bluuebunny/crossref_metadata_2025 huggingface dataset:
Beliefs of UK Transplant Recipients about Living Kidney Donation and Transplantation: Findings from a Multicentre Questionnaire-Based Case–Control Study
Authors: Bailey Pippa K. , Caskey Fergus J. , MacNeill Stephanie , Tomson Charles , Dor Frank J. M. F. , Ben-Shlomo Yoav
Published: December 2019

Differing beliefs about the acceptability of living-donor kidney transplants (LDKTs) have been proposed as explaining age, ethnic and socioeconomic disparities in their uptake. We investigated whether certain patient groups hold beliefs incompatible with LDKTs. This questionnaire-based case–control study was based at 14 hospitals in the United Kingdom. Participants were adults transplanted between 1 April 2013 and 31 March 2017. LDKT recipients were compared to deceased-donor kidney transplant (DDKT) recipients. Beliefs were determined by the direction and strength of agreement with ten statements. Multivariable logistic regression was used to investigate the association between beliefs and LDKT versus DDKT. Sex, age, ethnicity, religion, and education were investigated as predictors of beliefs. A total of 1240 questionnaires were returned (40% response). DDKT and LDKT recipients responded in the same direction for 9/10 statements. A greater strength of agreement with statements concerning the ‘positive psychosocial effects’ of living kidney donation predicted having an LDKT over a DDKT. Older age, Black, Asian and Minority Ethnic (BAME) group ethnicity, and having a religion other than Christianity were associated with greater degree of uncertainty regarding a number of statements, but there was no evidence that individuals in these groups hold strong beliefs against living kidney donation and transplantation. Interventions should address uncertainty, to increase LDKT activity in these groups.
Impact of MRI, CT, and Clinical Characteristics on Microbial Pathogen Detection Using CT-Guided Biopsy for Suspected Spondylodiscitis
Authors: Braun Alexander , Germann Thomas , Wünnemann Felix , Weber Marc-André , Schiltenwolf Marcus , Akbar Michael , Burkholder Iris , Kauczor Hans-Ulrich , Rehnitz Christoph
Published: December 2019

Spondylodiscitis accounts for 2–7% of osteomyelitis cases and is characterized by pain, systemic inflammation, and permanent neurological deficits. We aimed to identify imaging characteristics and clinical parameters to successfully predict microbiological pathogens by computed tomography (CT)-guided biopsy in suspected spondylodiscitis cases. Forty consecutive patients (mean age 65.1 years) with suspected spondylodiscitis underwent CT-guided biopsy. CT features (non-sclerotic endplate erosions (NSEs)), magnetic resonance criteria (paravertebral/epidural abscess (PA/EA) formation), and clinical data (C-reactive protein (CRP) > 50 mg/L) were assessed for their predictive potential. NSEs were detected in 6/11 (54.5%) and 1/29(3.4%) patients with positive and negative microbiology, respectively. PA and EA, respectively, were present in 7/11(63.6%) and 3/11 patients with positive microbiology and 7/29 (24.1%) and 2/29 patients with negative microbiology. CRP > 50 was observed in 7/11 (63.6%) and in 7/29 (24.1%) patients with positive and negative microbiology, respectively. Three double combinations possessed near-perfect specificity (PA + NSE, 100%; PA + CRP > 50, 96.6%; NSE + CRP > 50, 96.6%). The top three Youden indices included combinations with NSE. Since CT/magnetic resonance (MR) imaging and CRP are routinely used to evaluate spondylodiscitis, the presented diagnostic criteria and combinations can aid decision-making for biopsy.
Effects of Blood Pressure on Cognitive Performance: A Systematic Review
Authors: Forte Giuseppe , De Pascalis Vilfredo , Favieri Francesca , Casagrande Maria
Published: December 2019

Background: High blood pressure has been associated with an increased risk of developing cognitive impairment. However, this relationship is unclear. This study aims to systematically review the effects of blood pressure on executive functioning, language, memory, attention and processing speed. Methods: The review process was conducted according to the PRISMA-Statement, using the PubMed, PsycINFO, PsycARTICLES and MEDLINE databases. Restrictions were made by selecting studies, which included one or more cognitive measures and reported blood pressure recordings. Studies that included participants with medical conditions or people diagnosed with dementia, psychiatric disorders, stroke and head trauma were excluded. The review allows selecting fifty studies that included 107,405 participants. The results were reported considering different cognitive domains separately: global cognitive functioning, attention, processing speed, executive functions, memory and visuospatial abilities. Results: Higher blood pressure appears to influence cognitive performance in different domains in the absence of dementia and severe cardiovascular diseases, such as strokes. This relationship seems to be independent of demographic factors (gender and education), medical co-morbidity (diabetes), and psychiatric disorders (depression). Furthermore, it presents different patterns considering ageing. In the elderly, a sort of “cardiovascular paradox” is highlighted, which allows considering higher blood pressure as a protective factor for cognitive functioning. Conclusions: The results underline that higher blood pressure is associated with a higher risk of cognitive decline in people without dementia or stroke. These findings highlight the need to introduce early management of blood pressure, even in the absence of clinical hypertension, to prevent the risk of a decline of cognitive functioning typically associated with ageing.
Theoretical Performance Evaluation of a Marine Solid Propellant Water-Breathing Ramjet Propulsor
Authors: Eisen Nachum E. , Gany Alon
Published: December 2019

