scholarly journals Modeling and Simulation of Thermo-Fluid-Electrochemical Ion Flow in Biological Channels

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Riccardo Sacco ◽  
Fabio Manganini ◽  
Joseph W. Jerome
Keyword(s):  
Driving Forces ◽  
The Novel ◽  
Thermodynamical Equilibrium ◽  
Finite Element Scheme ◽  
Equilibrium Conditions ◽  
Solution Map ◽  
Ion Flow ◽  
Stabilized Finite Element ◽  
A Cell ◽  
Biological Channels

AbstractIn this articlewe address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the well-known velocity-extended Poisson-Nernst-Planck (vPNP) electrodiffusion model. Two extensions of the vPNP system are proposed: the velocity-extended Thermo-Hydrodynamic model (vTHD) and the velocity-extended Electro-Thermal model (vET). Both formulations are based on the principles of conservation of mass, momentum and energy, and collapse into the vPNP model under thermodynamical equilibrium conditions. Upon introducing a suitable one-dimensional geometrical representation of the channel,we discuss appropriate boundary conditions that depend only on effectively accessible measurable quantities. Then, we describe the novel models, the solution map used to iteratively solve them, and the mixed-hybrid flux-conservative stabilized finite element scheme used to discretize the linearized equations. Finally,we successfully apply our computational algorithms to the simulation of two different realistic biological channels: 1) the Gramicidin-A channel considered in [12]; and 2) the bipolar nanofluidic diode considered in [45].

Rīgas humānistu motīvs Roalda Dobrovenska romānā „Magnus, dāņu princis”

2021 ◽  
pp. 172-180
Author(s):  
Ausma Cimdiņa
Keyword(s):  
Life Story ◽  
Driving Forces ◽  
Historical Narrative ◽  
Human Society ◽  
The Novel ◽  
Historical Sources ◽  
Nation States ◽  
Russian State ◽  
History Of ◽  
Historical Role

The novel “Magnus, the Danish Prince” by the Russian diaspora in Latvia writer Roald Dobrovensky is seen as a specific example of a biographical and historical genre, which embodies the historical experience of different eras and nations in the confrontation of globalisation and national self-determination. At the heart of the novel are the Livonian War and the historical role and human destiny of Magnus (1540–1683) – the Danish prince of the Oldenburg dynasty, the first and the only king of Livonia. The motif of Riga’s humanists is seen both as one of the main ideological driving forces of the novel and as a marginal reflection in Magnus’s life story. Acknowledged historical sources have been used in the creation of the novel: Baltazar Rusov’s “Livonian Chronicle”; Nikolai Karamzin’s “History of the Russian State”; Alexander Janov’s “Russia: 1462–1584. The Beginning of the Tragedy. Notes of the Nature and Formation of Russian Statehood” etc. In connection with the concept of Riga humanists, another fictitious document created by the writer Dobrovensky himself is especially important, namely, the diary of Johann Birke – Magnus’s interpreter, a person with a double identity, “half-Latvian”, “half-German”. It is a message of an alternative to the well-known historical documents, which allows to turn the Livonian historical narrative in the direction of “letocentrism” and raises the issue of the ethnic identity of Riga’s humanists. Along with the deconstruction of the historically documented image of Livonian King Magnus, the thematic structure of the novel is dominated by identity aspects related to the Livonian historical narrative. Dobrovensky, with his novel, raises an important question – what does the medieval Livonia, Europe’s common intellectual heritage, mean for contemporary Latvia and the human society at large? Dobrovensky’s work is also a significant challenge in strengthening emotional ties with Livonia (which were weakened in the early stages of national historiography due to conflicts over the founding of nation-states).

scholarly journals Complete Genome Sequence of Human Norovirus Strain GII.P7-GII.6 Detected in a Patient in the United States in 2014

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Zhihui Yang ◽  
Jan Vinjé ◽  
Christopher A. Elkins ◽  
Michael Kulka
Keyword(s):  
United States ◽  
Genetic Variation ◽  
Homologous Recombination ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Driving Forces ◽  
The United States ◽  
The Novel ◽  
Human Norovirus ◽  
Norovirus Gastroenteritis

Homologous recombination is one of the driving forces contributing to the genetic variation of human norovirus, which is an important cause of sporadic and epidemic acute gastroenteritis globally. We report the near-complete genome of the novel recombinant norovirus strain GII.P7-GII.6, detected in an adult with norovirus gastroenteritis in the United States.

