julilili42/papers huggingface dataset:
Effects of extraction conditions on the redox properties of soil organic matter (SOM) and its ability to stimulate microbial iron(III) mineral reduction by electron shuttling
2019-09-09

Abstract. Soil organic matter (SOM), including humic substances (HS), is redox-active, can be microbially reduced, and transfers electrons in an abiotic reaction to Fe(III) minerals thus serving as electron shuttle. The standard procedure to extract HS from soil and separate them into humic acids (HA) and fulvic acids (FA) involves alkaline and acidic solutions potentially leading to unwanted changes in SOM chemical and redox properties. To determine the effects of extraction conditions on the redox and electron shuttling properties of SOM extracts, we prepared HS and SOM extracts from a forest soil applying either a combination of 0.1 M NaOH and 6 M HCl, or water (pH 7). Both chemical extractions (NaOH / HCl) and water extractions were done in separate setups under either oxic or anoxic conditions. Furthermore, we applied the NaOH / HCl treatment to a subsample of the water-extracted-SOM. We found that soil extraction with NaOH lead to ca. 100 times more extracted C and the extracted HS had 2–3 times higher electron exchange capacities (EEC) than SOM extracted by water. For water-extracted SOM, anoxic extraction conditions lead to about 7 times more extracted C and 1.5 times higher EEC than under oxic extraction conditions. This difference was probably due to the occurrence of microbial reduction and dissolution of Fe(III) minerals in the soil during the water extraction at neutral pH and the concomitant release of Fe(III) mineral-bound organic matter. NaOH / HCl treatment of the water-extracted SOM lead to 2 times higher EEC values in the HA isolated from the SOM compared to the water-extracted SOM itself, suggesting the chemical treatment with NaOH and HCl caused changes of redox-active functional groups of the extracted organic compounds. Higher EEC of extracts in turn resulted in a higher stimulation of microbial Fe(III) mineral reduction by electron shuttling, i.e. faster initial Fe(III) reduction rates, and in most cases also in higher reduction extents. Our findings suggest that SOM extracted with water at neutral pH should be used to better reflect environmental SOM redox processes in lab experiments and that potential artefacts of the chemical extraction method and anoxic extraction condition need to be considered when evaluating and comparing abiotic and microbial SOM redox processes.
Iridium Catalyzed Deoxygenation of Epoxides with Carbon Monoxide
2019-09-09

This work describes the selective desoxygenation of epoxides to olefins using carbon monoxide as the reducing agent and an iridium pincer complex as the homogeneous catalyst. A lithium salt additive acts as co-catalyst in various steps of the catalytic cycle. The mechanism is elucidated including the isolation of intermediates.
Germanium nanospheres as high precision optical tweezers probes (Conference Presentation)
2019-09-09

Force spectroscopy on single molecular machines is often performed using optical tweezers. However, the use of common microspheres composed of silica or polystyrene may have limitations in the maximum force, measurement precision, or the degrees of freedom that can be measured. For example, the ultimate precision of the experiment is limited by the drag coefficient, i.e. the size of the microsphere. Thus, ideally, microspheres should be as small as possible. However, if microspheres are too small, maximum trapping forces are smaller than biological motor-generated forces creating a lower practical size limit of about 200 nm for polystyrene. Here, we have developed germanium nanospheres with diameters ranging from 30--200 nm. With a high refractive index of 4.4, their trapping efficiency is more than 10-fold improved compared to silica. Using 70-nm-diameter germanium nanospheres, we measured the stepping behavior of the molecular motor kinesin-1. With an improved precision, we could measure intermediate steps. In the long-term, the development of novel probes enables novel applications.
Iridium Catalyzed Deoxygenation of Epoxides with Carbon Monoxide
2019-09-09

This work describes the selective desoxygenation of epoxides to olefins using carbon monoxide as the reducing agent and an iridium pincer complex as the homogeneous catalyst. A lithium salt additive acts as co-catalyst in various steps of the catalytic cycle. The mechanism is elucidated including the isolation of intermediates.&lt;br&gt;
Sediment Respiration Pulses in Intermittent Rivers and Ephemeral Streams
2019-09-10

Abstract Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO 2 ) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO 2 . We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32‐fold to 66‐fold upon sediment rewetting. Structural equation modeling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use, and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO 2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting‐drying cycles on respiration and CO 2 emissions in stream networks.
The Severe Typhoid Fever in Africa Program: Study Design and Methodology to Assess Disease Severity, Host Immunity, and Carriage Associated With Invasive Salmonellosis
2019-09-10

Abstract Background Invasive salmonellosis is a common community-acquired bacteremia in persons residing in sub-Saharan Africa. However, there is a paucity of data on severe typhoid fever and its associated acute and chronic host immune response and carriage. The Severe Typhoid Fever in Africa (SETA) program, a multicountry surveillance study, aimed to address these research gaps and contribute to the control and prevention of invasive salmonellosis. Methods A prospective healthcare facility–based surveillance with active screening of enteric fever and clinically suspected severe typhoid fever with complications was performed using a standardized protocol across the study sites in Burkina Faso, the Democratic Republic of Congo (DRC), Ethiopia, Ghana, Madagascar, and Nigeria. Defined inclusion criteria were used for screening of eligible patients for enrollment into the study. Enrolled patients with confirmed invasive salmonellosis by blood culture or patients with clinically suspected severe typhoid fever with perforation were eligible for clinical follow-up. Asymptomatic neighborhood controls and immediate household contacts of each case were enrolled as a comparison group to assess the level of Salmonella-specific antibodies and shedding patterns. Healthcare utilization surveys were performed to permit adjustment of incidence estimations. Postmortem questionnaires were conducted in medically underserved areas to assess death attributed to invasive Salmonella infections in selected sites. Results Research data generated through SETA aimed to address scientific knowledge gaps concerning the severe typhoid fever and mortality, long-term host immune responses, and bacterial shedding and carriage associated with natural infection by invasive salmonellae. Conclusions SETA supports public health policy on typhoid immunization strategy in Africa.
A new perspective on membrane-embedded Bax oligomers using DEER and bioresistant orthogonal spin labels
2019-09-10

