julilili42/papers huggingface dataset:
Pyrite formation from FeS and H2S is mediated by a novel type of microbial energy metabolism
2018-08-21

Abstract The exergonic reaction of FeS with H 2 S to form FeS 2 (pyrite) and H 2 was postulated to have operated as an early form of energy metabolism on primordial Earth. Since the Archean, sedimentary pyrite formation played a major role in the global iron and sulfur cycles, with direct impact on the redox chemistry of the atmosphere. To date, pyrite formation was considered a purely geochemical reaction. Here, we present microbial enrichment cultures, which grew with FeS, H 2 S, and CO 2 as their sole substrates to produce FeS 2 and CH 4 . Cultures grew over periods of three to eight months to cell densities of up to 2–9×10 6 cells mL −1 . Transformation of FeS with H 2 S to FeS 2 was followed by 57 Fe Mössbauer spectroscopy and showed a clear biological temperature profile with maximum activity at 28°C and decreasing activities towards 4°C and 60°C. CH 4 was formed concomitantly with FeS 2 and exhibited the same temperature dependence. Addition of either penicillin or 2-bromoethanesulfonate inhibited both FeS 2 and CH 4 production, indicating a syntrophic coupling of pyrite formation to methanogenesis. This hypothesis was supported by a 16S rRNA gene-based phylogenetic analysis, which identified at least one archaeal and five bacterial species. The archaeon was closely related to the hydrogenotrophic methanogen Methanospirillum stamsii while the bacteria were most closely related to sulfate-reducing Deltaproteobacteria , as well as uncultured Firmicutes and Actinobacteria . We identified a novel type of microbial metabolism able to conserve energy from FeS transformation to FeS 2 , which may serve as a model for a postulated primordial iron-sulfur world. Significance statement Pyrite is the most abundant iron-sulfur mineral in sediments. Over geological times, its burial controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. Its formation in sediments is so far considered a purely geochemical process that is at most indirectly supported by microbial activity. We show that lithotrophic microorganisms can directly transform FeS and H 2 S to FeS 2 and use this exergonic reaction as a novel form of energy metabolism that is syntrophically coupled to methanogenesis. Our results provide insights into a syntrophic relationship that could sustain part of the deep biosphere and lend support to the iron-sulfur-world theory that postulated FeS transformation to FeS 2 as a key energy-delivering reaction for life to emerge.
Vectashield-induced fluorescence quenching hinders conventional and super resolution microscopy
2018-08-21

Abstract Finding the right combination of a fluorescent dye and a mounting medium is crucial for optimal microscopy of fixed samples. It was recently shown that Vectashield, one of the most commonly used mounting media for conventional microscopy, can also be applied to super-resolution direct stochastic optical reconstruction microscopy (dSTORM). dSTORM utilizes conventional dyes and starts with samples in a fluorescent ON state. This helps identifying structures of interests. Subsequently, labelled samples are brought to blinking, which is necessary for localization of single molecules and reconstruction of super-resolution images. This is only possible with certain fluorescent dyes and imaging buffers. One of the most widely used dyes for dSTORM, Alexa Fluor (AF) 647, blinks in Vectashield. However, after adding Vectashield to our samples, we noticed that the fluorescence intensity of AF647 and its improved variant, AF647+, is quenched. Since structures of interest cannot be identified in quenched samples, loss of fluorescence intensity hinders imaging of AF647 in Vectashield. This has consequences for both conventional and dSTORM imaging. To overcome this, we provide: 1) a quantitative analysis of AF647 intensity in different imaging media, 2) practical advice on how to use Vectashield for dSTORM imaging of AF647 and AF647+.
Tree species richness increases ecosystem carbon storage in subtropical forests
2018-08-22