The novel myokine irisin interacts with hyaluronic acid in a cell-specific way and in association with COPD progression and severity

2016 ◽  
Author(s):  
Eleni Papakonstantinou ◽  
Michael Roth ◽  
Jyotshna Mandal ◽  
Michael Tamm ◽  
Daiana Stolz
Keyword(s):  
Hyaluronic Acid ◽  
The Novel ◽  
A Cell

scholarly journals A Cell-Based Biosensor System for Listeria monocytogenes Detection in Food

Proceedings ◽  
2020 ◽  
Vol 60 (1) ◽  
pp. 49
Author(s):  
Agni Hadjilouka ◽  
Konstantinos Loizou ◽  
Theofylaktos Apostolou ◽  
Lazaros Dougiakis ◽  
Antonios Inglezakis ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Limit Of Detection ◽  
Food Contamination ◽  
Food Samples ◽  
The Novel ◽  
Food Borne ◽  
Biosensor System ◽  
A Cell ◽  
Food Substrate

Listeria monocytogenes is an intracellular bacterium that causes serious epidemic and sporadic food-borne illnesses in humans. Rapid and trustworthy methods are necessary for the detection of the pathogen to prevent potential food contamination. The aim of this study was to test a newly developed L. monocytogenes biosensor on actual food samples and validate its ability to detect the presence of pathogens robustly and accurately. The newly developed method uses a cell-based biosensor technology (BERA) and a portable device developed by EMBIO Diagnostics called B.EL.D, and provides results within 3 min. Tests were conducted on ready-to-eat lettuce salads, milk and halloumi cheese and the results indicate that the novel system was able to identify inoculated samples with 98%, 90%, and 91% accuracy, respectively. Furthermore, the limit of detection was determined to be as low as 0.6 log CFU mL−1 or g−1 in all food types. Classification of the samples Above or Below the detection limit was accessed through a newly developed algorithm for each food substrate. Samples were also analyzed with the ISO 11290-1:2017 and 11290-2:2017, in parallel. Thus, it was concluded that the newly developed biosensor can be a useful tool in the food supply chain, decreasing the required time for the detection of pathogens and increasing the number of tested samples before they reach the market.

An econometric analysis of the factors affecting consumers' bread waste and consumption behaviour: a case study of Isparta province, Turkey

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Deniz Sarica ◽  
Vecdi Demircan ◽  
Aybike Erturk ◽  
Nilay Arslantas
Keyword(s):  
Driving Forces ◽  
Econometric Analysis ◽  
The Novel ◽  
Monthly Income ◽  
Key Factors ◽  
Content Type ◽  
Factors Affecting ◽  
Consumption Behaviour ◽  
Underlying Causes

PurposeThe purpose of the research is to identify the various factors affecting bread wastage and bread consumption of consumers in Isparta, Turkey.Design/methodology/approachThis study uses the categorical regression (CATREG) model to estimate the driving forces of bread waste and consumption. The study concentrates on data obtained from 384 respondents speaking for the same number of households placed in the province of Isparta in Turkey.FindingsThe results indicate that both models are statistically significant at the 1% level. Parents' profession, storage method, type of bread consumed, daily bread expenditure, monthly income and the idea of “bread is cheap” are the most important variables affecting bread wastage. Regarding bread consumption, parents' profession, fathers' education level, monthly income, inadequate control in bakeries, household size and the idea of “bread makes people fat” are found to play significant roles.Practical implicationsThe results could be helpful to develop influential policies on healthy eating and aiming plans to reduce bread consumption to healthy levels and prevent bread waste.Social implicationsThis research contributes to knowledge regarding the underlying causes of the bread consumption and wastage of Turkish consumers in the light of the data analysis for Isparta province.Originality/valueThis paper contains unique and original understandings concerning bread consumption and wastage attitudes and determinants for consumers from Isparta, Turkey. The novel findings of this research have conduced to a better understanding of the key factors that affect bread consumption and waste. The paper also applies an econometric analysis using a CATREG model to analyse the factors influencing consumers' bread waste and consumption behaviour in Isparta province, Turkey.

Misfit Dislocations and Elastic Relaxation

1995 ◽  
Vol 399 ◽  
Author(s):  
H.P Strunk ◽  
S. Christiansen ◽  
M. Albrecht
Keyword(s):  
Driving Forces ◽  
Maximum Shear Stress ◽  
Strain Tensor ◽  
Three Dimensional ◽  
Local Strain ◽  
Misfit Strain ◽  
Relaxation Mechanism ◽  
Misfit Dislocations ◽  
Thermodynamical Equilibrium ◽  
Three Dimensional Finite Element

ABSTRACTPrior to relaxation of misfit strain by formation of misfit dislocations, a growing heteroepitaxial layer can relax elastically by forming surface undulations called ripples. With increasing amplitude of the ripples the misfit strain and thus stress fields grow markedly inhomogeneous, and dislocation formation may thus be triggered in areas of maximum shear stress. The surface directly above such a new dislocation then represents a band of preferential growth and develops into a ridge, which in turn redistributes the strain in the growing layer. This interwoven elastic/plastic relaxation mechanism can comparably easily be deduced from transmission electron and atomic force microscopy studies of SiGe layers grown onto silicon by liquid phase epitaxy. This growth technique exerts only very small driving forces and thus operates very near thermodynamical equilibrium. The local strain tensor and strain energy density are calculated for the actual layer geometries by three dimensional finite element method and provide for quantification of the mechanism.