This work analyzes and presents theoretical performance of a marine water-breathing ramjet propulsor. A conceptual scheme of the motor is shown, the equation of thrust is presented, and the dependence on cruise velocity and depth are discussed. Different propellant compositions, representing a wide variety of formulations suitable for propelling a water-breathing ramjet, are investigated. The theoretical results reveal that the specific impulse of a water-breathing ramjet can increase by as much as 30% compared to a standard rocket, when using a conventional hydroxyl terminated polybutadiene (HTPB)-ammonium perchlorate (AP) propellant, which does not react chemically with the water. When employing a water-reactive propellant containing metal particles such as magnesium or aluminum, the specific impulse may be more than doubled. The thrust coefficient of the propulsor was computed at different cruise velocities and depths and was found to be greater than the predictable drag even at significant depth.
Special Issue: Mucorales and Mucormycosis
Authors: Dannaoui Eric , Lackner Michaela
Published: December 2019

Mucormycosis is a life-threatening infection, occurring mainly in immunocompromised patients, but also in immunocompetent patients after traumatic injuries [...]
Quantum Treatment of Inelastic Interactions for the Modeling of Nanowire Field-Effect Transistors
Authors: Lee Youseung , Logoteta Demetrio , Cavassilas Nicolas , Lannoo Michel , Luisier Mathieu , Bescond Marc
Published: December 2019

During the last decades, the Nonequilibrium Green’s function (NEGF) formalism has been proposed to develop nano-scaled device-simulation tools since it is especially convenient to deal with open device systems on a quantum-mechanical base and allows the treatment of inelastic scattering. In particular, it is able to account for inelastic effects on the electronic and thermal current, originating from the interactions of electron–phonon and phonon–phonon, respectively. However, the treatment of inelastic mechanisms within the NEGF framework usually relies on a numerically expensive scheme, implementing the self-consistent Born approximation (SCBA). In this article, we review an alternative approach, the so-called Lowest Order Approximation (LOA), which is realized by a rescaling technique and coupled with Padé approximants, to efficiently model inelastic scattering in nanostructures. Its main advantage is to provide a numerically efficient and physically meaningful quantum treatment of scattering processes. This approach is successfully applied to the three-dimensional (3D) atomistic quantum transport OMEN code to study the impact of electron–phonon and anharmonic phonon–phonon scattering in nanowire field-effect transistors. A reduction of the computational time by about ×6 for the electronic current and ×2 for the thermal current calculation is obtained. We also review the possibility to apply the first-order Richardson extrapolation to the Padé N/N − 1 sequence in order to accelerate the convergence of divergent LOA series. More in general, the reviewed approach shows the potentiality to significantly and systematically lighten the computational burden associated to the atomistic quantum simulations of dissipative transport in realistic 3D systems.
The Properties of Composites with Recycled Cement Mortar Used as a Supplementary Cementitious Material
Authors: Kalinowska-Wichrowska Katarzyna , Kosior-Kazberuk Marta , Pawluczuk Edyta
Published: December 2019

The process of recycling concrete rubble is accompanied by the formation of a large amount of fine fraction, which cannot be reused as aggregate. The results of research on the possibility of using recycled cement mortar (RCM), obtained during concrete recycling, as a cementitious supplementary material, are presented. The experimental research was carried out on the basis of two variables determining the recycling process: X1—temperature (range of variation 288–712 °C) and X2—time (range of variation 30–90 min) of thermal treatment of concrete rubble. The experiment included 10 series of new composites made with RCMs subjected to different variants of thermal treatment, and two additional control series. The best treatment parameters were determined based on the assessment of selected physical and mechanical properties of the new cement composites, as well as the analysis of characteristics and microstructure of RCM. The test results showed that proper thermal treatment of concrete rubble makes it possible to obtain a high-quality fine fraction, which has the properties of an active addition and can be used as a partial replacement for cement in mortars and concretes.
Biological Responses to the Transitional Area of Dental Implants: Material- and Structure-Dependent Responses of Peri-Implant Tissue to Abutments
Authors: Kim Jung-Ju , Lee Jae-Hyun , Kim Jeong Chan , Lee Jun-Beom , Yeo In-Sung Luke
Published: December 2019

