Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-genetic individuality in Escherichia coli motor switching

By analyzing 30 min, high-resolution recordings of single Escherichia coli flagellar motors in the physiological regime, we show that two main properties of motor switching—the mean clockwise and mean counter-clockwise interval durations—vary significantly. When we represent these quantities on a two-dimensional plot for several cells, the data do not fall on a one-dimensional curve, as expected with a single control parameter, but instead spread in two dimensions, pointing to motor individuality. The largest variations are in the mean counter-clockwise interval, and are attributable to variations in the concentration of the internal signaling molecule CheY-P. In contrast, variations in the mean clockwise interval are interpreted in terms of motor individuality. We argue that the sensitivity of the mean counter-clockwise interval to fluctuations in CheY-P is consistent with an optimal strategy of run and tumble. The concomittent variability in mean run length may allow populations of cells to better survive in rapidly changing environments by ‘hedging their bets’.
Objects Localisation from Motion with Constraints

This paper presents a method to estimate the 3D object position and occupancy given a set of object detections in multiple images and calibrated cameras. This problem is modelled as the estimation of a set of quadrics given 2D conics fit to the object bounding boxes. Although a closed form solution has been recently proposed, the resulting quadrics can be inaccurate or even be non valid ellipsoids in presence of noisy and inaccurate detections. This effect is especially important in case of small baselines, resulting in dramatic failures. To cope with this problem, we propose a set of linear constraints by matching the centres of the reprojected quadrics with the centres of the observed conics. These constraints can be solved with a linear system thus providing a more computationally efficient solution with respect to a non-linear alternative. Experiments on real data show that the proposed approach improves significantly the accuracy and the validity of the ellipsoids.
Increase of total creatine in human brain after oral supplementation of creatine-monohydrate.

The effect of oral creatine supplementation on brain metabolite concentrations was investigated in gray matter, white matter, cerebellum, and thalamus of healthy young volunteers by means of quantitative localized proton magnetic resonance spectroscopy in vivo (2.0 T, stimulated echo acquisition mode sequence; repetition time = 6,000 ms, echo time = 20 ms, middle interval = 10 ms, automated spectral evaluation). Oral consumption of 4 × 5 g creatine-monohydrate/day for 4 wk yielded a statistically significant increase (8.7% corresponding to 0.6 mM, P < 0.001) of the mean concentration of total creatine (tCr) when averaged across brain regions and subjects ( n = 6). The data revealed considerable intersubject variability (3.5-13.3%), with the smallest increases observed for the two male volunteers with the largest body weights. A regional analysis resulted in significant increases of tCr in gray matter (4.7%), white matter (11.5%), and cerebellum (5.4%) and was most pronounced in thalamus (14.6% corresponding to 1.0 mM). Other findings were significant decreases of N-acetyl-containing compounds in cerebellum and thalamus as well as of choline-containing compounds in thalamus. All cerebral metabolic alterations caused by oral Cr were reversible, as evidenced by control measurements at least 3 mo after the diet. This work demonstrates that excess consumption of Cr yields regionally dependent increases of the tCr concentration in human brain over periods of several weeks.
Use of Yeast Probiotics in Ruminants: Effects and Mechanisms of Action on Rumen pH, Fibre Degradation, and Microbiota According to the Diet

© 2012 Chaucheyras-Durand et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Use of Yeast Probiotics in Ruminants: Effects and Mechanisms of Action on Rumen pH, Fibre Degradation, and Microbiota According to the Diet
Seesaw model with softly broken Le−Lμ−Lτ

We enlarge the lepton sector of the Standard Model by adding to it two right-handed neutrino singlets, and propose a model based on the seesaw mechanism and on the lepton number = Le−Lμ−Lτ. The model is innovative from the theoretical point of view in that the -invariant mass term of the right-handed neutrinos is associated with the large mass scale responsible for the seesaw mechanism, whereas is softly broken at a smaller scale by the remaining Majorana mass terms of the right-handed neutrinos. While being very economical, the model has predictive power: one neutrino is massless (m3 = 0), the lepton mixing matrix U features Ue3 = 0, and the solar-neutrino oscillations have maximal amplitude.
Novel bioactive functionally graded coatings on Ti6Al4V

Bioactive glass coatings are very promising for implant materials due to their good adhesion, mechanical stability, and bioactivity. A new family of silicate-based glasses has been prepared and applied to metallic implants using a simple enameling technique. The graded approach used here reduces stress between layers, and preliminary indentation tests indicate a strong glass/metal adhesion.
Allogeneic Mesenchymal Stem Cells Ameliorate Aging Frailty: A Phase II Randomized, Double-Blind, Placebo-Controlled Clinical Trial

