cellular polypeptides and to control their homeostasis in response to external stress and changing environmental conditions. Among this set of chaperones, the CbpA protein has been shown to play a regulatory role in heat-shock gene regulation by directly interacting with the master stress-responsive repressor HspR. Apart from this regulatory role, little is known so far about CbpA functional activities. Using biochemistry and molecular biology approaches, we have started the in vitro functional characterization of H. pylori CbpA. Specifically, we show that CbpA is a multifunctional protein, being able to bind DNA and to stimulate the ATPase activity of the major chaperone DnaK. In addition, we report a preliminary observation suggesting that CbpA DNA-binding activity can be affected by the direct interaction with the heat-shock master repressor HspR, supporting the hypothesis of a reciprocal crosstalk between these two proteins. Thus, our work defines novel functions for H. pylori CbpA and stimulates further studies aimed at the comprehension of the complex regulatory interplay among chaperones and heat-shock transcriptional regulators.
Recovery of Copper from Leached Tailing Solutions by Biosorption
Authors: Cortés Sonia , Soto Elizabeth E. , Ordóñez Javier I.
Published: February 2020

Due to the progressive fall of the ore grades and the increasingly refractory composition of minerals, concentrating plants have increased which has led to an increase in the generation of tailings. Tailings, especially those obtained in the past, have remaining copper and other valuable species in quantities that can potentially be recovered, such as gold, silver, vanadium, and rare earth elements which transforms this abundant waste into a potential source of precious or strategic metals for secondary mining. One of the techniques of solid–liquid separation that processes solutions with low concentrations of metals corresponds to adsorption, and more recently biosorption, which is based on the use of biological matrices that do not constitute an environmental liability after application. Biosorption occurs as a consequence of the wide variety of active functional groups present in different types of biomass. Bacterial, fungal, plant, and algal biomasses have been described as biosorbents, mainly for the treatment of diluted and simple solutions. This work aims to recover copper from leached tailings using biomass of the red algae Gracilaria chilensis as a biosorbent. The tailing samples were taken from an abandoned deposit, in the north of Chile, and after an acid leaching copper was biosorbed, kinetics of adsorption and the equilibrium isotherms were studied, applying the Freundlich and Langmuir models. Operational parameters such as adsorbent dose, pH, and initial metal concentration were studied.
The Birth of Mineral Physics at the ANU in the 1970s
Authors: Liebermann Robert Cooper
Published: February 2020

In 1970, I established the first mineral physics laboratory in Australia at the Australian National University (ANU) under the auspices of A.E. (Ted) Ringwood. Over the next six years, we published 25 research papers in peer-reviewed journals, many of them in collaboration with graduate students, Ian Jackson and Leonie Jones. This research was focused on measurements of sound velocities in minerals (and their structural analogues) at high pressures and temperatures, as well as studies of melting and elastic shear instabilities in materials and applications of these experimental data to interpreting seismic models of the Earth’s interior.
Development of a Stress Sensor for In-Situ High-Pressure Deformation Experiments Using Radial X-Ray Diffraction
Authors: Girard Jennifer , Silber Reynold E. , Mohiuddin Anwar , Chen Haiyan , Karato Shun-ichiro
Published: February 2020

We developed a stress sensor for in-situ deformation experiments using synchrotron radial X-ray diffraction. This stress sensor provided nearly diffraction-plane-independent stress that, when used in series with a sample, reduced the uncertainty of the average stress estimation acting on a sample. Here, we present the results of a study where pyrope was used as a stress sensor. Using a Deformation-DIA (D-DIA) high-pressure deformation apparatus, pyrope, olivine and alumina were deformed in the same run/cell assembly placed in series along the compression direction. Deformation experiments were conducted at pressures between 4 and 5 GPa and temperatures between 730 and 1273 K with strain-rates between 10−5 and 10−6 s−1. Stresses estimated from various (hkl) planes in pyrope were nearly the same; i.e., pyrope is plastically isotropic with ≤10 % variation with (hkl). However, stresses from various (hkl) planes in olivine and alumina varied by approximately a factor of 3. Comparisons between average stresses inferred from pyrope and those from different diffraction planes in olivine and alumina showed that the average stress in these materials evolved from low-end stress, estimated from various (hkl) planes at small strain, to high-end stress at a large strain. This suggests that the rate-controlling slip system in these materials changes from the soft to the hard slip system with strain.
Stability of Cu-Sulfides in Submarine Tailing Disposals: A Case Study from Repparfjorden, Northern Norway
Authors: Mun Yulia , Strmić Palinkaš Sabina , Forwick Matthias , Junttila Juho , Pedersen Kristine Bondo , Sternal Beata , Neufeld Kai , Tibljaš Darko , Kullerud Kåre
Published: February 2020