The stability of peri-implant tissue is essential for the long-term success of dental implants. Although various types of implant connections are used, little is known about the effects of the physical mechanisms of dental implants on the stability of peri-implant tissue. This review summarizes the relevant literature to establish guidelines regarding the effects of connection type between abutments and implants in soft and hard tissues. Soft tissue seals can affect soft tissue around implants. In external connections, micromobility between the abutment and the hex component of the implant, resulting from machining tolerance, can destroy the soft tissue seal, potentially leading to microbial invasion. Internal friction connection implants induce strain on the surrounding bone via implant wall expansion that translates into masticatory force. This strain is advantageous because it increases the amount and quality of peri-implant bone. The comparison of internal and external connections, the two most commonly used connection types, reveals that internal friction has a positive influence on both soft and hard tissues.
Evidence of Structural Inhomogeneities in Hard-Soft Dimeric Particles without Attractive Interactions
Authors: Munaò Gianmarco , Saija Franz
Published: December 2019

We perform Monte Carlo simulations of a simple hard-soft dimeric model constituted by two tangent spheres experiencing different interactions. Specifically, two hard spheres belonging to different dimers interact via a bare hard-core repulsion, whereas two soft spheres experience a softly repulsive Hertzian interaction. The cross correlations are soft as well. By exploring a wide range of temperatures and densities we investigate the capability of this model to document the existence of structural inhomogeneities indicating the possible onset of aggregates, even if no attraction is set. The fluid phase behavior is studied by analyzing structural and thermodynamical properties of the observed structures, in particular by computing radial distribution functions, structure factors and cluster size distributions. The numerical results are supported by integral equation theories of molecular liquids which allow for a finer and faster spanning of the temperature-density diagram. Our results may serve as a framework for a more systematic investigation of self-assembled structures of functionalized hard-soft dimers able to aggregate in a variety of structures widely oberved in colloidal dispersion.
Investigation of Fresh Gastric Normal and Cancer Tissues Using Terahertz Time-Domain Spectroscopy
Authors: Grigorev Roman , Kuzikova Anna , Demchenko Petr , Senyuk Artem , Svechkova Anna , Khamid Abdo , Zakharenko Alexander , Khodzitskiy Mikhail
Published: December 2019

In recent times, terahertz (THz) technologies have been actively applied in many biomedical research work, including gastric cancer diagnosis. In order to provide an effective removal of tumor during surgery, it is necessary to clearly distinguish it from different membranes of the stomach. In this work, we reported an investigation of various normal and cancer fresh gastric tissues using terahertz time-domain spectroscopy in the reflection mode. Refractive index and absorption coefficient of moderately differentiated and poorly differentiated gastric adenocarcinomas, as well as both serosa and mucosa were obtained in the frequency range from 0.2 to 1 THz. All cancer tissues were distinguishable from normal ones. The influence of the morphology of the investigated tissues on the obtained optical properties is discussed. The obtained results demonstrated a potential of THz time-domain spectroscopy to discriminate a tumor from normal serous and mucous gastric membranes. Thus, this method might be applied to gastric cancer diagnosis.
Geometric Numerical Integration in Ecological Modelling
Authors: Diele Fasma , Marangi Carmela
Published: December 2019

A major neglected weakness of many ecological models is the numerical method used to solve the governing systems of differential equations. Indeed, the discrete dynamics described by numerical integrators can provide spurious solution of the corresponding continuous model. The approach represented by the geometric numerical integration, by preserving qualitative properties of the solution, leads to improved numerical behaviour expecially in the long-time integration. Positivity of the phase space, Poisson structure of the flows, conservation of invariants that characterize the continuous ecological models are some of the qualitative characteristics well reproduced by geometric numerical integrators. In this paper we review the benefits induced by the use of geometric numerical integrators for some ecological differential models.
Stability of Sets Criteria for Impulsive Cohen-Grossberg Delayed Neural Networks with Reaction-Diffusion Terms
Authors: Stamov Gani , Tomasiello Stefania , Stamova Ivanka , Spirova Cvetelina
Published: December 2019

The paper proposes an extension of stability analysis methods for a class of impulsive reaction-diffusion Cohen-Grossberg delayed neural networks by addressing a challenge namely stability of sets. Such extended concept is of considerable interest to numerous systems capable of approaching not only one equilibrium state. Results on uniform global asymptotic stability and uniform global exponential stability with respect to sets for the model under consideration are established. The main tools are expansions of the Lyapunov method and the comparison principle. In addition, the obtained results for the uncertain case contributed to the development of the stability theory of uncertain reaction-diffusion Cohen-Grossberg delayed neural networks and their applications. Moreover, examples are given to demonstrate the feasibility of our results.
FCS-MBFLEACH: Designing an Energy-Aware Fault Detection System for Mobile Wireless Sensor Networks
Authors: Shamshirband Shahaboddin , Joloudari Javad Hassannataj , GhasemiGol Mohammad , Saadatfar Hamid , Mosavi Amir , Nabipour Narjes
Published: December 2019

