Miracle-dz/UniFAR-FTUs huggingface dataset:
Kolmogorov-Sinai entropy and dissipation in driven classical Hamiltonian systems

Many connections between physics and information theory have been revealed since the development of classical information theory by Shannon. A key concept in this connection is entropy, which represents the amount of information transferred to the observer who performs measurements in an experiment. Statistical mechanics is a physical theory deeply connected to information by Jaynes’ Maximum Entropy principle, which defines equilibrium probability distributions as the ones that maximizes entropy under some physical constraints. In this way, these distributions are the less unbiased probabilities that can be assignment to an event. Following this path, the dissipated energy in a classical Hamiltonian process (also known as the thermodynamic entropy production) was connected to the relative entropy between the forward and backward probability densities. A recent work by Still et al. has revealed that energetic inefficiency and model inefficiency are equivalent concepts in Markovian processes, where the latter is defined as the difference in mutual information that the system’s state shares with the future and past environmental variables. This raises the question whether model unpredictability and energetic inefficiency are connected in the framework of classical physics. The aim of this study is to connect the concepts of random behavior of a classical Hamiltonian system with its energetic inefficiency. The random behavior of a classical system is quantified by the Kolmogorov-Sinai entropy associated with its dynamics, an information-theoretic approach to chaos, whereas energetic inefficiency is measured by the dissipated work.
Intestinal disposition of quercetin and its phase‐II metabolites after oral administration in healthy volunteers

Quercetin is one of the main dietary flavonoids and undergoes a substantial intestinal phase‐II metabolism. Quercetin conjugates have been detected in plasma and in urine, but their presence in the small intestine has not been assessed. This study aimed to investigate the intestinal metabolism and metabolite excretion of quercetin by the human small intestinal wall after oral dosing.
Digital Commons @ Michigan Tech Digital Commons @ Michigan Tech Brown carbon in tar balls from smoldering biomass combustion Brown carbon in tar balls from smoldering biomass combustion

We report the direct observation of laboratory production of spherical, carbonaceous particles – “tar balls” – from smoldering combustion of two commonly occurring dry mid-latitude fuels. Real-time measurements of spectrally varying absorption ˚Angstr ¨ om coefﬁcients (AAC) indicate that a class of light absorbing organic carbon (OC) with wavelength dependent imaginary part of its refractive index – optically deﬁned as “brown carbon” – is an important component of tar balls. The spectrum of the imaginary parts of their complex refractive indices can be described with a Lorentzian-like model with an effective resonance wavelength in the ultraviolet (UV) spectral region. Sensitivity calculations for containing (no absorption at and UV and total inclusion of the properties of tar into forcing models optical of UV in the
Geological Model of Mae Tang-Mae Ngad Diversion Tunnel Project, Northern Thailand

Most of infrastructure projects around the world have to focus on a clear understanding of geological model which may be determined from various sources of information. The limitation in geotechnical data and budget affects the accuracy of the geological model, particularly for projects of long and deep tunnel of which accessibility to the excavation points is difficult and far reaching. Therefore, an approach adopted for interpretation plays an important role in the level of uncertainty of the derived geological model. This paper focuses on the determination of the geological models at the site of a long water diversion tunnel project in a complex geologic setting in northern Thailand from an approach to understand the relationship between regional tectonic setting and local tectonic condition so that geological structures and rock mass conditions along the tunnel alignment can be assessed for a better planning of tunnel design and construction. The paper describes tectonic settings at regional scale (Northern Thailand and Eastern Myanmar), tectonic features and geologic condition in project area, geotechnical investigation and data along tunnel alignment and predicted tunnel ground behavior.
Phosphate Leaching from Green Roof Substrates—Can Green Roofs Pollute Urban Water Bodies?

