bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fourth law of thermodynamics: steepest entropy ascent
Authors: Beretta Gian Paolo 
Published: March 2020

When thermodynamics is understood as the science (or art) of constructing effective models of natural phenomena by choosing a minimal level of description capable of capturing the essential features of the physical reality of interest, the scientific community has identified a set of general rules that the model must incorporate if it aspires to be consistent with the body of known experimental evidence. Some of these rules are believed to be so general that we think of them as laws of Nature, such as the great conservation principles, whose ‘greatness’ derives from their generality, as masterfully explained by Feynman in one of his legendary lectures. The second law of thermodynamics is universally contemplated among the great laws of Nature. In this paper, we show that in the past four decades, an enormous body of scientific research devoted to modelling the essential features of non-equilibrium natural phenomena has converged from many different directions and frameworks towards the general recognition (albeit still expressed in different but equivalent forms and language) that another rule is also indispensable and reveals another great law of Nature that we propose to call the ‘fourth law of thermodynamics’. We state it as follows: every non-equilibrium state of a system or local subsystem for which entropy is well defined must be equipped with a metric in state space with respect to which the irreversible component of its time evolution is in the direction of steepest entropy ascent compatible with the conservation constraints. To illustrate the power of the fourth law, we derive (nonlinear) extensions of Onsager reciprocity and fluctuation–dissipation relations to the far-non-equilibrium realm within the framework of the rate-controlled constrained-equilibrium approximation (also known as the quasi-equilibrium approximation).This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Formulation of moment equations for rarefied gases within two frameworks of non-equilibrium thermodynamics: RET and GENERIC
Authors: Öttinger Hans Christian , Struchtrup Henning , Torrilhon Manuel 
Published: March 2020

In this work, we make a further step in bringing together different approaches to non-equilibrium thermodynamics. The structure of the moment hierarchy derived from the Boltzmann equation is at the heart of rational extended thermodynamics (RET, developed by Ingo Müller and Tommaso Ruggeri). Whereas the full moment hierarchy has the structure expressed in the general equation for the nonequilibrium reversible–irreversible coup- ling (GENERIC), the Poisson bracket structure of reversible dynamics postulated in that approach is a major obstacle for truncating moment hierarchies, which seems to work only in exceptional cases (most importantly, for the five moments associated with conservation laws). The practical importance of truncated moment hierarchies in rarefied gas dynamics and microfluidics motivates us to develop a new strategy for establishing the full GENERIC structure of truncated moment equations, based on non-entropy-producing irreversible processes associated with Casimir symmetry. Detailed results are given for the special case of 10 moments.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
A new continuum model for general relativistic viscous heat-conducting media
Authors: Romenski E. , Peshkov I. , Dumbser M. , Fambri F. 
Published: March 2020

The lack of formulation of macroscopic equations for irreversible dynamics of viscous heat-conducting media compatible with the causality principle of Einstein’s special relativity and the Euler–Lagrange structure of general relativity is a long-lasting problem. In this paper, we propose a possible solution to this problem in the framework of SHTC equations. The approach does not rely on postulates of equilibrium irreversible thermodynamics but treats irreversible processes from the non-equilibrium point of view. Thus, each transfer process is characterized by a characteristic velocity of perturbation propagation in the non-equilibrium state, as well as by an intrinsic time/length scale of the dissipative dynamics. The resulting system of governing equations is formulated as a first-order system of hyperbolic equations with relaxation-type irreversible terms. Via a formal asymptotic analysis, we demonstrate that classical transport coefficients such as viscosity, heat conductivity, etc., are recovered in leading terms of our theory as effective transport coefficients. Some numerical examples are presented in order to demonstrate the viability of the approach.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Rational extended thermodynamics of dense polyatomic gases incorporating molecular rotation and vibration
Authors: Arima Takashi , Ruggeri Tommaso , Sugiyama Masaru 
Published: March 2020