Wireless sensor networks (WSNs) include large-scale sensor nodes that are densely distributed over a geographical region that is completely randomized for monitoring, identifying, and analyzing physical events. The crucial challenge in wireless sensor networks is the very high dependence of the sensor nodes on limited battery power to exchange information wirelessly as well as the non-rechargeable battery of the wireless sensor nodes, which makes the management and monitoring of these nodes in terms of abnormal changes very difficult. These anomalies appear under faults, including hardware, software, anomalies, and attacks by raiders, all of which affect the comprehensiveness of the data collected by wireless sensor networks. Hence, a crucial contraption should be taken to detect the early faults in the network, despite the limitations of the sensor nodes. Machine learning methods include solutions that can be used to detect the sensor node faults in the network. The purpose of this study is to use several classification methods to compute the fault detection accuracy with different densities under two scenarios in regions of interest such as MB-FLEACH, one-class support vector machine (SVM), fuzzy one-class, or a combination of SVM and FCS-MBFLEACH methods. It should be noted that in the study so far, no super cluster head (SCH) selection has been performed to detect node faults in the network. The simulation outcomes demonstrate that the FCS-MBFLEACH method has the best performance in terms of the accuracy of fault detection, false-positive rate (FPR), average remaining energy, and network lifetime compared to other classification methods.
Effect of Hydrogen Charging on Pop-in Behavior of a Zr-Based Metallic Glass
Authors: Tian Lin , Tönnies Dominik , Hirsbrunner Moritz , Sievert Tim , Shan Zhiwei , Volkert Cynthia A.
Published: December 2019

In this work, structural and mechanical properties of hydrogen-charged metallic glass are studied to evaluate the effect of hydrogen on early plasticity. Hydrogen is introduced into samples of a Zr-based (Vit 105) metallic glass using electrochemical charging. Nanoindentation tests reveal a clear increase in modulus and hardness as well as in the load of the first pop-in with increasing hydrogen content. At the same time, the probability of a pop-in occurring decreases, indicating that hydrogen hinders the onset of plastic instabilities while allowing local homogeneous deformation. The hydrogen-induced stiffening and hardening is rationalized by hydrogen stabilization of shear transformation zones (STZs) in the amorphous structure, while the improved ductility is attributed to the change in the spatial correlation of the STZs.
Experimental Investigation of the Influence of Wire Arc Additive Manufacturing on the Machinability of Titanium Parts
Authors: Alonso Unai , Veiga Fernando , Suárez Alfredo , Artaza Teresa
Published: December 2019

The manufacturing of titanium airframe parts involves significant machining and low buy-to-fly ratios. Production costs could be greatly reduced by the combination of an additive manufacturing (AM) process followed by a finishing machining operation. Among the different AM alternatives, wire arc additive manufacturing (WAAM) offers deposition rates of kg/h and could be the key for the production of parts of several meters economically. In this study, the influence of the manufacturing process of Ti6Al4V alloy on both its material properties and machinability is investigated. First, the mechanical properties of a workpiece obtained by WAAM were compared to those in a conventional laminated plate. Then, drilling tests were carried out in both materials. The results showed that WAAM leads to a higher hardness than laminated Ti6Al4V and satisfies the requirements of the standard in terms of mechanical properties. As a consequence, higher cutting forces, shorter chips, and lower burr height were observed for the workpieces produced by AM. Furthermore, a metallographic analysis of the chip cross-sectional area also showed that a serrated chip formation is also present during drilling of Ti6Al4V produced by WAAM. The gathered information can be used to improve the competitiveness of the manufacturing of aircraft structures in terms of production time and cost.
On the Superplastic Deformation in Vanadium-Alloyed High-Nitrogen Steel
Authors: Astafurova Elena , Moskvina Valentina , Panchenko Marina , Maier Galina , Melnikov Eugene , Reunova Kseniya , Galchenko Nina , Astafurov Sergey
Published: December 2019

The experimental evidence for the realization of a superplastic behavior with 900% elongation in V-alloyed high-nitrogen austenitic Fe-19Cr-22Mn-1.5V-0.3C-0.6N steel was proposed. Using thermomechanical processing, a misoriented grain/subgrain austenitic microstructure with a high density of deformation-assisted defects and precipitates was developed in the steel. During high-temperature tensile deformation in a temperature interval from 850 to 1000 °C and strain-rate range from 4 × 10−4 s−1 to 6 × 10−3 s−1, this microstructure demonstrated the characteristics of superplastic flow: elongation in the interval 400–900%, strain-rate sensitivity exponent m = 0.40–0.49, grain boundary sliding mechanism. The maximum elongation to failure (900%) was reached at deformation temperature 950 °C and strain rate 4 × 10−4 s−1.
Metatranscriptomic Analysis of the Mouse Gut Microbiome Response to the Persistent Organic Pollutant 2,3,7,8-Tetrachlorodibenzofuran
Authors: Nichols Robert G. , Zhang Jingtao , Cai Jingwei , Murray Iain A. , Koo Imhoi , Smith Philip B. , Perdew Gary H. , Patterson Andrew D.
Published: December 2019