Green roofs are an effective stormwater measure due to high water retention capacity and the ability of delaying stormwater runoff. However, low importance is still given to the pollutant leaching potential of substrates used in green roof construction. The aim of the study is to estimate the concentrations and loads of P-PO43− in runoff from extensive and intensive substrates. To achieve this goal, several commonly-used fresh substrates were analyzed for P-PO43− leaching potential in different scale experiments, from laboratory batch tests, leaching column experiments, and long-term monitoring of open air green roof containers. The results of the study confirmed that fresh green roof substrates contain phosphorus in significant amounts of 17–145 mg∙P-PO43−/kg and, thus, can contribute to eutrophication of freshwater ecosystems. High correlation between phosphate content estimated by HCl extraction and cumulative load in leachate tests suggests that the batch HCl extraction test can be recommended for the comparison and selection of substrates with low potential P leaching. Volume-weighted mean concentrations and UALs of P-PO43− leaching from fresh substrates were higher in cases of intensive substrates, but there was no clear relationship between substrate type and the observed P-PO43− concentration range. To avoid increasing eutrophication of urban receivers the implementation of P reduction measures is strongly recommended.
Towards an online-coupled chemistry-climate model: evaluation of trace gases and aerosols in COSMO-ART

Abstract. The online-coupled, regional chemistry transport model COSMO-ART is evaluated for periods in all seasons against several measurement datasets to assess its ability to represent gaseous pollutants and ambient aerosol characteristics over the European domain. Measurements used in the comparison include long-term station observations, satellite and ground-based remote sensing products, and complex datasets of aerosol chemical composition and number size distribution from recent field campaigns. This is the first time these comprehensive measurements of aerosol characteristics in Europe are used to evaluate a regional chemistry transport model. We show a detailed analysis of the simulated size-resolved chemical composition under different meteorological conditions. Mean, variability and spatial distribution of the concentrations of O3 and NOx are well reproduced. SO2 is found to be overestimated, simulated PM2.5 and PM10 levels are on average underestimated, as is AOD. We find indications of an overestimation of shipping emissions. Time evolution of aerosol chemical composition is captured, although some biases are found in relative composition. Nitrate aerosol components are on average overestimated, and sulfates underestimated. The accuracy of simulated organics depends strongly on season and location. While strongly underestimated during summer, organic mass is comparable in spring and autumn. We see indications for an overestimated fractional contribution of primary organic matter in urban areas and an underestimation of SOA at many locations. Aerosol number concentrations compare well with measurements for larger size ranges, but overestimations of particle number concentration with factors of 2–5 are found for particles smaller than 50 nm. Size distribution characteristics are often close to measurements, but show discrepancies at polluted sites. Suggestions for further improvement of the modeling system consist of the inclusion of a revised secondary organic aerosols scheme, aqueous-phase chemistry and improved aerosol boundary conditions. Our work sets the basis for subsequent studies of aerosol characteristics and climate impacts with COSMO-ART, and highlights areas where improvements are necessary for current regional modeling systems in general.
Genomic Heterogeneity and the Small Renal Mass

Purpose: Tumor heterogeneity may represent a barrier to preoperative genomic characterization by needle biopsy in clear cell renal cell carcinoma (ccRCC). The extent of heterogeneity in small renal tumors remains unknown. Therefore, we set out to evaluate heterogeneity in resected large and small renal tumors. Experimental Design: We conducted a study from 2013 to 2016 that evaluated 47 consecutive ccRCC tumors resected during radical or partial nephrectomy. Cases were designated as small (<4 cm) and large (>7 cm) tumors. Each tumor had three regions sampled. Copy-number variation (CNV) was assessed and gene expression analysis was performed to characterize the clear-cell A and B (ccA/ccB) profile and the cell-cycle progression (CCP) score. Genomic heterogeneity between three regions was evaluated using CNV subclonal events, regional expression profiles, and correlation between gene expression. Results: Twenty-three small and 24 large tumors were analyzed. Total CNVs and subclonal CNVs events were less frequent in small tumors (P < 0.001). Significant gene expression heterogeneity was observed for both CCP scores and ccA/ccB classifications. Larger tumors had more variance in CCP scores (P = 0.026). The distribution of ccA/ccB differed between small and large tumors with mixed ccA/ccB tumors occurring more frequently in the larger tumors (P = 0.024). Analysis of five mixed tumors (with both ccA/ccB regions) demonstrated the more aggressive ccB phenotype had greater CNV events (P = 0.014). Conclusions: Small renal tumors have much less genomic complexity and fewer subclonal events. Pretreatment genomic characterization with single-needle biopsy in small tumors may be useful to assess biologic potential and may influence therapy. Clin Cancer Res; 24(17); 4137–44. ©2018 AACR.
In Vitro Activity of Clofazimine against Nontuberculous Mycobacteria Isolated in Beijing, China