Abstract Background Aging frailty, characterized by decreased physical and immunological functioning, is associated with stem cell depletion. Human allogeneic mesenchymal stem cells (allo-hMSCs) exert immunomodulatory effects and promote tissue repair. Methods This is a randomized, double-blinded, dose-finding study of intravenous allo-hMSCs (100 or 200-million [M]) vs placebo delivered to patients (n = 30, mean age 75.5 ± 7.3) with frailty. The primary endpoint was incidence of treatment-emergent serious adverse events (TE-SAEs) at 1-month postinfusion. Secondary endpoints included physical performance, patient-reported outcomes, and immune markers of frailty measured at 6 months postinfusion. Results No therapy-related TE-SAEs occurred at 1 month. Physical performance improved preferentially in the 100M-group; immunologic improvement occurred in both the 100M- and 200M-groups. The 6-minute walk test, short physical performance exam, and forced expiratory volume in 1 second improved in the 100M-group (p = .01), not in the 200M- or placebo groups. The female sexual quality of life questionnaire improved in the 100M-group (p = .03). Serum TNF-α levels decreased in the 100M-group (p = .03). B cell intracellular TNF-α improved in both the 100M- (p < .0001) and 200M-groups (p = .002) as well as between groups compared to placebo (p = .003 and p = .039, respectively). Early and late activated T-cells were also reduced by MSC therapy. Conclusion Intravenous allo-hMSCs were safe in individuals with aging frailty. Treated groups had remarkable improvements in physical performance measures and inflammatory biomarkers, both of which characterize the frailty syndrome. Given the excellent safety and efficacy profiles demonstrated in this study, larger clinical trials are warranted to establish the efficacy of hMSCs in this multisystem disorder. Clinical Trial Registration www.clinicaltrials. gov: CRATUS (#NCT02065245).
An Inert Continuous Microreactor for the Isolation and Analysis of a Single Microbial Cell

Studying biological phenomena of individual cells is enabled by matching the scales of microbes and cultivation devices. We present a versatile, chemically inert microfluidic lab-on-a-chip (LOC) device for biological and chemical analyses of isolated microorganisms. It is based on the Envirostat concept and guarantees constant environmental conditions. A new manufacturing process for direct fusion bonding chips with functional microelectrodes for selective and gentle cell manipulation via negative dielectrophoresis (nDEP) was generated. The resulting LOC system offered a defined surface chemistry and exceptional operational stability, maintaining its structural integrity even after harsh chemical treatment. The microelectrode structures remained fully functional after thermal bonding and were proven to be efficient for single-cell trapping via nDEP. The microfluidic network consisted solely of glass, which led to enhanced chip reusability and minimized interaction of the material with chemical and biological compounds. We validated the LOC for single-cell studies with the amino acid secreting bacterium Corynebacterium glutamicum. Intracellular l-lysine production dynamics of individual bacteria were monitored based on a genetically encoded fluorescent nanosensor. The results demonstrate the applicability of the presented LOC for pioneering chemical and biological studies, where robustness and chemically inert surfaces are crucial parameters for approaching fundamental biological questions at a single-cell level.
Nitroglycerin induces late preconditioning against myocardial stunning via a PKC-dependent pathway.

Previous studies have shown that administration of nitric oxide (NO) donors induces a delayed cardioprotective effect indistinguishable from the late phase of ischemic preconditioning (PC). However, the ability of clinically relevant NO donors to elicit this phenomenon has not been evaluated. In this study we tested whether an NO-releasing agent that is nitroglycerin (NTG), which is widely used clinically, can mimic the late phase of ischemic PC. Four groups of conscious rabbits underwent six cycles of 4-min occlusion (O)/4-min reperfusion (R) for 3 consecutive days ( days 1, 2, and 3). The severity of myocardial stunning was assessed as the total deficit of systolic wall thickening (WTh) after the last O/R cycle. In the control group ( group I, n = 6), the total deficit of WTh was reduced by 50% and 51% on days 2 and 3 vs. day 1, respectively, indicating late PC against stunning. Pretreatment with NTG (2 μg ⋅ kg-1 ⋅ min-1iv over 1 h) on day 0 ( group II, n = 6) was as effective as ischemic PC in mitigating myocardial stunning 24 h later ( day 1); on days 2 and 3, no further reduction of stunning was seen. Coadministration of the PKC inhibitor chelerythrine (5 mg/kg) with NTG ( group III, n = 6) completely abrogated the NTG-induced protection. Pretreatment with chelerythrine alone ( group IV, n = 5) did not alter stunning. These results demonstrate that a relatively brief infusion of NTG induces a robust protective effect against stunning 24 h later via a protein kinase C (PKC)-dependent signaling mechanism. The magnitude of NTG-induced protection is equivalent to that observed during the late phase of ischemic PC. Late PC induced by brief treatment with NTG could be a useful therapeutic strategy for myocardial protection in patients with ischemic heart disease.
Extracellular Conformational Changes in the Capsid of Human Papillomaviruses Contribute to Asynchronous Uptake into Host Cells