Persistent organic pollutants (POPs) are important environmental chemicals and continued study of their mechanism of action remains a high priority. POPs, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,7,8-tetrachlorodibenzofuran (TCDF), and polychlorinated biphenyls (PCBs), are widespread environmental contaminants that are agonists for the aryl hydrocarbon receptor (AHR). Activation of the AHR modulates the gut microbiome community structure and function, host immunity, and the host metabolome. In the current study, male C57BL6/J mice were exposed, via the diet, to 5 µg/kg body weight (BW) TCDF or 24 µg/kg BW of TCDF every day for 5 days. The functional and structural changes imparted by TCDF exposure to the gut microbiome and host metabolome were explored via 16S rRNA gene amplicon sequencing, metabolomics, and bacterial metatranscriptomics. Significant changes included increases in lipopolysaccharide (LPS) biosynthesis gene expression after exposure to 24 µg/kg BW of TCDF. Increases in LPS biosynthesis were confirmed with metabolomics and LPS assays using serum obtained from TCDF-treated mice. Significant increases in gene expression within aspartate and glutamate metabolism were noted after exposure to 24 µg/kg BW of TCDF. Together, these results suggest that after exposure to 24 µg/kg BW of TCDF, the gut microbiome increases the production of LPS and glutamate to promote localized gut inflammation, potentially using glutamate as a stress response.
Possible Use of Blood Tryptophan Metabolites as Biomarkers for Coronary Heart Disease in Sudden Unexpected Death
Authors: Santisukwongchote Kobchai , Amornlertwatana Yutti , Sastraruji Thanapat , Jaikang Churdsak
Published: December 2019

Coronary heart disease (CHD) is the major cause of death in sudden unexpected death (SUD) cases. Tryptophan (TRP) and its metabolites are correlated with the CHD patient but less studies in the SUD. The aim of this study was to evaluate the relationship of TRP and its metabolites with the CHD in the SUD cases. Blood samples and heart tissues were collected from CHD subjects (n = 31) and the control group (n = 72). Levels of kynurenine (KYN), kynurenic acid (KYA), xanthurenic acid (XAN), 3-hydroxyanthranillic acid (HAA), quinolinic acid (QA), picolinic acid (PA) and 5-hydroxyindoleacetic acid (HIAA) were determined by HPLC-DAD. A severity of heart occlusion was categorized into four groups, and the relationship was measured with the TRP metabolites. The HIAA and The KYN levels significantly differed (p < 0.01) between the CHD group and the control group. Lower levels of QA/XAN, PA/KA, HAA/XAN, KYN/XAN and KYN/TRP were found in the CHD group. However, PA/HAA, PA/HIAA, PA/KYN and XAN/KA values in the CHD group were higher than the control group (p < 0.05). This study revealed that the values of PA/KA and PA/HAA provided better choices for a CHD biomarker in postmortem bodies.
A High-Throughput Microfluidic Magnetic Separation (µFMS) Platform for Water Quality Monitoring
Authors: Castillo-Torres Keisha Y. , McLamore Eric S. , Arnold David P.
Published: December 2019

The long-term aim of this work is to develop a biosensing system that rapidly detects bacterial targets of interest, such as Escherichia coli, in drinking and recreational water quality monitoring. For these applications, a standard sample size is 100 mL, which is quite large for magnetic separation microfluidic analysis platforms that typically function with <20 µL/s throughput. Here, we report the use of 1.5-µm-diameter magnetic microdisc to selectively tag target bacteria, and a high-throughput microfluidic device that can potentially isolate the magnetically tagged bacteria from 100 mL water samples in less than 15 min. Simulations and experiments show ~90% capture efficiencies of magnetic particles at flow rates up to 120 µL/s. Also, the platform enables the magnetic microdiscs/bacteria conjugates to be directly imaged, providing a path for quantitative assay.
Tetracycline Resistant Campylobacter jejuni Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline are Longitudinally Transmitted within the Production Continuum but are Not Detected in Ground Beef
Authors: Inglis G. Douglas , Gusse Jenny F. , House Kathaleen E. , Shelton Tara G. , Taboada Eduardo N.
Published: December 2019