ABSTRACT Due to the natural resistance of nontuberculous mycobacteria (NTM) to many antibiotics, the treatment of diseases caused by NTM is often long-term but unsuccessful. The main goal of this study was to evaluate the in vitro susceptibilities to clofazimine of 209 isolates consisting of different NTM species isolated in Beijing, China. Furthermore, 47 reference strains were also tested, including 30 rapidly growing mycobacterium (RGM) species and 17 slowly growing mycobacterium (SGM) species. The potential molecular mechanism contributing to clofazimine resistance of NTM was investigated as well. Clofazimine exhibited excellent activity against both reference strains and clinical isolates of different SGM species, and most of the strains had MICs far below 1 μg/ml. Although the majority of the clinical isolates of Mycobacterium abscessus and Mycobacterium fortuitum had MICs higher than 2 μg/ml, 17 out of the 30 reference strains of different RGM species had MICs below 1 μg/ml in vitro. According to the MIC distributions, the tentative epidemiological cutoff (ECOFF) values for Mycobacterium kansasii, Mycobacterium avium, and Mycobacterium intracellulare were defined at 0.5 μg/ml, 1 μg/ml, and 2 μg/ml, respectively. Intriguingly, single-direction cross-resistance between bedaquiline- and clofazimine (Cfz)-resistant isolates was observed among the tested NTM species. This study demonstrates that clofazimine had strong activity against most SGM species in vitro, as well as some RGM species. The data provide important insights into the possible clinical application of Cfz to treat NTM infections.
Thin Slices of Athletes’ Nonverbal Behavior Give Away Game Location: Testing the Territoriality Hypothesis of the Home Game Advantage

The present research investigated whether perceivers could detect who is playing at home or away in soccer matches based on thin slices of professional (Experiment 1) and amateur (Experiment 3) athletes’ nonverbal behavior prior to the match and whether perceivers rated athletes playing at home relatively higher on behavioral dimensions (Experiments 2 and 3) linked to territoriality. In Experiment 1 (N = 80), participants watched short videos depicting soccer players prior to a UEFA Champions League match and rated whether athletes were more likely to be playing at home or away. In Experiment 2 (two groups N = 102 and N = 101), perceivers rated these videos in terms of assertiveness, dominance, and aggression. In Experiment 3, we replicated the procedure of Experiments 1 and 2 with different stimulus material from amateur soccer (N = 112). Participants could significantly differentiate between home playing and away playing athletes (Experiment 1: d = 0.44 and Experiment 3: d = 1.07). Experiments 2 and 3 showed that perceivers rated professional and amateur soccer players higher on assertiveness (d = 0.34–0.63), dominance (d = 0.20–0.55), and aggression (d = 0.16–0.49) when playing at home compared to playing away. Findings are supportive of evolutionary accounts of nonverbal behavior, ecological approaches to person perception, and the thin slices of behavior hypothesis by demonstrating that humans change their nonverbal behavior depending on game location. We discuss the relevance of the present findings for the home advantage in sports.
Effects of Physical Exercise on Adiponectin, Leptin, and Inflammatory Markers in Childhood Obesity: Systematic Review and Meta-Analysis