Mine tailings that were produced during the exploitation of the Ulveryggen siliciclastic sediment-hosted Cu deposit in northern Norway were disposed into the inner part of Repparfjorden from 1972 to 1978/1979. This study focuses on the mineralogy and geochemistry of the submarine mine tailings and underlying natural marine sediments from the inner part of Repparfjorden, as well as on the primary Ulveryggen ore. The ore mineralization from the neighboring Nussir carbonate sediment-hosted Cu deposit was studied too, due to the forthcoming mining of both deposits. Bornite and chalcopyrite are the major Cu-sulfides, and are characterized by low concentrations of potentially toxic elements including Cd, Hg, and As. The tailing material occupies the uppermost 9 cm of Repparfjorden sediments. It is characterized by predomination of a silty component with elevated Cu (up to 747.7 ppm), Ni (up to 87 ppm), and Cr (up to 417 ppm) concentrations. The high Cu concentration is related to the deposition of mine tailings. In contrast, Ni and Cr concentrations are close to those in naturally occurring stream sediments from the feeding river, Repparfjordelva, reflecting the compatibility of these elements with hosting mafic volcanics, which are widely spread in the Repparfjord Tectonic Window. Copper in the uppermost part of the sediments is bound to the acid-soluble fraction while Ni and Cr are bound to the residual fraction. Artificial placement of large masses of fine-grained material, i.e., smothering, resulted in a diminished biological activity and/or physical distortion of mostly benthic fauna, which was reflected in total organic carbon (TOC) values as low as 0.15% in the uppermost strata. Sulfide minerals are found both in natural marine sediments and in the mine tailings. They are generally well-preserved with an exception for chalcopyrite from the uppermost part of the submarine tailing, which shows signs of incipient weathering. Thermodynamic modeling confirmed that redox potential and pH are important factors in the weathering of sulfides. Available ligands contribute to the Cu speciation. In near-neutral to slightly alkaline conditions a presence of carbonates can lead to the mobilization of Cu in form of CuCO3 complexes.
Association between the Degree of Processing of Consumed Foods and Sleep Quality in Adolescents
Authors: Sousa Raíssa da Silva , Bragança Maylla Luanna Barbosa Martins , Oliveira Bianca Rodrigues de , Coelho Carla Cristine Nascimento da Silva , Silva Antônio Augusto Moura da
Published: February 2020

The aim of this study was to evaluate the association between food consumption by the degree of processing and sleep quality in adolescents from São Luís, Maranhão, Brazil. A cross-sectional study with 2499 adolescents (aged 18 to 19 years) was developed. Exposure variables included energy contributions of food groups stratified by the NOVA classification: fresh or minimally processed foods (FMPF), processed foods (PF), and ultra-processed foods (UPF), categorized into quartiles. The outcome variable was sleep quality assessed with the Pittsburgh Sleep Quality Index. Associations between these variables were estimated by Poisson regression, with robust estimation of variance. Most of the adolescents had poor sleep quality (57.1%). There were associations between FMPF in the third (57.1%–66.0% of total calories; prevalence ratio PR = 0.88; 95% CI: 0.80, 0.97) and fourth quartile (66.1%–95.8% of total calories; PR = 0.87; 95% CI: 0.78, 0.96) and lower prevalence of poor sleep quality. The fourth quartile of UPF (44.3%–81.8% of total calories; PR = 1.14; 95% CI: 1.03, 1.27) was associated with a higher prevalence of poor sleep quality. Higher intake of FMPF is a protective factor for poor sleep quality, whereas higher UPF consumption is a risk factor for poor sleep quality.
Effects of Maternal Dietary Patterns during Pregnancy on Early Childhood Growth Trajectories and Obesity Risk: The CANDLE Study
Authors: Hu Zunsong , Tylavsky Frances A. , Kocak Mehmet , Fowke Jay H. , Han Joan C. , Davis Robert L. , LeWinn Kaja Z. , Bush Nicole R. , Sathyanarayana Sheela , Karr Catherine J. , Zhao Qi
Published: February 2020