The impacts of the antimicrobial growth promoter (AGP), chlortetracycline with sulfamethazine (AS700), on the development of antimicrobial resistance and longitudinal transmission of Campylobacter jejuni within the beef production continuum were empirically determined. Carriage of tetracycline resistance determinants in the enteric bacterial community increased at a greater rate for AS700-treatment cattle. The majority of the bacteria from animals administered AS700 carried tetW. Densities of C. jejuni shed in feces increased over the confined feeding period, and the administration of AS700 did not conspicuously reduce C. jejuni densities in feces or within the intestine. The majority of C. jejuni isolates recovered were resistant to tetracycline, but the resistance rates to other antibiotics was low (≤20.1%). The richness of C. jejuni subtypes recovered from AS700-treated animals that were either resistant or susceptible to tetracycline was reduced, indicating selection pressure due to AGP administration. Moreover, a degree of subtype-specific resistance to tetracycline was observed. tetO was the primary tetracycline resistance determinant conferring resistance in C. jejuni isolates recovered from cattle and people. Clinically-relevant C. jejuni subtypes (subtypes that represent a risk to human health) that were resistant to tetracycline were isolated from cattle feces, digesta, hides, the abattoir environment, and carcasses, but not from ground beef. Thus, study findings indicate that clinically-relevant C. jejuni subtypes associated with beef cattle, including those resistant to antibiotics, do not represent a significant foodborne risk.
Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum β-Lactamase Activity
Authors: Oueslati Saoussen , Retailleau Pascal , Marchini Ludovic , Dortet Laurent , Bonnin Rémy A. , Iorga Bogdan I. , Naas Thierry
Published: December 2019

OXA-48-producing Enterobacterales have now widely disseminated globally. A sign of their extensive spread is the identification of an increasing number of OXA-48 variants. Among them, three are particularly interesting, OXA-163, OXA-247 and OXA-405, since they have lost carbapenem activities and gained expanded-spectrum cephalosporin hydrolytic activity subsequent to a four amino-acid (AA) deletion in the β5–β6 loop. We investigated the mechanisms responsible for substrate specificity of OXA-405. Kinetic parameters confirmed that OXA-405 has a hydrolytic profile compatible with an ESBL (hydrolysis of expanded spectrum cephalosporins and susceptibility to class A inhibitors). Molecular modeling techniques and 3D structure determination show that the overall dimeric structure of OXA-405 is very similar to that of OXA-48, except for the β5–β6 loop, which is shorter for OXA-405, suggesting that the length of the β5–β6 loop is critical for substrate specificity. Covalent docking with selected substrates and molecular dynamics simulations evidenced the structural changes induced by substrate binding, as well as the distribution of water molecules in the active site and their role in substrate hydrolysis. All this data may represent the structural basis for the design of new and efficient class D inhibitors.
Mutation and Recombination Rates Vary Across Bacterial Chromosome
Authors: Kivisaar Maia
Published: December 2019

Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.
Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli
Authors: Parekh Virali J. , Niccum Brittany A. , Shah Rachna , Rivera Marisa A. , Novak Mark J. , Geinguenaud Frederic , Wien Frank , Arluison Véronique , Sinden Richard R.
Published: December 2019

Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression.
Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines
Authors: Jacksch Susanne , Kaiser Dominik , Weis Severin , Weide Mirko , Ratering Stefan , Schnell Sylvia , Egert Markus
Published: December 2019

Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.
Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae
Authors: Villalobos-Cid Manuel , Salinas Francisco , Kessi-Pérez Eduardo I. , De Chiara Matteo , Liti Gianni , Inostroza-Ponta Mario , Martínez Claudio
Published: December 2019

Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the “1002 yeast genomes project”. We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the “1002 yeast genomes project”. We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.
Multi-Tool (LA-ICPMS, EMPA and XRD) Investigation on Heavy Minerals from Selected Holocene Peat-Bog Deposits from the Upper Vistula River Valley, Poland
Authors: Szopa Krzysztof , Skreczko Sylwia , Chew David , Krzykawski Tomasz , Szymczyk Artur
Published: December 2019

Peat sediments represent important environmental and climatic archives, as well as recording information on the processes affecting the formation of these deposits; combined these data can be used for paleoreconstruction of peat-bogs. In this paper we characterize heavy mineral-rich sandy layers from two peat-bog sites in Mizerów and Strumień (Poland). In both cases, the most common identified mineral suite is: epidote, staurolite, tourmaline (dravite and schörl), garnet, spinel, Al2SiO5 polymorphs (sillimanite, kyanite, andalusite), amphibole (mainly hornblende), pyroxene (e.g., richterite, diopside), perovskite, topaz, cordierite, apatite, monazite, chromite, ilmenite, chlorite, iron oxides, rutile and siderite. This mineral suite is characteristic of a metamorphic aureole surrounding a magmatic body. Pyrite is likely authigenic in origin. Apatite and monazite were employed for U-Pb and CHIME dating, respectively. Based on the U-Pb age information composition and textural features of selected minerals, different provenance areas were indicated: the Tatra Massif, the Bohemian Massif, and the Silesian Basin area. Transport of the investigated mineral phases was linked to development of both the Odra (praOdra) and the Vistula valleys.
Factors Controlling the Chromium Isotope Compositions in Podiform Chromitites
Authors: Economou-Eliopoulos Maria , Frei Robert , Mitsis Ioannis
Published: December 2019