ABSTRACT Human papillomavirus 16 (HPV16) is the leading cause of cervical cancer. For initial infection, HPV16 utilizes a novel endocytic pathway for host cell entry. Unique among viruses, uptake occurs asynchronously over a protracted period of time, with half-times between 9 and 12 h. To trigger endocytic uptake, the virus particles need to undergo a series of structural modifications after initial binding to heparan sulfate proteoglycans (HSPGs). These changes involve proteolytic cleavage of the major capsid protein L1 by kallikrein-8 (KLK8), exposure of the N terminus of the minor capsid protein L2 by cyclophilins, and cleavage of this N terminus by furin. Overall, the structural changes are thought to facilitate the engagement of an elusive secondary receptor for internalization. Here, we addressed whether structural changes are the rate-limiting steps during infectious internalization of HPV16 by using structurally primed HPV16 particles. Our findings indicate that the structural modifications mediated by cyclophilins and furin, which lead to exposure and cleavage, respectively, of the L2 N terminus contribute to the slow and asynchronous internalization kinetics, whereas conformational changes elicited by HSPG binding and KLK8 cleavage did not. However, these structural modifications accounted for only 30 to 50% of the delay in internalization. Therefore, we propose that limited internalization receptor availability for engagement of HPV16 causes slow and asynchronous internalization in addition to rate-limiting structural changes in the viral capsid. IMPORTANCE HPVs are the main cause of anogenital cancers. Their unique biology is linked to the differentiation program of skin or mucosa. Here, we analyzed another unique aspect of HPV infections using the prototype HPV16. After initial cell binding, HPVs display an unusually protracted residence time on the plasma membrane prior to asynchronous uptake. As viruses typically do not expose themselves to host immune sensing, we analyzed the underlying reasons for this unusual behavior. This study provides evidence that both extracellular structural modifications and possibly a limited availability of the internalization receptor contribute to the slow internalization process of the virus. These findings indicate that perhaps a unique niche for initial infection that could allow for rapid infection exists. In addition, our results may help to develop novel, preventive antiviral measures.
An Exploration of Social Functioning in Young People with Eating Disorders: A Qualitative Study

Previous research indicates adults with eating disorders (EDs) report smaller social networks, and difficulties with social functioning, alongside demonstrating difficulties recognising and regulating emotions in social contexts. Concurrently, those recovered from the illness have discussed the vital role offered by social support and interaction in their recovery. To date, little is known about the social skills and social networks of adolescents with EDs and this study aimed to conduct focus groups to explore the social functioning of 17 inpatients aged 12–17. Data were analysed using thematic analysis and six core themes were identified: group belonging, self-monitoring, social sensitivity, impact of hospitalisation, limited coping strategies and strategies for service provision. Key areas for service provision were: management of anxiety, development and/or maintenance of a social network and development of inter and intrapersonal skills. The most salient finding was that adolescents with EDs reported social difficulties which appeared to persist over and above those typically experienced at this point in the lifespan and therefore a key area for future focus is the development of appropriate coping strategies and solutions to deal with these reported difficulties.
VIOLA—A Multi-Purpose and Web-Based Visualization Tool for Neuronal-Network Simulation Output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity, and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. In order to cover the surface area captured by today's experimental techniques and to achieve sufficient self-consistency, such models contain millions of nerve cells. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based, and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model incorporating distance-dependent connectivity subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Interactive multi-view analysis therefore assists existing data analysis workflows. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis, and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.
Extracellular Ca2+ decreases chloride reabsorption in rat CTAL by inhibiting cAMP pathway.

The effect of activation of the Ca2+-sensing receptor on net Cl flux ( J Cl) has been investigated on microperfused cortical (C) thick ascending limb (TAL) from rat kidney. Increasing bath Ca2+ from 0.5 to 3 mM or adding 200 μM of the specific Ca2+-sensing receptor agonist neomycin reduced basal as well as antidiuretic hormone (ADH)-stimulated J Cl by 27.7 ± 5.0% and 25.9 ± 4.1%, respectively. J Cl remained unchanged in time control tubules. The effect of neomycin/Ca2+ on J Cl was blocked by two protein kinase A inhibitors, H-9 or H-89, but not by a protein kinase C inhibitor, GF-109203X, regardless of whether ADH was present or not. Moreover, H-89 decreased basal J Cl and prevented a further effect of 3 mM Ca2+. When J Cl was increased by 8-bromo-cAMP plus IBMX, no effect of 3 mM Ca2+ was observed. Inhibitors of phospholipase A2 and cytochrome P-450 monooxygenase failed to modify the effect of 3 mM Ca2+, although these agents dampened significantly the inhibitory effect of bradykinin on medullary TAL. We conclude that extracellular Ca2+ decreases basal and ADH-stimulated Cl reabsorption in CTAL by inhibiting the cAMP pathway, independently of protein kinase C or phospholipase A2 stimulation.
Evaluation of the validity of treatment decisions based on surrogate country models before introduction of the Polish FRAX and recommendations in comparison to current practice