scholarly journals Identification of a Direct Biosynthetic Pathway for UDP–N-Acetylgalactosamine from Glucosamine-6-Phosphate in Thermophilic Crenarchaeon Sulfolobus tokodaii

2018 ◽  
Vol 200 (10) ◽  
pp. e00048-18
Author(s):  
Mohammad Dadashipour ◽  
Mariko Iwamoto ◽  
Mohammad Murad Hossain ◽  
Jun-ichi Akutsu ◽  
Zilian Zhang ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Cell Extract ◽  
Biosynthetic Pathways ◽  
The Novel ◽  
Nucleotide Sugar ◽  
Content Type ◽  
Sulfolobus Tokodaii ◽  
Archaeal Species ◽  
A Cell ◽  
Bacterial Type

ABSTRACT Most organisms, from Bacteria to Eukarya, synthesize UDP–N-acetylglucosamine (UDP-GlcNAc) from fructose-6-phosphate via a four-step reaction, and UDP–N-acetylgalactosamine (UDP-GalNAc) can only be synthesized from UDP-GlcNAc by UDP-GlcNAc 4-epimerase. In Archaea, the bacterial-type UDP-GlcNAc biosynthetic pathway was reported for Methanococcales. However, the complete biosynthetic pathways for UDP-GlcNAc and UDP-GalNAc present in one archaeal species are unidentified. Previous experimental analyses on enzymatic activities of the ST0452 protein, identified from the thermophilic crenarchaeon Sulfolobus tokodaii, predicted the presence of both a bacterial-type UDP-GlcNAc and an independent UDP-GalNAc biosynthetic pathway in this archaeon. In the present work, functional analyses revealed that the recombinant ST2186 protein possessed an glutamine:fructose-6-phosphate amidotransferase activity and that the recombinant ST0242 protein possessed a phosphoglucosamine-mutase activity. Along with the acetyltransferase and uridyltransferase activities of the ST0452 protein, the activities of the ST2186 and ST0242 proteins confirmed the presence of a bacterial-type UDP-GlcNAc biosynthetic pathway in S. tokodaii. In contrast, the UDP-GlcNAc 4-epimerase homologue gene was not detected within the genomic data. Thus, it was expected that galactosamine-1-phosphate or galactosamine-6-phosphate (GalN-6-P) was provided by conversion of glucosamine-1-phosphate or glucosamine-6-phosphate (GlcN-6-P). A novel epimerase converting GlcN-6-P to GalN-6-P was detected in a cell extract of S. tokodaii, and the N-terminal sequence of the purified protein indicated that the novel epimerase was encoded by the ST2245 gene. Along with the ST0242 phosphogalactosamine-mutase activity, this observation confirmed the presence of a novel UDP-GalNAc biosynthetic pathway from GlcN-6-P in S. tokodaii. Discovery of the novel pathway provides a new insight into the evolution of nucleotide sugar metabolic pathways. IMPORTANCE In this work, a novel protein capable of directly converting glucosamine-6-phosphate to galactosamine-6-phosphate was successfully purified from a cell extract of the thermophilic crenarchaeon Sulfolobus tokodaii. Confirmation of this novel activity using the recombinant protein indicates that S. tokodaii possesses a novel UDP-GalNAc biosynthetic pathway derived from glucosamine-6-phosphate. The distributions of this and related genes indicate the presence of three different types of UDP-GalNAc biosynthetic pathways: a direct pathway using a novel enzyme and two conversion pathways from UDP-GlcNAc using known enzymes. Additionally, Crenarchaeota species lacking all three pathways were found, predicting the presence of one more unknown pathway. Identification of these novel proteins and pathways provides important insights into the evolution of nucleotide sugar biosynthesis, as well as being potentially important industrially.

scholarly journals Light Attention Predicts Protein Location from the Language of Life

2021 ◽  
Author(s):  
Hannes Staerk ◽  
Christian Dallago ◽  
Michael Heinzinger ◽  
Burkhard Rost
Keyword(s):  
Network Architecture ◽  
Language Models ◽  
Sequence Length ◽  
Evolutionary Information ◽  
Biological Processes ◽  
The Novel ◽  
Neural Network Architecture ◽  
Percentage Points ◽  
Protein Functions ◽  
A Cell

Although knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expertly chosen input features leveraging evolutionary information that is resource expensive to generate. We showcase using embeddings from protein language models for competitive localization predictions not relying on evolutionary information. Our lightweight deep neural network architecture uses a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention (LA). The method significantly outperformed the state-of-the-art for ten localization classes by about eight percentage points (Q10). The novel models are available as a web-service and as a stand-alone application at embed.protein.properties.

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