The application of Cr isotope compositions to the investigation of magmatic and post-magmatic effects on chromitites is unexplored. This study presents and compiles the first Cr stable isotope data (δ53Cr values) with major and trace element, contents from the Balkan Peninsula, aiming to provide an overview of the compositional variations of δ53Cr values in ophiolite-hosted chromitites and to delineate geochemical constraints controlling the composition of chromitites. The studied chromitites exhibit δ53Cr values ranging from −0.184‰ to +0.159‰, falling in the range of so-called “igneous Earth” or “Earth’s mantle inventory” with values −0.12 ± 0.11‰ to 0.079 ± 0.129‰ (2sd). A characteristic feature is the slightly positively fractionated δ53Cr values of all chromitite samples from Othrys (+0.043 ± 0.03‰), and the occurrence of a wide range of δ53Cr values spanning from positively, slightly negatively to the most negatively fractionated signatures (Pindos, δ53Cr = −0.147 to +0.009‰; Skyros, δ53Cr = −0.078 to +0.159‰). The observed negative trend between δ53Cr values and Cr/(Cr + Al) ratios may reflect a decrease in the δ53Cr values of chromitites with increasing partial melting degree. Alternatively, it may point to processes related to magmatic differentiation, as can be seen in our data from Mikrokleisoura (Vourinos).
Chia Seeds (Salvia Hispanica L.): An Overview—Phytochemical Profile, Isolation Methods, and Application
Authors: Knez Hrnčič Maša , Ivanovski Maja , Cör Darija , Knez Željko
Published: December 2019

Chia (Salvia hispanica L.) is a small seed that comes from an annual herbaceous plant, Salvia hispanica L. In recent years, usage of Chia seeds has tremendously grown due to their high nutritional and medicinal values. Chia was cultivated by Mesopotamian cultures, but then disappeared for centuries until the middle of the 20th century, when it was rediscovered. Chia seeds contain healthy ω-3 fatty acids, polyunsaturated fatty acids, dietary fiber, proteins, vitamins, and some minerals. Besides this, the seeds are an excellent source of polyphenols and antioxidants, such as caffeic acid, rosmarinic acid, myricetin, quercetin, and others. Today, chia has been analyzed in different areas of research. Researches around the world have been investigating the benefits of chia seeds in the medicinal, pharmaceutical, and food industry. Chia oil is today one of the most valuable oils on the market. Different extraction methods have been used to produce the oil. In the present study, an extensive overview of the chemical composition, nutritional properties, and antioxidant and antimicrobial activities, along with extraction methods used to produce chia oil, will be discussed.
SLC22A5 (OCTN2) Carnitine Transporter—Indispensable for Cell Metabolism, a Jekyll and Hyde of Human Cancer
Authors: Juraszek Barbara , Nałęcz Katarzyna A.
Published: December 2019

Oxidation of fatty acids uses l-carnitine to transport acyl moieties to mitochondria in a so-called carnitine shuttle. The process of β-oxidation also takes place in cancer cells. The majority of carnitine comes from the diet and is transported to the cell by ubiquitously expressed organic cation transporter novel family member 2 (OCTN2)/solute carrier family 22 member 5 (SLC22A5). The expression of SLC22A5 is regulated by transcription factors peroxisome proliferator-activated receptors (PPARs) and estrogen receptor. Transporter delivery to the cell surface, as well as transport activity are controlled by OCTN2 interaction with other proteins, such as PDZ-domain containing proteins, protein phosphatase PP2A, caveolin-1, protein kinase C. SLC22A5 expression is altered in many types of cancer, giving an advantage to some of them by supplying carnitine for β-oxidation, thus providing an alternative to glucose source of energy for growth and proliferation. On the other hand, SLC22A5 can also transport several chemotherapeutics used in clinics, leading to cancer cell death.
Non-Lamellar Liquid Crystalline Nanocarriers for Thymoquinone Encapsulation
Authors: Yaghmur Anan , Tran Boi Vi , Moghimi Seyed Moein
Published: December 2019

Owing to their unique structural features, non-lamellar liquid crystalline nanoparticles comprising cubosomes and hexosomes are attracting increasing attention as versatile investigative drug carriers. Background: Depending on their physiochemical characteristics, drug molecules on entrapment can modulate and reorganize structural features of cubosomes and hexosomes. Therefore, it is important to assess the effect of guest molecules on broader biophysical characteristics of non-lamellar liquid crystalline nanoparticles, since drug-induced architectural, morphological, and size modifications can affect the biological performance of cubosomes and hexosomes. Methods: We report on alterations in morphological, structural, and size characteristics of nanodispersions composed from binary mixtures of glycerol monooleate and vitamin E on thymoquinone (a molecule with wide therapeutic potentials) loading. Results: Thymoquinone loading was associated with a slight increase in the mean hydrodynamic nanoparticle size and led to structural transitions from an internal biphasic feature of coexisting inverse cubic Fd3m and hexagonal (H2) phases to an internal inverse cubic Fd3m phase (micellar cubosomes) or an internal inverse micellar (L2) phase (emulsified microemulsions, EMEs). We further report on the presence of “flower-like” vesicular populations in both native and drug-loaded nanodispersions. Conclusions: These nanodispersions have the potential to accommodate thymoquinone and may be considered as promising platforms for the development of thymoquinone nanomedicines.
α-Ionone, an Apocarotenoid, Induces Plant Resistance to Western Flower Thrips, Frankliniella occidentalis, Independently of Jasmonic Acid
Authors: Murata Mika , Kobayashi Tetsuya , Seo Shigemi
Published: December 2019