Forest ecosystems are an integral component of the global carbon cycle as they take up and release large amounts of C over short time periods (C flux) or accumulate it over longer time periods (C stock). However, there remains uncertainty about whether and in which direction C fluxes and in particular C stocks may differ between forests of high versus low species richness. Based on a comprehensive dataset derived from field-based measurements, we tested the effect of species richness (3–20 tree species) and stand age (22–116 years) on six compartments of above- and below-ground C stocks and four components of C fluxes in subtropical forests in southeast China. Across forest stands, total C stock was 149 ± 12 Mg ha −1 with richness explaining 28.5% and age explaining 29.4% of variation in this measure. Species-rich stands had higher C stocks and fluxes than stands with low richness; and, in addition, old stands had higher C stocks than young ones. Overall, for each additional tree species, the total C stock increased by 6.4%. Our results provide comprehensive evidence for diversity-mediated above- and below-ground C sequestration in species-rich subtropical forests in southeast China. Therefore, afforestation policies in this region and elsewhere should consider a change from the current focus on monocultures to multi-species plantations to increase C fixation and thus slow increasing atmospheric CO 2 concentrations and global warming.
Outbreaks in a Rapidly Changing Central Africa — Lessons from Ebola
2018-08-22

Outbreaks in a Rapidly Changing Central Africa Economic and demographic change across Central Africa exacerbates the risk of infectious disease epidemics. But population growth and increasing income and education can also spur demand for infrastructure to support sustainable development, including basic health services.
Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution
2018-08-22

Neuropeptides are neurosecretory signaling molecules in protostomes and deuterostomes (together Nephrozoa). Little, however, is known about the neuropeptide complement of the sister group of Nephrozoa, the Xenacoelomorpha, which together form the Bilateria. Because members of the xenacoelomorph clades Xenoturbella, Nemertodermatida, and Acoela differ extensively in their central nervous system anatomy, the reconstruction of the xenacoelomorph and bilaterian neuropeptide complements may provide insights into the relationship between nervous system evolution and peptidergic signaling. Here, we analyzed transcriptomes of seven acoels, four nemertodermatids, and two Xenoturbella species using motif searches, similarity searches, mass spectrometry and phylogenetic analyses to characterize neuropeptide precursors and neuropeptide receptors. Our comparison of these repertoires with previously reported nephrozoan and cnidarian sequences shows that the majority of annotated neuropeptide GPCRs in cnidarians are not orthologs of specific bilaterian neuropeptide receptors, which suggests that most of the bilaterian neuropeptide systems evolved after the cnidarian–bilaterian evolutionary split. This expansion of more than 20 peptidergic systems in the stem leading to the Bilateria predates the evolution of complex nephrozoan organs and nervous system architectures. From this ancient set of neuropeptides, acoels show frequent losses that correlate with their divergent central nervous system anatomy. We furthermore detected the emergence of novel neuropeptides in xenacoelomorphs and their expansion along the nemertodermatid and acoel lineages, the two clades that evolved nervous system condensations. Together, our study provides fundamental insights into the early evolution of the bilaterian peptidergic systems, which will guide future functional and comparative studies of bilaterian nervous systems.
Faster processing of moving compared with flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion
2018-08-22

When the brain has determined the position of a moving object, because of anatomical and processing delays the object will have already moved to a new location. Given the statistical regularities present in natural motion, the brain may have acquired compensatory mechanisms to minimize the mismatch between the perceived and real positions of moving objects. A well-known visual illusion—the flash lag effect—points toward such a possibility. Although many psychophysical models have been suggested to explain this illusion, their predictions have not been tested at the neural level, particularly in a species of animal known to perceive the illusion. To this end, we recorded neural responses to flashed and moving bars from primary visual cortex (V1) of awake, fixating macaque monkeys. We found that the response latency to moving bars of varying speed, motion direction, and luminance was shorter than that to flashes, in a manner that is consistent with psychophysical results. At the level of V1, our results support the differential latency model positing that flashed and moving bars have different latencies. As we found a neural correlate of the illusion in passively fixating monkeys, our results also suggest that judging the instantaneous position of the moving bar at the time of flash—as required by the postdiction/motion-biasing model—may not be necessary for observing a neural correlate of the illusion. Our results also suggest that the brain may have evolved mechanisms to process moving stimuli faster and closer to real time compared with briefly appearing stationary stimuli. NEW &amp; NOTEWORTHY We report several observations in awake macaque V1 that provide support for the differential latency model of the flash lag illusion. We find that the equal latency of flash and moving stimuli as assumed by motion integration/postdiction models does not hold in V1. We show that in macaque V1, motion processing latency depends on stimulus luminance, speed and motion direction in a manner consistent with several psychophysical properties of the flash lag illusion.
Exploring teacher popularity: associations with teacher characteristics and student outcomes in primary school
2018-08-22