The paper aims to construct a rational extended thermodynamics (RET) theory of dense polyatomic gases by taking into account the experimental evidence that the relaxation time of molecular rotation and that of molecular vibration are quite different from each other. For simplicity, we focus on gases with only one dissipative process due to bulk viscosity. In fact, in some polyatomic gases, the effect of bulk viscosity is much larger than that of shear viscosity and heat conductivity. The present theory includes the previous RET theory of dense gases with six fields as a particular case, and it also includes the RET theory of rarefied polyatomic gases with seven fields in the rarefied-gas limit. The closure is carried out by using the universal principles, that is, Galilean invariance and objectivity, entropy principle, and thermodynamic stability (convexity of entropy), where the duality principle connecting rarefied gases to dense gases also plays an important role. A detailed discussion is devoted to the expression of the production terms in the system of balance equations. As typical examples, we study a gas with virial equations of state and a van der Waals gas. Lastly the dispersion relation of a linear wave is derived, and its comparison with experimental data is made.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Intrinsic properties of conservation-dissipation formalism of irreversible thermodynamics
Authors: Yong Wen-An 
Published: March 2020

This paper proposes four fundamental requirements for establishing PDEs (partial differential equations) modelling irreversible processes. We show that the PDEs derived via the CDF (conservation-dissipation formalism) meet all the requirements. In doing so, we find useful constraints on the freedoms of CDF and point out that a shortcoming of the formalism can be remedied with the help of the Maxwell iteration. It is proved that the iteration preserves the gradient structure and strong dissipativeness of the CDF-based PDEs. A refined formulation of the second law of thermodynamics is given to characterize the strong dissipativeness, while the gradient structure corresponds to nonlinear Onsager relations. Further advantages and limitations of CDF will also be presented.This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Variational principles and nonequilibrium thermodynamics
Authors: Ván P. , Kovács R. 
Published: March 2020

Variational principles play a fundamental role in deriving the evolution equations of physics. They work well in the case of non-dissipative evolution, but for dissipative systems, the variational principles are not unique and not constructive. With the methods of modern nonequilibrium thermodynamics, one can derive evolution equations for dissipative phenomena and, surprisingly, in several cases, one can also reproduce the Euler–Lagrange form and symplectic structure of the evolution equations for non-dissipative processes. In this work, we examine some demonstrative examples and compare thermodynamic and variational techniques. Then, we argue that, instead of searching for variational principles for dissipative systems, there is another viable programme: the second law alone can be an effective tool to construct evolution equations for both dissipative and non-dissipative processes.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Weak invariants in dissipative systems: action principle and Noether charge for kinetic theory
Authors: Abe Sumiyoshi 
Published: March 2020

In non-equilibrium classical thermostatistics, the state of a system may be described by not only dynamical/thermodynamical variables but also a kinetic distribution function. This ‘double structure’ bears some analogy with that in quantum thermodynamics, where both dynamical variables and the Hilbert space are involved. Recently, the concept of weak invariants has repeatedly been discussed in the context of quantum thermodynamics. A weak invariant is defined in such a way that its value changes in time but its expectation value is conserved under time evolution prescribed by a kinetic equation. Here, a new aspect of a weak invariant is revealed for the classical Fokker–Planck equation as an example of classical kinetic equations. The auxiliary field formalism is applied to the construction of the action for the kinetic equation. Then, it is shown that the auxiliary field is a weak invariant and is the Noether charge. The action is invariant under the transformation generated by the weak invariant. The result may shed light on possible roles of the symmetry principle in the kinetic descriptions of non-equilibrium systems.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Gradient and GENERIC time evolution towards reduced dynamics
Authors: Grmela M. , Klika V. , Pavelka M. 
Published: March 2020