Apocarotenoids, such as β-cyclocitral, α-ionone, β-ionone, and loliolide, are derived from carotenes via chemical or enzymatic processes. Recent studies revealed that β-cyclocitral and loliolide play an important role in various aspects of plant physiology, such as stress responses, plant growth, and herbivore resistance. However, information on the physiological role of α-ionone is limited. We herein investigated the effects of α-ionone on plant protection against herbivore attacks. The pretreatment of whole tomato (Solanum lycopersicum) plants with α-ionone vapor decreased the survival rate of western flower thrips (Frankliniella occidentalis) without exhibiting insecticidal activity. Exogenous α-ionone enhanced the expression of defense-related genes, such as basic β-1,3-glucanase and basic chitinase genes, in tomato leaves, but not that of jasmonic acid (JA)- or loliolide-responsive genes. The pretreatment with α-ionone markedly decreased egg deposition by western flower thrips in the JA-insensitive Arabidopsis (Arabidopsis thaliana) mutant coi1-1. We also found that common cutworm (Spodoptera litura) larvae fed on α-ionone-treated tomato plants exhibited a reduction in weight. These results suggest that α-ionone induces plant resistance to western flower thrips through a different mode of action from that of JA and loliolide.
IR and NMR Studies of the Status of Al and Acid Sites in Desilicated Zeolite Y
Authors: Gackowski Mariusz , Podobiński Jerzy , Broclawik Ewa , Datka Jerzy
Published: December 2019

The desilication of zeolite Y (of Si/Al = 31) that was previously dealuminated by steaming and acid treatment was studied. Desilication of zeolites of high Si/Al module in alkali solutions extracts both Si and Al from zeolite crystals, but while Si remains in solution, Al is reinserted into the zeolite grain. The main goal of our study was to follow the status of Al reinserted into zeolite during the desilication procedure, and its role in the formation of acid sites of the Brønsted and Lewis types. The properties of Al were followed by 27Al MAS NMR spectroscopy (for parent samples and zeolites treated either with NaOH or NaOH/tetrabutylammonium hydroxide), whereas the acid sites generated in the final stages were studied by IR spectroscopy with NH3 and CO as probe molecules. In non-desilicated zeolite, most of the Al was in a typically zeolitic tetrahedral coordination, while both NMR and quantitative IR studies of NH3 sorption evidenced that Al that was extracted by desilication and was subsequently reinserted had a tetrahedral coordination similar to amorphous aluminosilicates and showed an ion exchange ability. After the exchange of Na+ to NH4+ and decomposition of NH4+ ions, reinserted Al forms generated protonic sites from which some condensed at higher temperatures producing Lewis acid sites (with stoichiometry typical for zeolites i.e., the condensation of two protonic sites produces one Lewis site) but some other kept their character.
Antimicrobial Susceptibility and Antibacterial Mechanism of Limonene against Listeria monocytogenes
Authors: Han Yingjie , Sun Zhichang , Chen Wenxue
Published: December 2019

Limonene is a monoterpenoid compound, which is founded in a lot of plants’ essential oils with good antibacterial activity against food-borne pathogens, but it has an ambiguous antimicrobial susceptibility and mechanism against Listeria monocytogenes (L. monocytogenes). In this study, the antimicrobial susceptibility of Limonene to L. monocytogenes was studied, and some new sights regarding its antibacterial mechanism were further explored. Scanning electron microscopy (SEM) verified that limonene caused the destruction of the cell integrity and wall structure of L. monocytogenes. The increase in conductivity and the leakage of intracellular biomacromolecules (nucleic acids and proteins) confirmed that limonene had an obvious effect on cell membrane permeability. The results of Propidium Iodide (PI) fluorescence staining were consistent with the results of the conductivity measurements. This indicated that limonene treatment caused damage to the L. monocytogenes cell membrane. Furthermore, the decrease in ATP content, ATPase (Na+K+-ATPase, Ca2+-ATPase) activity and respiratory chain complex activity indicated that limonene could hinder ATP synthesis by inhibiting the activity of the respiratory complex and ATPase. Finally, differential expression of proteins in the respiratory chain confirmed that limonene affected respiration and energy metabolism by inhibiting the function of the respiratory chain complex.