We investigated the associations between maternal dietary patterns during pregnancy and early childhood growth trajectories and overweight/obesity risk in offspring. Maternal diet was assessed using a food frequency questionnaire during the second trimester, and dietary patterns were derived by reduced rank regression. The associations between maternal dietary pattern scores and body mass index (BMI) trajectories from birth to age four (rising-high, moderate, and low BMI trajectories) as well as overweight/obesity risk at age four were analyzed (n = 1257). Two maternal dietary patterns were identified. The fast food pattern included a higher intake of fried chicken and fish, fruit juices, mayonnaise, and sugar-sweetened beverages, while the processed food pattern included a higher intake of dairy, salad dressing, processed meat, and cold breakfast cereal. Women with greater adherence to the fast food pattern were more likely to have children in the rising-high BMI trajectory group [OR (95% CI) = 1.32 (1.07–1.62); p = 0.008] or having overweight/obesity at age four [OR (95% CI) = 1.31 (1.11–1.54); p = 0.001]. The processed food pattern was not associated with these outcomes. The maternal dietary pattern during pregnancy represented by fried foods and sugar-sweetened beverages may contribute to rapid early childhood growth and increased risk for obesity in offspring.
Enhanced GIP Secretion in Obesity Is Associated with Biochemical Alteration and miRNA Contribution to the Development of Liver Steatosis
Authors: Góralska Joanna , Raźny Urszula , Polus Anna , Dziewońska Agnieszka , Gruca Anna , Zdzienicka Anna , Dembińska-Kieć Aldona , Solnica Bogdan , Micek Agnieszka , Kapusta Maria , Słowińska-Solnica Krystyna , Malczewska-Malec Małgorzata
Published: February 2020

Nutrient excess enhances glucose-dependent insulinotropic polypeptide (GIP) secretion, which may in turn contribute to the development of liver steatosis. We hypothesized that elevated GIP levels in obesity may affect markers of liver injury through microRNAs. The study involved 128 subjects (body mass index (BMI) 25–40). Fasting and postprandial GIP, glucose, insulin, and lipids, as well as fasting alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), cytokeratin-18, fibroblast growth factor (FGF)-19, and FGF-21 were determined. TaqMan low density array was used for quantitative analysis of blood microRNAs. Fasting GIP was associated with ALT [β = 0.16 (confidence interval (CI): 0.01–0.32)], triglycerides [β = 0.21 (95% CI: 0.06–0.36], and FGF-21 [β = 0.20 (95%CI: 0.03–0.37)]; and postprandial GIP with GGT [β = 0.17 (95%CI: 0.03–0.32)]. The odds ratio for elevated fatty liver index (>73%) was 2.42 (95%CI: 1.02–5.72) for high GIP versus low GIP patients. The miRNAs profile related to a high GIP plasma level included upregulated miR-136-5p, miR-320a, miR-483-5p, miR-520d-5p, miR-520b, miR-30e-3p, and miR-571. Analysis of the interactions of these microRNAs with gene expression pathways suggests their potential contribution to the regulation of the activity of genes associated with insulin resistance, fatty acids metabolism, and adipocytokines signaling. Exaggerated fasting and postprandial secretion of GIP in obesity are associated with elevated liver damage markers as well as FGF-21 plasma levels. Differentially expressed microRNAs suggest additional, epigenetic factors contributing to the gut–liver cross-talk.
Animal Models for Gammaherpesvirus Infections: Recent Development in the Analysis of Virus-Induced Pathogenesis
Authors: Fujiwara Shigeyoshi , Nakamura Hiroyuki
Published: February 2020