Abstract Background: New findings on adipose tissue physiology and obesity-associated inflammation status suggest that modification of the adipokine level can be relevant for the long-term prevention of obesity-associated chronic disease. Objectives: The scope of the present study was to investigate the effectiveness of physical exercise in reducing the systemic inflammation related to obesity in children. Methods: We conducted a systematic review with meta-analysis of controlled randomized trials, identified through electronic database search, which investigated the effect of physical exercise, without concomitant dietary intervention, on adiponectin, leptin, and/or other inflammatory markers in children up to age 18 years with a body mass index greater than the 95th percentile for age and sex. Results: Seven trials were included in the meta-analysis, with a total of 250 participants. Compared with the control group without any lifestyle modification, the physical exercise resulted in a reduction in leptin [standardized mean difference (SMD) −1.13; 95% confidence interval (95%CI): −1.89 to −0.37; I2 = 79.9%] and interleukin-6 (SMD −0.84; 95%CI: −1.45 to −0.23, I2 = 0.9%) and an increase in adiponectin plasma concentration (SMD 0.69; 95%CI: 0.02–1.35; I2 = 74.3%). Conclusions: These results indicate that physical exercise improved the inflammatory state in children with obesity. It is unclear whether this effect can reduce the risk of cardiovascular and metabolic disease in adulthood. Clinical trials with a uniform intervention protocol and outcome measurements are required to put our knowledge on adipose tissue biology into a clinical perspective.
Comparison of Synthetic Media Designed for Expansion of Adipose-Derived Mesenchymal Stromal Cells

Mesenchymal stromal cells (MSCs) are multipotent cells that can differentiate into various cell types, such as osteoblasts, myocytes, and adipocytes. This characteristic makes the cells a useful tool in developing new therapies for a number of common maladies and diseases. The utilization of animal-derived growth serum, such as fetal bovine serum (FBS), for the expansion of MSCs has traditionally been used for cell culture. However, in clinical applications, animal-derived products present limitations and safety concerns for the recipient, as exposure to animal (xeno-) antigens and infectious agents is possible. Multiple synthetic, xeno-free media have been developed to combat these limitations of animal-derived growth serum and have the potential to be used in ex vivo MSC expansion for clinical use. The goal of this study was to determine if xeno-free media are adequate to significantly and efficiently expand MSCs derived from adipose tissue. MSCs were cultured in both standard FBS-containing as well as xeno-free media. The media were compared for cell yield, viability, and phenotypic expression via flow cytometry and directed differentiation. The xeno-free media that were tested were StemMACS MSC Expansion Media (Miltenyi Biotec, Bergisch Gladbach, Germany), PLTMax Human Platelet Lysate (Sigma-Aldrich, St. Louis, MO, USA), and MesenCult-hPL media (Stemcell Technologies, Vancouver, BC, Canada). All xeno-free media showed promise as a feasible replacement for animal-derived growth serums. The xeno-free media expanded MSCs more quickly than the FBS-containing medium and also showed great similarity in cell viability and phenotypic expression. In fact, each xeno-free media produced a greater viable cell yield than the standard FBS-containing medium.
Multiple phosphorylation sites on γ‐tubulin are essential and contribute to the biogenesis of basal bodies in Tetrahymena

The mechanisms that regulate γ‐tubulin, including its post‐translational modifications, are poorly understood. γ‐Tubulin is important for the duplication of centrioles and structurally similar basal bodies (BBs), organelles which contain a ring of nine triplet microtubules. The ciliate Tetrahymena thermophila carries hundreds of cilia in a single cell and provides an excellent model to specifically address the role of γ‐tubulin in the BBs assembly and maintenance. The genome of Tetrahymena contains a single γ‐tubulin gene. We show here that there are multiple isoforms of γ‐tubulin that are likely generated by post‐translational modifications. We identified evolutionarily conserved serine and threonine residues as potential phosphosites of γ‐tubulin, including S80, S129, S131, T283, and S360. Several mutations that either prevent (S80A, S131A, T283A, S360A) or mimic (T283D) phosphorylation were conditionally lethal and at a higher temperature phenocopied a loss of γ‐tubulin. Cells that overproduced S360D γ‐tubulin displayed phenotypes consistent with defects in the microtubule‐dependent functions, including an asymmetric division of the macronucleus and abnormalities in the pattern of BB rows, including gaps, fragmentation, and misalignment. In contrast, overexpression of S129D γ‐tubulin affected the orientation, docking, and structure of the BBs, including a loss of either the B‐ or C‐subfibers or the entire triplets. We conclude that conserved potentially phosphorylated amino acids of γ‐tubulin are important for either the assembly or stability of BBs.
C7 vertebra homeotic transformation in domestic dogs – are Pug dogs breaking mammalian evolutionary constraints?

