julilili42/papers huggingface dataset:
Effects of Microplastic on Human Gut Microbiome: Detection of Plastic-Degrading Genes in Human Gut Exposed to Microplastics—Preliminary Study
2022-11-09

Microplastics are major pollutants in the environment, and it is currently established that microplastics have already entered human food chains and been incorporated into the human body through ingestion and inhalation. Several works in animal models have already reported the adverse effect of microplastic exposure on biological systems; however, the effect of microplastic contamination on human health is still far from understood. In previous work, we reported microplastic contamination in the digestive tract of the Indonesian coastal and highland population. Using the same stool samples, we extended our previous work by investigating gut microbial composition in samples with and without microplastic contamination using next-generation sequencing. We found that microplastic contamination does not affect overall gut microbial composition and the abundance of gut-health-related genes. However, we found a negative and positive correlation between specific types of microplastics with certain bacterial taxa, especially from the genera Roseburia, Clostridium, and Prevotella. Despite the lack of a profound effect on the gut microbiome, we detected for the first time the presence of genes encoding plastic-degrading enzymes in the human gut microbiome, suggesting an adaptation of gut microbiome to microplastic contamination.
Mapping the circumnuclear regions of the Circinus galaxy with the Imaging X-ray Polarimetry Explorer
2022-11-09

ABSTRACT We report on the Imaging X-ray Polarimetry Explorer (IXPE) observation of the closest and X-ray brightest Compton-thick active galactic nucleus (AGN), the Circinus galaxy. We find the source to be significantly polarized in the 2–6 keV band. From previous studies, the X-ray spectrum is known to be dominated by reflection components, both neutral (torus) and ionized (ionization cones). Our analysis indicates that the polarization degree is 28 ± 7 per cent (at 68 per cent confidence level) for the neutral reflector, with a polarization angle of 18° ± 5°, roughly perpendicular to the radio jet. The polarization of the ionized reflection is unconstrained. A comparison with Monte Carlo simulations of the polarization expected from the torus shows that the neutral reflector is consistent with being an equatorial torus with a half-opening angle of 45°–55°. This is the first X-ray polarization detection in a Seyfert galaxy, demonstrating the power of X-ray polarimetry in probing the geometry of the circumnuclear regions of AGNs, and confirming the basic predictions of standard Unification Models.
Morpho‐Functional Changes of Nigral Dopamine Neurons in an α‐Synuclein Model of Parkinson's Disease
2022-11-09

Abstract Background The accumulation of α‐synuclein (α‐syn) fibrils in intraneuronal inclusions called Lewy bodies and Lewy neurites is a pathological signature of Parkinson's disease (PD). Although several aspects linked to α‐syn–dependent pathology (concerning its spreading, aggregation, and activation of inflammatory and neurodegenerative processes) have been under intense investigation, less attention has been devoted to the real impact of α‐syn overexpression on structural and functional properties of substantia nigra pars compacta (SNpc) dopamine (DA) neurons, particularly at tardive stages of α‐syn buildup, despite this has obvious relevance to comprehending mechanisms beyond PD progression. Objectives We aimed to determine the consequences of a prolonged α‐syn overexpression on somatodendritic morphology and functions of SNpc DA neurons. Methods We performed immunohistochemistry, stereological DA cell counts, analyses of dendritic arborization, ex vivo patch‐clamp recordings, and in vivo DA microdialysis measurements in a 12‐ to 13‐month‐old transgenic rat model overexpressing the full‐length human α‐syn ( Snca +/+ ) and age‐matched wild‐type rats. Results Aged Snca +/+ rats have mild loss of SNpc DA neurons and decreased basal DA levels in the SN. Residual nigral DA neurons display smaller soma and compromised dendritic arborization and, in parallel, increased firing activity, switch in firing mode, and hyperexcitability associated with hypofunction of fast activating/inactivating voltage‐gated K + channels and Ca 2+ ‐ and voltage‐activated large conductance K + channels. These intrinsic currents underlie the repolarization/afterhyperpolarization phase of action potentials, thus affecting neuronal excitability. Conclusions Besides clarifying α‐syn–induced pathological landmarks, such evidence reveals compensatory functional mechanisms that nigral DA neurons could adopt during PD progression to counteract neurodegeneration. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Modeling disks and magnetic outflows around a forming massive star
2022-11-09