In this study, we investigated conditions and consequences of teacher popularity in primary schools. Teacher popularity is embedded in a theoretical framework that describes relationships between teacher competence, teaching quality, and student outcomes. In the empirical analyses, we used multilevel modeling to distinguish between individual students' liking of the teacher and a teacher's popularity as rated by the whole class (N=1070 students, 54 teachers). The classroom level composite of the extent to which students liked their teacher was a reliable indicator of teacher popularity. Teacher popularity was associated with teacher self-reports of self-efficacy and teaching enthusiasm and with external observers' ratings of teaching quality. The grades students received were not related to the popularity ratings. In a longitudinal study, teacher popularity predicted students' learning gains and interest development over and above the effects of teaching quality. These results suggest that teacher popularity can be a useful and informative indicator in research on students' academic development and teacher effectiveness. (DIPF/Orig.)
An Unusual Case of DMEK Graft Loss into the Vitreous and Its Successful Retrieval and Survival
2018-08-22

&lt;b&gt;&lt;i&gt;Purpose:&lt;/i&gt;&lt;/b&gt; The aim of this article is to report an unusual case of postoperative graft loss into the vitreous cavity after Descemet membrane endothelial keratoplasty (DMEK) in a patient with an unstable iris-lens diaphragm (scleral-fixated intraocular lens [sf-IOL]) and its successful retrieval with a favourable outcome. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; This is a retrospective case report. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; DMEK procedure was performed in a vitrectomized eye of an 80-year-old woman with pre-existing sf-IOL due to pseudophakic bullous keratopathy. In the setting of an inadvertently created oversized Ando iridectomy and unstable iris-lens diaphragm due to sf-IOL, repeated loss of an anterior chamber gas tamponade occurred. At the 3rd postoperative day, the patient noticed a change in visual perception, and we could detect a loss of the graft into the vitreous via B-scan ultrasound. A 23-G vitrectomy was performed promptly to recover the graft using a bimanual hand-over-hand technique. Six months after DMEK, the patient had a clear cornea without dehiscences with a central corneal thickness of 533 μm and endothelial cell count of 1,219 cells/mm&lt;sup&gt;2&lt;/sup&gt;. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; This case demonstrates the possibility of graft recovery from the vitreous after DMEK and subsequent corneal clearing despite unstable iris-lens diaphragm and vitrectomized eye.
Crystallographic preferred orientations of ice deformed in direct-shear experiments at low temperatures
2018-08-22

Abstract. We sheared synthetic polycrystalline ice at temperatures of −5, −20 and −30 °C, to different shear strains, up to γ = 2.6 (equivalent strain of 1.5). Cryo-electron backscatter diffraction (EBSD) shows that basal intra-crystalline slip planes become preferentially oriented parallel to the shear plane, in all experiments. This is visualized as a primary cluster of crystal c-axes (the c-axis is perpendicular to the basal plane) perpendicular to the shear plane. In all except the two highest-strain experiments at −30 °C, a secondary cluster of c-axes is observed, at an angle to the primary cluster. With increasing strain, the primary c-axis cluster strengthens. With increasing temperature, both clusters strengthen. In the −5 °C experiments, the angle between the two clusters reduces with increasing strain. The c-axis clusters are elongated perpendicular to the shear direction. This elongation increases with increasing shear strain and with decreasing temperature. Highly curved grain boundaries are more prevalent in samples sheared at higher temperatures. At each temperature, the proportion of and irregularity of curved boundaries decreases with increasing shear strain. Subgrains are observed in all samples. Recrystallized grains and subgrains are similar in size and are both smaller than the original grains. Microstructural interpretations and comparisons of the data from experimentally sheared samples with numerical models suggest that the observed crystallographic orientation patterns result from a balance of the rates of lattice rotation (during dislocation creep) and growth of grains by strain-induced grain boundary migration (GBM). GBM is faster at higher temperatures and becomes less important as shear strain increases. These observations and interpretations provide a hypothesis to be tested in further experiments and using numerical models, with the ultimate goal of aiding the interpretation of crystallographic preferred orientations in naturally deformed ice.
Pre-clinical Imaging of Invasive Candidiasis Using ImmunoPET/MR
2018-08-23