Introduction Patients diagnosed before the Polish FRAX was introduced may require re-evaluation and treatment changes if the diagnosis was established according to a surrogate country FRAX score. The aim of the study was to evaluate the validity of treatment decisions based on the surrogate country model before introduction of the Polish FRAX and to provide recommendations based on the current practice. Material and methods We evaluated a group of 142 postmenopausal women (70.7 ±8.9 years) who underwent bone mineral density measurements. We used 22 country-specific FRAX models and compared these to the Polish model. Results The mean risk values for hip and major osteoporotic fractures within 10 years were 4.575 (from 0.82 to 8.46) and 12.47% (from 2.18 to 21.65), respectively. In the case of a major fracture, 94.4% of women would receive lifestyle advice, and 5.6% would receive treatment according to the Polish FRAX using the guidelines of the National Osteoporosis Foundation (NOF). Polish treatment thresholds would implement pharmacotherapy in 32.4% of the study group. In the case of hip fractures, 45% of women according to the NOF would require pharmacotherapy but only 9.8% of women would qualify according to Polish guidelines. Nearly all surrogate FRAX calculator scores proved significantly different form Polish (p > 0.05). Conclusions More patients might have received antiresorptive medication before the Polish FRAX. This study recommends re-evaluation of patients who received medical therapy before the Polish FRAX was introduced and a review of the recommendations, considering the side effects of antiresorptive medication.
SIMPLE‐type preconditioners for cell‐centered, colocated finite volume discretization of incompressible Reynolds‐averaged Navier–Stokes equations

This paper contains a comparison of four SIMPLE‐type methods used as solver and as preconditioner for the iterative solution of the (Reynolds‐averaged) Navier–Stokes equations, discretized with a finite volume method for cell‐centered, colocated variables on unstructured grids. A matrix‐free implementation is presented, and special attention is given to the treatment of the stabilization matrix to maintain a compact stencil suitable for unstructured grids. We find SIMPLER preconditioning to be robust and efficient for academic test cases and industrial test cases. Compared with the classical SIMPLE solver, SIMPLER preconditioning reduces the number of nonlinear iterations by a factor 5–20 and the CPU time by a factor 2–5 depending on the case. The flow around a ship hull at Reynolds number 2E9, for example, on a grid with cell aspect ratio up to 1:1E6, can be computed in 3 instead of 15 h.Copyright © 2012 John Wiley & Sons, Ltd.
Stability Improvement of CO 2 Foam for Enhanced Oil Recovery Applications Using Polyelectrolytes and Polyelectrolyte Complex Nanoparticles

CO2 foam for enhanced oil-recovery applications has been traditionally used in order to address mobility-control problems that occur during CO2 flooding. However, the supercritical CO2 foam generated by surfactant has a few shortcomings, such as loss of surfactant to the formation due to adsorption and lack of a stable front in the presence of crude oil. These problems arise because surfactants dynamically leave and enter the foam interface. We discuss the addition of polyelectrolytes and polyelectrolyte complex nanoparticles (PECNP) to the surfactant solution to stabilize the interface using electrostatic forces to generate stronger and longer-lasting foams. An optimized ratio and pH of the polyelectrolytes was used to generate the nanoparticles. Thereafter we studied the interaction of the polyelectrolyte–surfactant CO2 foam and the polyelectrolyte complex nanoparticle–surfactant CO2 foam with crude oil in a high-pressure, high-temperature static view cell. The nanoparticle–surfactant CO2 foam system was found to be more durable in the presence of crude oil. Understanding the rheology of the foam becomes crucial in determining the effect of shear on the viscosity of the foam. A high-pressure, high-temperature rheometer setup was used to shear the CO2 foam for the three different systems, and the viscosity was measured with time. It was found that the viscosity of the CO2 foams generated by these new systems of polyelectrolytes was slightly better than the surfactant-generated CO2 foams. Core-flood experiments were conducted in the absence and presence of crude oil to understand the foam mobility and the oil recovered. The core-flood experiments in the presence of crude oil show promising results for the CO2 foams generated by nanoparticle–surfactant and polyelectrolyte–surfactant systems. This paper also reviews the extent of damage, if any, that could be caused by the injection of nanoparticles. It was observed that the PECNP–surfactant system produced 58.33% of the residual oil, while the surfactant system itself produced 47.6% of the residual oil in place. Most importantly, the PECNP system produced 9.1% of the oil left after the core was flooded with the surfactant foam system. This proves that the PECNP system was able to extract more oil from the core when the surfactant foam system was already injected. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 44491.