Context. Similar to their lower mass siblings, massive protostars can be expected to: (a) be surrounded by circumstellar disks, and (b) launch magnetically driven jets and outflows. The disk formation and global evolution is thereby controlled by advection of angular momentum from large scales, the efficiency of magnetic braking and the resistivity of the medium, and the internal thermal and magnetic pressures of the disk. Aims. We determine the dominant physical mechanisms that shape the appearance of these circumstellar disks, their sizes, and aspect ratios. Methods. We performed a series of 30 simulations of a massive star forming from the gravitational collapse of a molecular cloud threaded by an initially uniform magnetic field, starting from different values for the mass of the cloud, its initial density and rotation profiles, its rotational energy content, the magnetic field strength, and the resistivity of the material. The gas and dust was modeled with the methods of resistive magnetohydrodynamics, also considering radiation transport of thermal emission and self-gravity. We checked for the impact of spatial resolution in a dedicated convergence study. Results. After the initial infall phase dominated by the gravitational collapse, an accretion disk was formed, shortly followed by the launching of magnetically driven outflows. Two layers can be distinguished in the accretion disk: a thin layer, vertically supported by thermal pressure, and a thick layer, vertically supported by magnetic pressure. Both regions exhibit Keplerian-like rotation and grow outward over time. We observed the effects of magnetic braking in the inner ~50 au of the disk at late times in our fiducial case. The parameter study reveals that the size of the disk is mostly determined by the density and rotation profiles of the initial mass reservoir and not by the magnetic field strength. We find that the disk size and protostellar mass gain scale with the initial mass of the cloud. Magnetic pressure can slightly increase the size of the accretion disk, while magnetic braking is more relevant in the innermost parts of the disk as opposed to the outer disk. From the parameter study, we infer that multiple initial conditions for the onset of gravitational collapse are able to produce a given disk size and protostellar mass.
Assessment of penetration and permeation of caffeine by confocal Raman spectroscopy in vivo and ex vivo by tape stripping
2022-11-09

Abstract Objective Tape stripping is an often‐used non‐invasive destructive method to investigate the skin penetration of a substance. In recent years, however, the suitability of confocal Raman spectroscopy (CRS) as a non‐invasive method of non‐destructive examination of the skin has become increasingly apparent. In this study, we compared invasion and depletion penetration and permeation kinetics of a 2% caffeine solution with and without 1,2‐pentanediol as a penetration enhancer measured with CRS and tape stripping. Methods Porcine skin was used for tape stripping and human skin for CRS. 2% caffeine solution was applied to the skin for different incubation times. Human skin was then examined by CRS while caffeine was extracted from porcine skin and quantified via reverse‐phase HPLC. Fluxes were also measured and calculated by sum of the total amounts of caffeine penetrated into the skin. Results Without penetration enhancers, there is hardly any difference between the penetration profiles of the two measurement methods for invasion, but the curves for depletion are different. Furthermore, the calculated flux values for the invasion are almost identical, but for the depletion the tape stripping values are about twice as high as the CRS values. Conclusion The relevance of conducting invasion and depletion studies became clear and was able to show the still existing problems in the comparability of CRS and tape stripping.
Environmental Risk of Arsenic Mobilization from Disposed Sand Filter Materials
2022-11-09

Arsenic (As)-bearing water treatment residuals (WTRs) from household sand filters are usually disposed on top of floodplain soils and may act as a secondary As contamination source. We hypothesized that open disposal of these filter-sands to soils will facilitate As release under reducing conditions. To quantify the mobilization risk of As, we incubated the filter-sand, the soil, and a mixture of the filter-sand and soil in anoxic artificial rainwater and followed the dynamics of reactive Fe and As in aqueous, solid, and colloidal phases. Microbially mediated Fe(III)/As(V) reduction led to the mobilization of 0.1-4% of the total As into solution with the highest As released from the mixture microcosms equaling 210 μg/L. Due to the filter-sand and soil interaction, Mössbauer and X-ray absorption spectroscopies indicated that up to 10% Fe(III) and 32% As(V) were reduced in the mixture microcosm. Additionally, the mass concentrations of colloidal Fe and As analyzed by single-particle ICP-MS decreased by 77-100% compared to the onset of reducing conditions with the highest decrease observed in the mixture setups (>95%). Overall, our study suggests that (i) soil provides bioavailable components (e.g., organic matter) that promote As mobilization via microbial reduction of As-bearing Fe(III) (oxyhydr)oxides and (ii) As mobilization as colloids is important especially right after the onset of reducing conditions but its importance decreases over time.
Re-evaluation of the morphology and phylogeny ofDiplocynodon levantinicumHuene & Nikoloff, 1963 and the stratigraphic age of the West Maritsa coal field (Upper Thrace Basin, Bulgaria)
2022-11-09