Reduction of a mesoscopic dynamical theory to equilibrium thermodynamics brings to the latter theory the fundamental thermodynamic relation (i.e. entropy as a function of the thermodynamic state variables). The reduction is made by following the mesoscopic time evolution to its conclusion, i.e. to fixed points at which the time evolution ceases to continue. The approach to fixed points is driven by entropy, that, if evaluated at the fixed points, becomes the thermodynamic entropy. Since the fixed points are parametrized by the thermodynamic state variables (by constants of motion), the thermodynamic entropy arises as a function of the thermodynamic state variables and thus the final outcome of the reduction is the fundamental thermodynamic relation. This reduction process extends also to reductions in which the reduced theory still involves the time evolution (e.g. reduction of kinetic theory to hydrodynamics). The essence of the extension is the replacement of the mesoscopic time evolution of the state variables with the corresponding mesoscopic time evolution of the vector field (i.e. of the fluxes). The fixed point in this flux time evolution is the vector field generating the reduced mesoscopic time evolution. The flux-entropy driving the flux time evolution becomes, if evaluated at the fixed point, the flux fundamental thermodynamic relation in the reduced dynamical theory. We show that the flux-entropy is a potential related to the entropy production.This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial
Authors: Chen Zhaowei , Hu Jijia , Zhang Zongwei , Jiang Shan , Han Shoumeng , Yan Dandan , Zhuang Ruhong , Hu Ben , Zhang Zhan 
Published: March 2020

AbstractAimsStudies have indicated that chloroquine (CQ) shows antagonism against COVID-19 in vitro. However, evidence regarding its effects in patients is limited. This study aims to evaluate the efficacy of hydroxychloroquine (HCQ) in the treatment of patients with COVID-19.Main methodsFrom February 4 to February 28, 2020, 62 patients suffering from COVID-19 were diagnosed and admitted to Renmin Hospital of Wuhan University. All participants were randomized in a parallel-group trial, 31 patients were assigned to receive an additional 5-day HCQ (400 mg/d) treatment, Time to clinical recovery (TTCR), clinical characteristics, and radiological results were assessed at baseline and 5 days after treatment to evaluate the effect of HCQ.Key findingsFor the 62 COVID-19 patients, 46.8% (29 of 62) were male and 53.2% (33 of 62) were female, the mean age was 44.7 (15.3) years. No difference in the age and sex distribution between the control group and the HCQ group. But for TTCR, the body temperature recovery time and the cough remission time were significantly shortened in the HCQ treatment group. Besides, a larger proportion of patients with improved pneumonia in the HCQ treatment group (80.6%, 25 of 31) compared with the control group (54.8%, 17 of 31). Notably, all 4 patients progressed to severe illness that occurred in the control group. However, there were 2 patients with mild adverse reactions in the HCQ treatment group. Significance: Among patients with COVID-19, the use of HCQ could significantly shorten TTCR and promote the absorption of pneumonia.SignificanceAmong patients with COVID-19, the use of HCQ could significantly shorten TTCR and promote the absorption of pneumonia.Trial registrationURL: https://www.clinicaltrials.gov/. The unique identifier: ChiCTR2000029559.
Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
Authors: Venkatakrishnan AJ , Puranik Arjun , Anand Akash , Zemmour David , Yao Xiang , Wu Xiaoying , Chilaka Ramakrishna , Murakowski Dariusz K. , Standish Kristopher , Raghunathan Bharathwaj , Wagner Tyler , Garcia-Rivera Enrique , Solomon Hugo , Garg Abhinav , Barve Rakesh , Anyanwu-Ofili Anuli , Khan Najat , Soundararajan Venky 
Published: March 2020