The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs. The aim of this study was to describe the prevalence of cervical ribs in a large group of domestic dogs of different breeds, and explore a possible relation with other congenital vertebral malformations (CVMs) in the breed with the highest prevalence of cervical ribs. By phenotyping we hoped to give clues as to the underlying genetic causes. Twenty computed tomography studies from at least two breeds belonging to each of the nine groups recognized by the Federation Cynologique Internationale, including all the brachycephalic ‘screw‐tailed’ breeds that are known to be overrepresented for CVMs, were reviewed. The Pug dog was more affected by cervical ribs than any other breed (46%; P < 0.001), and was selected for further analysis. No association was found between the presence of cervical ribs and vertebral body formation defect, bifid spinous process, caudal articular process hypoplasia/aplasia and an abnormal sacrum, which may infer they have a different aetiopathogenesis. However, Pug dogs with cervical ribs were more likely to have a transitional thoraco‐lumbar vertebra (P = 0.041) and a pre‐sacral vertebral count of 26 (P < 0.001). Higher C7/T1 dorsal spinous processes ratios were associated with the presence of cervical ribs (P < 0.001), supporting this is a true homeotic transformation. Relaxation of the stabilizing selection has likely occurred, and the Pug dog appears to be a good naturally occurring model to further investigate the aetiology of cervical ribs, other congenital vertebral anomalies and numerical alterations.
In Vitro Activity of Imipenem-Relebactam against Clinical Isolates of Gram-Negative Bacilli Isolated in Hospital Laboratories in the United States as Part of the SMART 2016 Program

ABSTRACT Relebactam is a non-β-lactam, bicyclic diazabicyclooctane β-lactamase inhibitor of class A and class C β-lactamases, including Klebsiella pneumoniae carbapenemases (KPCs). It is in phase 3 clinical development in combination with imipenem/cilastatin. The in vitro activities of imipenem-relebactam, imipenem, and comparators were determined using the Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution method for isolates of Enterobacteriaceae (n = 3,419) and Pseudomonas aeruginosa (n = 896) collected in 2016 by 21 U.S. hospital laboratories participating in the SMART (Study for Monitoring Antimicrobial Resistance Trends) global surveillance program. Relebactam was tested at a fixed concentration of 4 μg/ml. Imipenem-relebactam MICs were interpreted using CLSI breakpoints for imipenem. Rates of susceptibility to imipenem-relebactam and imipenem for non-Proteeae Enterobacteriaceae (n = 3,143) and P. aeruginosa were 99.1% (3,115/3,143) and 95.9% (3,013/3,143) and were 94.4% (846/896) and 74.7% (669/896), respectively. Relebactam restored imipenem susceptibility to 78.5% (102/130) of imipenem-nonsusceptible non-Proteeae Enterobacteriaceae and to 78.0% (177/227) of imipenem-nonsusceptible P. aeruginosa isolates. Susceptibility to imipenem-relebactam was 98.2% (444/452) and 82.2% (217/264) for multidrug-resistant (MDR) non-Proteeae Enterobacteriaceae and MDR P. aeruginosa, respectively. Given the ability of relebactam to restore susceptibility to imipenem in nonsusceptible isolates of both non-Proteeae Enterobacteriaceae and P. aeruginosa and to demonstrate potent activity against current MDR isolates of both non-Proteeae Enterobacteriaceae and P. aeruginosa, further development of imipenem-relebactam appears warranted.