The human commensal yeast <i>Candida</i> is the fourth most common cause of hospital-acquired bloodstream infections, with <i>Candida albicans</i> accounting for the majority of the >400,000 life-threatening infections annually. Diagnosis of invasive candidiasis (IC), a disease encompassing candidemia (blood-borne yeast infection) and deep-seated organ infections, is a major challenge since clinical manifestations of the disease are indistinguishable from viral, bacterial and other fungal diseases, and diagnostic tests for biomarkers in the bloodstream such as PCR, ELISA, and pan-fungal β-D-glucan lack either standardization, sensitivity, or specificity. Blood culture remains the gold standard for diagnosis, but test sensitivity is poor and turn-around time slow. Furthermore, cultures can only be obtained when the yeast resides in the bloodstream, with samples recovered from hematogenous infections often yielding negative results. Consequently, there is a pressing need for a diagnostic test that allows the identification of metastatic foci in deep-seated <i>Candida</i> infections, without the need for invasive biopsy. Here, we report the development of a highly specific mouse IgG3 monoclonal antibody (MC3) that binds to a putative β-1,2-mannan epitope present in high molecular weight mannoproteins and phospholipomannans on the surface of yeast and hyphal morphotypes of <i>C. albicans</i>, and its use as a [<sup>64</sup>Cu]NODAGA-labeled tracer for whole-body pre-clinical imaging of deep-seated <i>C. albicans</i> infections using antibody-guided positron emission tomography and magnetic resonance imaging (immunoPET/MRI). When used in a mouse intravenous (i.v.) challenge model that faithfully mimics disseminated <i>C. albicans</i> infections in humans, the [<sup>64</sup>Cu]NODAGA-MC3 tracer accurately detects infections of the kidney, the principal site of blood-borne candidiasis in this model. Using a strain of the emerging human pathogen <i>Candida auris</i> that reacts with MC3 <i>in vitro</i>, but which is non-infective in i.v. challenged mice, we demonstrate the accuracy of the tracer in diagnosing invasive infections <i>in vivo</i>. This pre-clinical study demonstrates the principle of using antibody-guided molecular imaging for detection of deep organ infections in IC, without the need for invasive tissue biopsy.
The gravitational field of a laser beam beyond the short wavelength approximation
2018-08-23

Light carries energy, and therefore, it is the source of a gravitational field. The gravitational field of a beam of light in the short wavelength approximation has been studied by several authors. In this article, we consider light of finite wavelengths by describing a laser beam as a solution of Maxwell's equations and taking diffraction into account. Then, novel features of the gravitational field of a laser beam become apparent, such as frame-dragging due to its spin angular momentum and the deflection of parallel co-propagating test beams that overlap with the source beam. Even though the effects are too small to be detected with current technology, they are of conceptual interest, revealing the gravitational properties of light.
No stable wormholes in Einstein-dilaton-Gauss-Bonnet theory
2018-08-24