AbstractThe COVID-19 pandemic demands assimilation of all available biomedical knowledge to decode its mechanisms of pathogenicity and transmission. Despite the recent renaissance in unsupervised neural networks for decoding unstructured natural languages, a platform for the real-time synthesis of the exponentially growing biomedical literature and its comprehensive triangulation with deep omic insights is not available. Here, we present the nferX platform for dynamic inference from over 45 quadrillion possible conceptual associations extracted from unstructured biomedical text, and their triangulation with Single Cell RNA-sequencing based insights from over 25 tissues. Using this platform, we identify intersections between the pathologic manifestations of COVID-19 and the comprehensive expression profile of the SARS-CoV-2 receptor ACE2. We find that tongue keratinocytes, airway club cells, and ciliated cells are likely underappreciated targets of SARS-CoV-2 infection, in addition to type II pneumocytes and olfactory epithelial cells. We further identify mature small intestinal enterocytes as a possible hotspot of COVID-19 fecal-oral transmission, where an intriguing maturation-correlated transcriptional signature is shared between ACE2 and the other coronavirus receptors DPP4 (MERS-CoV) and ANPEP (α-coronavirus). This study demonstrates how a holistic data science platform can leverage unprecedented quantities of structured and unstructured publicly available data to accelerate the generation of impactful biological insights and hypotheses.The nferX Platform Single-cell resource -https://academia.nferx.com/
Dispersion of a new coronavirus SARS-CoV-2 by airlines in 2020: Temporal estimates of the outbreak in Mexico
Authors: Cruz-Pacheco G , Bustamante-Castañeda J.F , Caputo J.G , Jiménez-Corona ME , Ponce-de-León S 
Published: March 2020

SummaryOn January 23, 2020, China imposed a quarantine on the city of Wuhan to contain the SARS-CoV-2 outbreak. Regardless of this measure the new infection has spread to several countries around the world. Here, we developed a method to study the dissemination of this infection by the airline routes and we give estimations of the time of arrival of the outbreaks to the different cities.In this work we show an analysis of the dispersion of this infection to other cities by airlines based on the classic model the Kermack and McKendrick complemented with diffusion on a graph composed of nodes which represent the cities and edges which represent the airline routes. We do several numerical simulations to estimate the date of arrival to different cities starting the infection at Wuhan, China and to show the robustness of the estimation respect to changes in the epidemiological parameters and to changes on the graph. we use Mexico City as an example. In this case, our estimate of the arrival time is between March 20 and March 30, 2020. This analysis is limited to the analysis of dispersion by airlines, so this estimate should be taken as an overestimate since the infection can arrive by other means.This model estimates the arrival of the infectious outbreak to Mexico between March 20 and March 30. This estimation gives a time period to implement and strengthen preventive measures aimed at the general population, as well as to strengthen hospital infrastructure and training of human resources in health.
Risk assessment of progression to severe conditions for patients with COVID-19 pneumonia: a single-center retrospective study
Authors: Zeng Lijiao , Li Jialu , Liao Mingfeng , Hua Rui , Huang Pilai , Zhang Mingxia , Zhang Youlong , Shi Qinlang , Xia Zhaohua , Ning Xinzhong , Liu Dandan , Mo Jiu , Zhou Ziyuan , Li Zigang , Fu Yu , Liao Yuhui , Yuan Jing , Wang Lifei , He Qing , Liu Lei , Qiao Kun 
Published: March 2020

AbstractBackgroundManagement of high mortality risk due to significant progression requires prior assessment of time-to-progression. However, few related methods are available for COVID-19 pneumonia.MethodsWe retrospectively enrolled 338 adult patients admitted to one hospital between Jan 11, 2020 to Feb 29, 2020. The final follow-up date was March 8, 2020. We compared characteristics between patients with severe and non-severe outcome, and used multivariate survival analyses to assess the risk of progression to severe conditions.ResultsA total of 76 (31.9%) patients progressed to severe conditions and 3 (0.9%) died. The mean time from hospital admission to severity onset is 3.7 days. Age, body mass index (BMI), fever symptom on admission, co-existing hypertension or diabetes are associated with severe progression. Compared to non-severe group, the severe group already demonstrated, at an early stage, abnormalities in biomarkers indicating organ function, inflammatory responses, blood oxygen and coagulation function. The cohort is characterized with increasing cumulative incidences of severe progression up to 10 days after admission. Competing risks survival model incorporating CT imaging and baseline information showed an improved performance for predicting severity onset (mean time-dependent AUC = 0.880).ConclusionsMultiple predisposition factors can be utilized to assess the risk of progression to severe conditions at an early stage. Multivariate survival models can reasonably analyze the progression risk based on early-stage CT images that would otherwise be misjudged by artificial analysis.
Selecting donors for faecal microbiota transplantation in ulcerative colitis
Authors: de Leeuw Marcel A. , Duval Manuel X. 
Published: March 2020

