julilili42/papers huggingface dataset:
Benefits at the nanoscale: a review of nanoparticle‐enabled processes favouring microbial growth and functionality
2020-07-23

Summary Nanoparticles are ubiquitous and co‐occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe‐mineral interactions at large, microbe‐nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano‐sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe‐nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size‐dependent solubility, with a focus on environmentally‐relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano‐tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle‐associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size‐dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.
Reconstituting social contracts in conflict-affected MENA countries: Whither Iraq and Libya?
2020-07-23

This article discusses the prospects for forging new social contracts in highly fragile and conflict affected countries. Building on analytical insights from the political settlements and state fragility literature, conceptualising peacebuilding processes as efforts to forge social contracts enables us to address the roles of governments, social groups, citizens and external stakeholders. We discuss the potential for peacebuilding processes to realise social contracts by assessing societal perceptions of the core public good that citizens expect the state to provide, namely protection. We address two cases where 'stateness' was destroyed by foreign intervention and civil war: Iraq (since 2003) and Libya (since 2011). We discuss the troubled recent trajectories of efforts to build peace in Iraq and Libya along the substantive, spatial and temporal dimensions of the social contract. Drawing on interviews, survey results and estimates of civilian casualties, we take a 'bottom-up' perspective of their societies' experiences and expectations regarding protection. We conclude that in both countries the provision of protection by the state and others runs counter to the expectations of significant parts of the population. At the national level, major social groups have been unable to overcome mutual distrust, while continued threats to physical security reduce the prospects that any social contract able to deliver other public goods can ever emerge. Existing political settlements in both countries have rewarded the politicization of ethno-sectarian identity (especially in Iraq) and have benefited economic war lordism (especially in Libya). We conclude that as social contracts at the national level are unlikely to emerge, the consequences of de-facto break ups of both countries must be acknowledged if social contracts at sub-national levels are to have any chance of delivering peace.
High-resolution X-ray spectroscopy of the stellar wind in Vela X-1 during a flare
2020-07-23

Context. We present a ~130 ks observation of the prototypical wind-accreting, high-mass X-ray binary Vela X-1 collected with XMM-Newton at orbital phases between 0.12 and 0.28. A strong flare took place during the observation that allows us to investigate the reaction of the clumpy stellar wind to the increased X-ray irradiation. Aims. To examine the wind’s reaction to the flare, we performed both time-averaged and time-resolved analyses of the RGS spectrum and examined potential spectral changes. Methods. We focused on the high-resolution XMM-Newton RGS spectra and divided the observation into pre-flare, flare, and post-flare phases. We modeled the time-averaged and time-resolved spectra with phenomenological components and with the self-consistent photoionization models calculated via CLOUDY and XSTAR in the pre-flare phase, where strong emission lines due to resonant transitions of highly ionized ions are seen. Results. In the spectra, we find emission lines corresponding to K-shell transitions in highly charged ions of oxygen, neon, magnesium, and silicon as well as radiative recombination continua (RRC) of oxygen. Additionally, we observe potential absorption lines of magnesium at a lower ionization stage and features identified as iron L lines. The CLOUDY and XSTAR photoionization models provide contradictory results, either pointing towards uncertainties in theory or possibly a more complex multi-phase plasma, or both. Conclusions. We are able to demonstrate the existence of a plethora of variable narrow features, including the firm detection of oxygen lines and RRC that RGS enables to observe in this source for the first time. We show that Vela X-1 is an ideal source for future high-resolution missions, such as XRISM and Athena .
GJ 357 b
2020-07-23

Aims. In this paper we present a deep X-ray observation of the nearby M dwarf GJ 357 and use it to put constraints on the atmospheric evolution of its planet, GJ 357 b. We also analyse the systematic errors in the stellar parameters of GJ 357 in order to see how they affect the perceived planetary properties. Methods. By comparing the observed X-ray luminosity of its host star, we estimate the age of GJ 357 b as derived from a recent XMM-Newton observation (log L x [erg s −1 ] = 25.73), with L x − age relations for M dwarfs. We find that GJ 357 presents one of the lowest X-ray activity levels ever measured for an M dwarf, and we put a lower limit on its age of 5 Gyr. Using this age limit, we performed a backwards reconstruction of the original primordial atmospheric reservoir. Furthermore, by considering the systematic errors in the stellar parameters, we find a range of possible planetary masses, radii, and densities. Results. From the backwards reconstruction of the irradiation history of GJ 357 b’s we find that the upper limit of its initial primordial atmospheric mass is ~38 M ⊕ . An initial atmospheric reservoir significantly larger than this may have survived through the X-ray and ultraviolet irradiation history, which would not be consistent with current observations that suggest a telluric composition. However, given the relatively small mass of GJ 357 b, even accreting a primordial envelope ≳10 M ⊕ would have been improbable as an unusually low protoplanetary disc opacity, large-scale migration, and a weak interior luminosity would have been required. For this reason, we discard the possibility that GJ 357 b was born as a Neptunian- or Jovian-sized body. In spite of the unlikelihood of a currently existing primordial envelope, volcanism and outgassing may have contributed to a secondary atmosphere. Under this assumption, we present three different synthetic IR spectra for GJ 357 b that one might expect, consisting of 100% CO 2 , 100% SO 2 , and 75% N 2 , 24% CO 2 and 1% H 2 O , respectively. Future observations with space-based IR spectroscopy missions will be able to test these models. Finally, we show that the uncertainties in the stellar and planetary quantities do not have a significant effect on the estimated mass or radius of GJ 357 b.
Surface Characteristics of Milled and 3D Printed Denture Base Materials Following Polishing and Coating: An In-Vitro Study
2020-07-24