Epstein–Barr virus (EBV) is involved in the pathogenesis of various lymphomas and carcinomas, whereas Kaposi’s sarcoma-associated herpesvirus (KSHV) participates in the pathogenesis of endothelial sarcoma and lymphomas. EBV and KSHV are responsible for 120,000 and 44,000 annual new cases of cancer, respectively. Despite this clinical importance, no chemotherapies or vaccines have been developed for virus-specific treatment and prevention of these viruses. Humans are the only natural host for both EBV and KSHV, and only a limited species of laboratory animals are susceptible to their experimental infection; this strict host tropism has hampered the development of their animal models and thereby impeded the study of therapeutic and prophylactic strategies. To overcome this difficulty, three main approaches have been used to develop animal models for human gammaherpesvirus infections. The first is experimental infection of laboratory animals with EBV or KSHV. New-world non-human primates (NHPs) and rabbits have been mainly used in this approach. The second is experimental infection of laboratory animals with their own inherent gammaherpesviruses. NHPs and mice have been mainly used here. The third, a recent trend, employs experimental infection of EBV or KSHV or both to immunodeficient mice reconstituted with human immune system components (humanized mice). This review will discuss how these three approaches have been used to reproduce human clinical conditions associated with gammaherpesviruses and to analyze the mechanisms of their pathogenesis.
The Samaritan and Jewish Versions of the Pentateuch: A Survey
Authors: Hjelm Ingrid
Published: February 2020

This article discusses the main differences between the Samaritan and the Jewish versions of the Pentateuch. The Samaritan Bible consists of the Torah—that is, the Five Books of Moses—also called the Samaritan Pentateuch (SP). The Jewish Bible contains in addition the Prophets and the Writings, a total of 39 books. The introduction seeks to present both traditions in their own right and in relation to other ancient textual traditions (the Dead Sea Scrolls, the ancient Greek and Latin, and the Septuagint). The focus of this article is on the shared tradition of the Pentateuch with special emphasis on the textual and theological character of the Samaritan Pentateuch: major variants in the SP, the Moses Layer, and the cult place. This article closes with discussion of editions and translations of the Samaritan Bible and the Masoretic Bible respectively.
Announcement for “Separations 2019 Outstanding Reviewer Award” Winner
Authors:   Separations Editorial Office
Published: February 2020

Peer review is an essential part of the publication process, ensuring that Separations maintains high quality standards for its published papers [...]
Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules
Authors: Xu Jingzhi , Li Xiaobo , Kang Guangbo , Bai Liang , Wang Ping , Huang He
Published: February 2020

A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.
Quantitative FRET-FLIM-BlaM to Assess the Extent of HIV-1 Fusion in Live Cells
Authors: Carlon-Andres Irene , Padilla-Parra Sergi
Published: February 2020

The first steps of human immunodeficiency virus (HIV) infection go through the engagement of HIV envelope (Env) with CD4 and coreceptors (CXCR4 or CCR5) to mediate viral membrane fusion between the virus and the host. New approaches are still needed to better define both the molecular mechanistic underpinnings of this process but also the point of fusion and its kinetics. Here, we have developed a new method able to detect and quantify HIV-1 fusion in single live cells. We present a new approach that employs fluorescence lifetime imaging microscopy (FLIM) to detect Förster resonance energy transfer (FRET) when using the β-lactamase (BlaM) assay. This novel approach allows comparing different populations of single cells regardless the concentration of CCF2-AM FRET reporter in each cell, and more importantly, is able to determine the relative amount of viruses internalized per cell. We have applied this approach in both reporter TZM-bl cells and primary T cell lymphocytes.