BackgroundInflammatory bowel disease (IBD) is a set of conditions characterized by non-infectious chronic inflammation of the gastrointestinal tract. These primarily include Crohn’s disease (CD), ulcerative colitis (UC) and indeterminate colitis. Fecal microbiota transplantation (FMT) has proven to be an effective treatment for some patients with active UC. There is currently no procedure allowing to predict the patients’ response and to select the most adequate donor(s).AimInvestigate microbiome characteristics in association with responder/non-responder status and develop selection criteria for donor samples to be used for UC FMT.MethodsAvailable UC longitudinal FMT microbiome data sets were in part combined and reanalyzed, with focus on species level changes in the microbiota, using state-of-the-art 16S analysis routines.ResultsWe predicted antibiotic resistance to be higher in non-responders (p=0.0064). Microbiomes of UC FMT responder donors have higher phylogenetic diversity (p=0.0026) and a higher proportion of facultative anaerobes (p=3.3E-5) as compared to non-responder donors. We predicted succinate and histamine to be increased in non-responder donors and non-responders, respectively. Sialic acid catabolism was also predicted to be increased in non-responder donors. Tryptamine and indole-3-acetaldehyde were predicted to be increased in responder donors.ConclusionsOur findings contribute to the establishment of selection criteria for UC FMT donor samples and composition guidelines for future synthetic microbial communities. Our results suggest that oxidative stress resistant facultative anaerobes are important for the establishment of an anaerobic environment and a successful UC FMT therapy. Several metabolites can be tested for additional optimization or prioritization of stool bank samples for UC FMT. Our results question the usefulness of antibiotics based preparation of the gut, prior to FMT.
The early scientific literature response to the novel Coronavirus outbreak: who published what?
Authors: Gori Davide , Boetto Erik , Fantini Maria Pia 
Published: March 2020

AbstractIntroductionRecent events highlight how emerging and re-emerging pathogens are becoming global challenges for public health. In December 2019, a novel coronavirus has emerged. This has suddenly turned out into global health concern.ObjectivesAim of this research is to focus on the bibliometric aspects in order to measure what is published in the first 30-days of a global epidemic outbreakMethodsWe searched PubMed database in order to find all relevant studies in the first 30-days from the first publication.ResultsFrom the initial 442 identified articles, 234 were read in-extenso. The majority of papers come from China, UK and USA. 63.7% of the papers were commentaries, editorials and reported data and only 17.5% of the sources used data directly collected on the field. Topics mainly addressed were “epidemiology”, “preparedness” and “generic discussion”. NNR showed a reduction for both the objectives assessed from January to February.Conclusions“Diagnosis” and effective preventive and therapeutic measures were the fields in which more research is still needed. The vast majority of scientific literature in the first 30-days of an epidemic outbreak is based on reported data rather than primary data. Nevertheless, the scientific statements and public health decisions rely on these data.Strengths of our studyThis is the first bibliometric research in Pubmed Database on the first 30 days of publications regarding the novel Coronavirus (SARS-nCoV-2) outbreak of 2019.The vast majority of publication in the first 30-days of an epidemic outbreak are reported data or comments, and only a small fraction of the papers have directly collected data.Limitations of our studyOur research is only PubMed based. It ill be auspicable to consult more than one relevant database in future papers.In addition, we excluded non-English publications leading to a potential bias due to the fact that the outbreak started in China.