(1) Background: To date, no information on the polishability of milled and 3D-printed complete denture bases has been provided, which is relevant in terms of plaque accumulation. (2) Methods: three groups (n = 30) were manufactured using the cold-polymerization polymethilmethacrilate, milling (SM) and 3D printing (AM). 10 specimens of each group were left untreated (reference). 10 more specimens were pre-polished (intermediate polishing) and 10 final specimens were highgloss polished. An additional 20 specimens were 3D printed and coated with the liquid resin (coated), 10 of which were additionally polished (coated + polished). For each group Ra and Rz values, gloss value and REM images were obtained. (3). The “highgloss-polished” specimens showed statistically lower Ra and Rz values in the SM, followed by AM and conventional groups. In the AM group statistically lower surfaces roughness was revealed for highgloss-polished, “coated + polished”, and “coated” specimens, respectively. (4) Conclusions: The milled specimens demonstrated superiors surface characteristics than 3D printed and conventionally produced after polishing. The polished specimens demonstrated superior surface characteristics over coated specimens. However, the surface roughness by both polished and coated specimens was within the clinically relevant threshold of 0.2 μm.
Optimal Coding and the Origins of Zipfian Laws
2020-07-24

The problem of compression in standard information theory consists of assigning codes as short as possible to numbers. Here we consider the problem of optimal coding – under an arbitrary coding scheme – and show that it predicts Zipf’s law of abbreviation, namely a tendency in natural languages for more frequent words to be shorter. We apply this result to investigate optimal coding also under so-called non-singular coding, a scheme where unique segmentation is not warranted but codes stand for a distinct number. Optimal non-singular coding predicts that the length of a word should grow approximately as the logarithm of its frequency rank, which is again consistent with Zipf’s law of abbreviation. Optimal non-singular coding in combination with the maximum entropy principle also predicts Zipf’s rank-frequency distribution. Furthermore, our findings on optimal non-singular coding challenge common beliefs about random typing. It turns out that random typing is in fact an optimal coding process, in stark contrast with the common assumption that it is detached from cost cutting considerations. Finally, we discuss the implications of optimal coding for the construction of a compact theory of Zipfian laws more generally as well as other linguistic laws.
Trends in sample preparation and separation methods for the analysis of very polar and ionic compounds in environmental water and biota samples
2020-07-24

Abstract Recent years showed a boost in knowledge about the presence and fate of micropollutants in the environment. Instrumental and methodological developments mainly in liquid chromatography coupled to mass spectrometry hold a large share in this success story. These techniques soon complemented gas chromatography and enabled the analysis of more polar compounds including pesticides but also household chemicals, food additives, and pharmaceuticals often present as traces in surface waters. In parallel, sample preparation techniques evolved to extract and enrich these compounds from biota and water samples. This review article looks at very polar and ionic compounds using the criterion log P ≤ 1. Considering about 240 compounds, we show that (simulated) log D values are often even lower than the corresponding log P values due to ionization of the compounds at our reference pH of 7.4. High polarity and charge are still challenging characteristics in the analysis of micropollutants and these compounds are hardly covered in current monitoring strategies of water samples. The situation is even more challenging in biota analysis given the large number of matrix constituents with similar properties. Currently, a large number of sample preparation and separation approaches are developed to meet the challenges of the analysis of very polar and ionic compounds. In addition to reviewing them, we discuss some trends: for sample preparation, preconcentration and purification efforts by SPE will continue, possibly using upcoming mixed-mode stationary phases and mixed beds in order to increase comprehensiveness in monitoring applications. For biota analysis, miniaturization and parallelization are aspects of future research. For ionic or ionizable compounds, we see electromembrane extraction as a method of choice with a high potential to increase throughput by automation. For separation, predominantly coupled to mass spectrometry, hydrophilic interaction liquid chromatography applications will increase as the polarity range ideally complements reversed phase liquid chromatography, and instrumentation and expertise are available in most laboratories. Two-dimensional applications have not yet reached maturity in liquid-phase separations to be applied in higher throughput. Possibly, the development and commercial availability of mixed-mode stationary phases make 2D applications obsolete in semi-targeted applications. An interesting alternative will enter routine analysis soon: supercritical fluid chromatography demonstrated an impressive analyte coverage but also the possibility to tailor selectivity for targeted approaches. For ionic and ionizable micropollutants, ion chromatography and capillary electrophoresis are amenable but may be used only for specialized applications such as the analysis of halogenated acids when aspects like desalting and preconcentration are solved and the key advantages are fully elaborated by further research.
Spatio-temporal dynamic of soil quality in the central Iranian desert modeled with machine learning and digital soil assessment techniques
2020-07-24