Diplocynodon levantinicum Huene &amp; Nikoloff, 1963 was described based on few bone fragments from the West-Maritsa lignite basin of Central Bulgaria. Huene &amp; Nikoloff, 1963 assumed a late Pliocene age, implying that this species represents the stratigraphically youngest crocodilian of Europe. In this current study, we re-evaluate the stratigraphy of the West-Maritsa Basin and conclude a late Oligocene age of ~26 Ma for the Kipra coal-seam, the fossiliferous horizon. Furthermore, topotypical and undescribed D. levantinicum specimens are accessible now and allowed for a deeper taxonomic and phylogenetic analysis. A comparison with other Diplocynodon species reveals D. levantinicum as a valid species, having (1) a long suborbital fenestra, (2) a very short dentary symphysis, (3) a large gap between the first and second dentary alveolus, (4) an occlusion pit in line with the tooth row posterior to the 14 th dentary alveolus, (5) a sulcus lateral to the glenoid fossa and, (6) a lingual foramen for the articular artery situated entirely on the surangular. The phylogenetic analyses find D. levantinicum deeply nested inside the Diplocynodontinae subfamily. After the disappearance of the Paratethyan influence (Solenovian regional stage) in the Upper Thrace Basin this species has roamed during the late Oligocene extensive freshwater lake and swamp ecosystems represented by the Maritsa Formation. Diplocynodon levantinicum represents the only nominal Diplocynodon taxon of late Oligocene (Chattian) age.
The grit crust: A poly-extremotolerant microbial community from the Atacama Desert as a model for astrobiology
2022-11-09

The grit crust is a recently discovered, novel type of biocrust made of prokaryotic cyanobacteria, eukaryotic green algae, fungi, lichens and other microbes that grow around and within granitoid stone pebbles of about 6 mm diameter in the Coastal Range of the Atacama Desert, Chile. The microbial community is very well adapted towards the extreme conditions of the Atacama Desert, such as the highest irradiation of the planet, strong temperature amplitudes and steep wet-dry cycles. It also has several other striking features making this biocrust unique compared to biocrusts known from other arid biomes on Earth. It has already been shown that the grit crust mediates various bio-weathering activities in its natural habitat. These activities prime soil for higher organisms in a way that can be envisioned as a proxy for general processes shaping even extra-terrestrial landscapes. This mini-review highlights the potential of the grit crust as a model for astrobiology in terms of extra-terrestrial microbial colonization and biotechnological applications that support human colonization of planets.
Review of: Sarah Lamdan: Data Cartels. The companies that control and monopolize our information. Stanford University Press 2023
2022-11-09

&lt;p&gt;In the book &lt;em&gt;Data Cartels&lt;/em&gt;, Sarah Lamdan examines the &quot;GAFAM ot curated information&quot;: Companies that have their origins in scientific information infrastructures and are now on their way to dominating not only the research life cycle, but large parts of where decisions are made for society: Law, News, Data Brokering. Without effective regulation, data cartels are not only spreading into these fields, but transforming them. Science, law, and information infrastructures thus find themselves in an ever tighter grip of digital oligopolies that threatens to destroy their sovereignty.&lt;/p&gt; &lt;p&gt;This text is a machine-based translation of my review in order to provide easier access for non-German speaking interested parties, also the german language quotes were therefore transferred. Consider this version a &raquo;post-print derivative&laquo; and please refer to the original in case of references or citations: Siems, R. (2022). Rezension zu: Data cartels : the companies that control and monopolize our information / Sarah Lamdan. O-Bib. Das Offene Bibliotheksjournal / Herausgeber VDB, 9(4), 1&ndash;8. https://doi.org/10.5282/o-bib/5902&lt;/p&gt;
Structural Basis for Inhibition of Mutant EGFR with Lazertinib (YH25448)
2022-11-10

Lazertinib (YH25448) is a novel third-generation tyrosine kinase inhibitor (TKI) developed as a treatment for EGFR mutant non-small cell lung cancer. To better understand the nature of lazertinib inhibition, we determined crystal structures of lazertinib in complex with both WT and mutant EGFR and compared its binding mode to that of structurally related EGFR TKIs. We observe that lazertinib binds EGFR with a distinctive pyrazole moiety enabling hydrogen bonds and van der Waals interactions facilitated through hydrophilic amine and hydrophobic phenyl groups, respectively. Biochemical assays and cell studies confirm that lazertinib effectively targets EGFR(L858R/T790M) and to a lesser extent HER2. The molecular basis for lazertinib inhibition of EGFR reported here highlights previously unexplored binding interactions leading to improved medicinal chemistry properties compared to clinically approved osimertinib (AZD9291) and offers novel strategies for structure-guided design of tyrosine kinase inhibitors.
I can't get no (job) satisfaction? Differences in teachers' job satisfaction from a career pathways perspective
2022-11-10