In [P. Kanti, B. Kleihaus, J. Kunz, Phys. Rev. Lett. 107, 271101 (2011)] it was shown that the four-dimensional Einstein-dilaton-Gauss-Bonnet theory allows for wormholes without introducing any exotic matter. The numerical solution for the wormhole was obtained there and it was claimed that this solution is gravitationally stable against radial perturbations, what, by now, would mean the only known theoretical possibility for existence of an apparently stable, four-dimensional and asymptotically flat wormhole without exotic matter. Here, more detailed analysis of perturbations shows that the Kanti-Kleihaus-Kunz wormhole is unstable against small perturbations for any values of its parameters. The exponential growth appears in the time domain after a long period of damped oscillations, in the same way as it takes place in the case of unstable higher-dimensional black holes in the Einstein-Gauss-Bonnet theory. The instability is driven by the purely imaginary mode, which is nonperturbative in the Gauss-Bonnet coupling .
Thermodynamics of the hard-disk fluid at a planar hard wall: Generalized scaled-particle theory and Monte Carlo simulation
2018-08-24

A generalized scaled-particle theory for the uniform hard-disk mixture is derived in the spirit of the White Bear II free energy of the hard-sphere fluid [H. Hansen-Goos and R. Roth, J. Phys. C: Condens. Matter 18, 8413 (2006)]. The theory provides a very simple result for the interfacial free energy γ of the hard-disk fluid at a planar hard wall (which in d = 2 is a line) in terms of the equation of state. To complement and assess the theory, we perform Monte Carlo simulations from which we obtain γ using Gibbs-Cahn integration. While we find excellent overall agreement between theory and simulation, it also becomes apparent that the set of scaled-particle variables available in d = 2 is too limited, prohibiting a quasi-exact result for γ. Furthermore, this is reflected in the mixture equation of state resulting from our theory, which, similar to a previous attempt by Santos et al. [Mol. Phys. 96, 1 (1999)], displays a small but systematic deviation from simulations.
One-Year Outcomes after PCI Strategies in Cardiogenic Shock
2018-08-25

Among patients with acute myocardial infarction and cardiogenic shock, the risk of death or renal-replacement therapy at 30 days was lower with culprit-lesion-only PCI than with immediate multivessel PCI, and mortality did not differ significantly between the two groups at 1 year of follow-up. (Funded by the European Union Seventh Framework Program and others; CULPRIT-SHOCK ClinicalTrials.gov number, NCT01927549 .).
Short-term effects of low-concentration atropine eye drops on pupil size and accommodation in young adult subjects
2018-08-25

At a dose of 0.01%, clinically significant short-term effects were detected on pupil size and accommodation for at least 24 h. At the lowest dose of 0.001%, only tiny effects on pupil size were detectable.
RESPONDER – diagnosis of pathological complete response by vacuum-assisted biopsy after neoadjuvant chemotherapy in breast Cancer - a multicenter, confirmative, one-armed, intra-individually-controlled, open, diagnostic trial
2018-08-25

The trial has been registered at clinicaltrials.gov with the identifier NCT02948764 on October 28, 2016 and at the German Clinical Trials Register ( DRKS00011761 ) on February 20, 2017. The date of enrolment of the first participant to the trial was on March 8, 2017.
The application of different 3D-scan-systems and photogrammetry at an excavation — A Neolithic dolmen from Switzerland
2018-08-25

The discovery of a Neolithic dolmen in Switzerland with inhumations, dating between 3500 and 3000 BCE, was an exceptional finding. To provide best conditions for subsequent studies on the archaeological remains our interdisciplinary team decided to apply 3D documentation. Depending on different factors, two scanning systems with four scanners and photogrammetry were applied and the obtained data was combined. Detailed excavation plans and simultaneously a reduction of excavation time without loss of information were the result. A virtual animation of the dolmen in its reconstructed ancient appearance combined with the context of the grave goods was created. The 3D documentation provided initial data for anthropological and paleogenetic analyses. The individuals buried in the dolmen might provide novel information to the Neolithic research of central Europe. Additionally, with the help of the 3D data, the dolmen was rebuilt to make this archaeological heritage accessible to the public.