Soil degradation reduces soil quality by a loss of organic matter, reduced soil fertility, and structural breakdown, erosion, undesirable changes in salinity, acidity or alkalinity and the effects of toxic chemicals, contaminants or excessive flooding. In this study, we investigated spatial and temporal changes of soil quality between 1986 and 2030 in the Central Iranian desert. 201 topsoil samples (0–20 cm) in Yazd-Ardakan plain of Iran were chosen with conditioned Latin hypercube sampling strategy and analysed for soil organic carbon, electrical conductivity, dry bulk density, aggregate stability, and soil heavy metals. A soil quality index was calculated using weighted index method. To predict the spatial distribution of the soil quality index, we implemented a random forest model based on a set of covariates with a coefficient of determination of 0.69 between soil quality index and covariates. The results of soil quality index changes from 1986 to 2030 show that during this period, the areal extent of the Very Low SQI Class (<0.4) increased by 78,242 ha (increase of 16.2%), while the extent of the Good SQI Class (>0.6) decreased by 366,018 ha (decrease of 75.8%). This indicates that the soil quality in the study area, over time, is progressively becoming poorer. The results of the study of soil quality changes can be used in land evaluation, environmental studies and integrated planning and management in order to properly and reasonably utilize natural resources and reduce future soil degradation.
Sample Size Recommendations for Continuous-Time Models: Compensating Shorter Time Series with Larger Numbers of Persons and Vice Versa
2020-07-24

Autoregressive modeling has traditionally been concerned with time-series data from one unit (<i>N</i> = 1). For short time series (<i>T</i> T, another source of information is often available for model estimation, that is, the persons (<i>N</i> &gt; 1). In this work, we illustrate the <i>N</i>/<i>T</i> compensation effect: With an increasing number of persons <i>N</i> at constant <i>T</i>, the model estimation performance increases, and vice versa, with an increasing number of time points <i>T</i> at constant <i>N</i>, the performance increases as well. Based on these observations, we develop sample size recommendations in the form of easily accessible <i>N</i>/<i>T</i> heatmaps for two popular autoregressive continuous-time models.
Increased mitochondrial respiration of adipocytes from metabolically unhealthy obese compared to healthy obese individuals
2020-07-24

Abstract Among obese subjects, metabolically healthy (MHO) and unhealthy obese (MUHO) subjects exist, the latter being characterized by whole-body insulin resistance, hepatic steatosis, and subclinical inflammation. Insulin resistance and obesity are known to associate with alterations in mitochondrial density, morphology, and function. Therefore, we assessed mitochondrial function in human subcutaneous preadipocytes as well as in differentiated adipocytes derived from well-matched donors. Primary subcutaneous preadipocytes from 4 insulin-resistant (MUHO) versus 4 insulin-sensitive (MHO), non-diabetic, morbidly obese Caucasians (BMI &gt; 40 kg/m 2 ), matched for sex, age, BMI, and percentage of body fat, were differentiated in vitro to adipocytes. Real-time cellular respiration was measured using an XF24 Extracellular Flux Analyzer (Seahorse). Lipolysis was stimulated by forskolin (FSK) treatment. Mitochondrial respiration was fourfold higher in adipocytes versus preadipocytes ( p = 1.6*10 –9 ). In adipocytes, a negative correlation of mitochondrial respiration with donors’ insulin sensitivity was shown ( p = 0.0008). Correspondingly, in adipocytes of MUHO subjects, an increased basal respiration ( p = 0.002), higher proton leak ( p = 0.04), elevated ATP production ( p = 0.01), increased maximal respiration ( p = 0.02), and higher spare respiratory capacity ( p = 0.03) were found, compared to MHO. After stimulation with FSK, the differences in ATP production, maximal respiration and spare respiratory capacity were blunted. The differences in mitochondrial respiration between MUHO/MHO were not due to altered mitochondrial content, fuel switch, or lipid metabolism. Thus, despite the insulin resistance of MUHO, we could clearly show an elevated mitochondrial respiration of MUHO adipocytes. We suggest that the higher mitochondrial respiration reflects a compensatory mechanism to cope with insulin resistance and its consequences. Preserving this state of compensation might be an attractive goal for preventing or delaying the transition from insulin resistance to overt diabetes.
Non-Invasive Assessment of Hypoxia and Neovascularization with MRI for Identification of Aggressive Breast Cancer
2020-07-24