Education policy stakeholders attempt to counteract teacher shortages by recruiting persons from outside of the teacher career. However, teachers' job satisfaction, a key predictor for teacher retention, often differs between those originally trained as a teacher and those from different career pathways. Applying multiple indicator multiple causes (MIMIC) bifactor models on PISA data (N = 125,764 teachers), we found that first career teachers show higher job satisfaction. Furthermore, the curricular preparedness by initial education is more important for those, who always intended to become teachers when compared to those arriving from alternative routes. Based on findings in this study, we recommend improvements of alternative certification programs, working conditions, and professional development opportunities for persons who did not initially plan to become teachers to increase overall teachers' job satisfaction.
Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
2022-11-10

Abstract Aim Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter‐gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene. Location Europe. Taxon Common vole ( Microtus arvalis ). Methods We generated a dataset comprised of 4.2 kb long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated. Results We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than most previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM) even at high latitudes. Main Conclusions The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.
Are Lay People Able to Estimate Breeding Bird Diversity?
2022-11-10

Studies about biodiversity and well-being used different approaches to assess biodiversity, e.g., scientific counts and censuses or perceived biodiversity estimated by the respondents. Here, we assessed whether laypeople could estimate the breeding bird diversity or species richness at specific places. For comparison, we carried out bird censuses with standard methods of professional ornithologists and used citizen science data from the internet platform Ornitho (Germany). Lay people from the public (1184 respondents) were surveyed between May and July 2022 at 40 different places in southwest Germany between Rottenburg/Tübingen and Stuttgart following the catchment of the river Neckar (30 people surveyed per place). People were asked to estimate the bird species richness/diversity at this current place. Here, we show that the data from the citizen science platform does not correlate with the professional census counts nor with the perceived species richness of laypeople. Laypeople have a generally good assessment of the bird species richness, correlating with the data of professionals (r = 0.325, p = 0.041). On average, the number of species assessed by laypeople lies in between the values of the professional morning and afternoon census. People were most often surveyed in the afternoon; therefore, their assessment must be done on other factors than actual birds present. This result is valuable for future studies on the connection between biodiversity and well-being.
Comparison of High-Resolution 14C and Luminescence-Based Chronologies of the MIS 2 Madaras Loess/Paleosol Sequence, Hungary: Implications for Chronological Studies
2022-11-10

Numerous loess/paleosol sequences (LPS) in the Carpathian Basin span the period of Marine Isotope Stage (MIS) 2 and the last glacial maximum (LGM). Nevertheless, only two known records—Madaras and Dunaszekcső—preserve highly resolved records with absolute chronologies with minimal uncertainties, which enable the meaningful assessment of feedbacks and short-term climatic fluctuations over this period. The Madaras profile is located at the northern margin fringe of the Bácska loess plateau; Dunaszekcső, located on the Danube to its west, yields a chronology built on over 100 14C dates yet spans only part of MIS 2, missing half of the LGM including its peak. Here, we add to the previously published 14C chronology for Madaras (15 dates) with an additional 17 14C and luminescence ages. Resulting age models built solely on quartz OSL and feldspar pIRIRSL data underestimate the 14C based chronology, which is likely based on inaccuracies related to luminescence signal behavior; we observe age underestimations associated with unusual quartz behavior and significant signal loss, a phenomenon also observed in Serbian and Romanian loess, which may relate to non-sensitized grains from proximal sources. Our new chronology provides higher resolution than hitherto possible, yielding consistent 2 sigma uncertainties of ~150–200 years throughout the entire sequence. Our study indicates that the addition of further dates may not increase the chronological precision significantly. Additionally, the new age model is suitable for tackling centennial-scale changes. The mean sedimentation rate based on our new age-depth model (10.78 ± 2.34 years/cm) is the highest yet recorded in the Carpathian Basin for MIS 2. The resolution of our age model is higher than that for the Greenland NGRIP ice core record. The referred horizons in our profile are all characterized by a drop in accumulation and a higher sand input, the latter most likely deriving from nearby re-exposed sand dunes.