The aim of this study was to investigate the potential of magnetic resonance imaging (MRI) for a non-invasive synergistic assessment of tumor microenvironment (TME) hypoxia and induced neovascularization for the identification of aggressive breast cancer. Fifty-three female patients with breast cancer underwent multiparametric breast MRI including quantitative blood-oxygen-level-dependent (qBOLD) imaging for hypoxia and vascular architecture mapping for neovascularization. Quantitative MRI biomarker maps of oxygen extraction fraction (OEF), metabolic rate of oxygen (MRO2), mitochondrial oxygen tension (mitoPO2), microvessel radius (VSI), microvessel density (MVD), and microvessel type indicator (MTI) were calculated. Histopathology was the standard of reference. Histopathological markers (vascular endothelial growth factor receptor 1 (FLT1), podoplanin, hypoxia-inducible factor 1-alpha (HIF-1alpha), carbonic anhydrase 9 (CA IX), vascular endothelial growth factor C (VEGF-C)) were used to confirm imaging biomarker findings. Univariate and multivariate regression analyses were performed to differentiate less aggressive luminal from aggressive non-luminal (HER2-positive, triple negative) malignancies and assess the interplay between hypoxia and neoangiogenesis markers. Aggressive non-luminal cancers (n = 40) presented with significantly higher MRO2 (i.e., oxygen consumption), lower mitoPO2 values (i.e., hypoxia), lower MTI, and higher MVD than less aggressive cancers (n = 13). Data suggest that a model derived from OEF, mitoPO2, and MVD can predict tumor proliferation rate. This novel MRI approach, which can be easily implemented in routine breast MRI exams, aids in the non-invasive identification of aggressive breast cancer.
“Germany Crashes Out of World Cup”: A Mixed-Method Study on the Effects of Crisis Communication on Facebook
2020-07-24

Using social media for crisis communication has been proposed as an effective strategy because it allows teams to build parasocial relationships with fans. The authors focused on the early elimination of Germany during the 2018 Fédération Internationale de Football Association World Cup to examine the effects of (crisis) communication on Facebook. The authors compared the Facebook posts of the German team, captain Manuel Neuer, and team member Thomas Müller and examined the emoji reactions each received. Although Neuer posted text identical to that of the team, his post received a smaller proportion of angry emoji reactions. Müller received fewer angry reactions than the team, but more than Neuer. The authors also used data from a two-wave panel to study changes in evaluation and parasocial relationships and perceived authenticity as potential mediators. Only the team was evaluated more negatively after the elimination than before. Parasocial relationships mediated the effect of exposure to social media posts on evaluation.
Vast amounts of encoded items nullify but do not reverse the effect of sleep on declarative memory
2020-07-24

Abstract Sleep strengthens memories by repeatedly reactivating associated neuron ensembles. Our studies show that although long-term memory for a medium number of word-pairs (160) benefits from sleep, a large number (320) does not. This suggest an upper limit to the amount of information that has access to sleep-dependent declarative memory consolidation, which is possibly linked to the availability of reactivation opportunities. Due to competing processes of global forgetting that are active during sleep, we hypothesised that even larger amounts of information would enhance the proportion of information that is actively forgotten during sleep. In the present study, we aimed to induce such forgetting by challenging the sleeping brain with vast amounts of to be remembered information. For this, 80 participants learned a very large number of 640 word-pairs over the course of an entire day and then either slept or stayed awake during the night. Recall was tested after another night of regular sleep. Results revealed comparable retention rates between the sleep and wake groups. Although this null-effect can be reconciled the concept of limited capacities available for sleep-dependent consolidation, it contradicts our hypothesis that sleep would increase forgetting compared to the wake group. Additional exploratory analyses relying on equivalence testing and Bayesian statistics reveal that there is evidence against sleep having a detrimental effect on the retention of declarative memory at high information loads. We argue that forgetting occurs in both wake and sleep states through different mechanisms, i.e., through increased interference and through global synaptic downscaling, respectively. Both of these processes might scale similarly with information load.