Abstract Bax is a Bcl-2 protein crucial for apoptosis initiation and execution, whose active conformation is only partially understood. Dipolar EPR spectroscopy has proven to be a valuable tool to determine coarse-grained models of membrane-embedded Bcl-2 proteins. Here we show how the combination of spectroscopically distinguishable nitroxide and gadolinium spin labels and Double Electron-Electron Resonance can help to gain new insights into the quaternary structure of active, membrane-embedded Bax oligomers. We show that attaching labels bulkier than the conventional MTSL may affect Bax fold and activity, depending on the protein/label combination. However, we identified a suitable pair of spectroscopically distinguishable labels, which allows to study complex distance networks in the oligomers that could not be disentangled before. Additionally, we compared the stability of the different spin-labeled protein variants in E . coli and HeLa cell extracts. We found that the gem -diethyl nitroxide-labeled Bax variants were reasonably stable in HeLa cell extracts. However, when transferred into human cells, Bax was found to be mislocalized, thus preventing its characterization in a physiological environment. The successful use of spectroscopically distinguishable labels on membrane-embedded Bax-oligomers opens an exciting new path towards structure determination of membrane-embedded homo- or hetero-oligomeric Bcl-2 proteins via EPR.
Haemostatic changes in urogenital schistosomiasis haematobium: a case-control study in Gabonese schoolchildren
2019-09-10

Abstract In many tropical areas schistosomiasis is a major health problem causing hepatosplenic, intestinal or urogenital complaints. Hepatosplenic schistosomiasis mansoni is also characterized by blood coagulation abnormalities. Liver pathology plays a role in the development of haemostatic changes and the parasitic infection may directly affect coagulation. However, these contributing factors cannot be studied separately in hepatosplenic schistosomiasis infections. This pilot study provides insight in haemostatic changes in urinary schistosomiasis by studying coagulation parameters in schistosomiasis haematobium-infected Gabonese schoolchildren. Selection on urinary schistosomiasis patients without hepatosplenic complaints allows for the investigation of the direct effects of the parasite on haemostasis. Levels of von Willebrand Factor (VWF) antigen, active VWF and osteoprotegerin were elevated, indicating inflammation-mediated endothelial activation. In contrast to hepatosplenic schistosomiasis, thrombin–antithrombin complex and D-dimer levels were not affected. Despite its small sample size, this study clearly indicates that Schistosoma haematobium directly alters the activation status of the endothelium, without initiation of coagulation.
Conflicting Disk Inclination Estimates for the Black Hole X-Ray Binary XTE J1550−564
2019-09-10

Abstract The dynamical characteristics of XTE J1550−564, a black hole X-ray binary, are well established, and the broadband spectral evolution of the source has been well studied. Its orbital inclination is known to be high, at ∼75°, with the jet estimated to align well with the orbital axis. We explore simultaneous observations made with the Advanced Satellite for Cosmology and Astrophysics and Rossi X-ray Timing Explorer covering the 1–200 keV band during the early stages of the first outburst of XTE J1550−564 in its hard-intermediate state on 1998 September 23/24. We show that the most up-to-date reflection models applied to these data yield an inclination estimate much lower than that found in previous studies at ∼40°, grossly disagreeing with the dynamically estimated orbital inclination. We discuss the possible explanations for this disagreement and its implications for reflection models, including possible physical scenarios in which either the inner disk is misaligned with both the binary orbit and the outer jet or the inner accretion flow, corona, and/or jet have vertical structure that leads to lower inferred disk inclination through various physical means.
Major shoreline retreat and sediment starvation following Snowball Earth
2019-09-10

Abstract While cap dolostones are integral to the Snowball Earth hypothesis, the current depositional model does not account for multiple geological observations. Here we propose a model that rationalises palaeomagnetic, sequence‐stratigraphic and sedimentological data and supports rapid deglaciation with protracted cap dolostone precipitation. The Snowball Earth hypothesis posits that a runaway ice‐albedo can explain the climate paradox of Neoproterozoic glacial deposits occurring at low palaeolatitudes. This scenario invokes volcanic degassing to increase atmospheric greenhouse gases to a critical threshold that overcomes the albedo effect and brings the planet back from the ice‐covered state. Once this occurs, Earth should shift rapidly from a snowball to an extreme greenhouse. However, cap dolostone units overlying glacial sediments, typically interpreted as transgressive deposits, exhibit multiple magnetic reversals indicating they accumulated in &gt;10 5 years. By reviewing modern post‐glacial systems, sequence stratigraphic concepts and principles of sedimentology, we suggest that cap dolostones are not restricted to the transgression but rather represent sediment starvation following a major landward shoreline migration associated with the demise of Snowball Earth. Thus, the duration in which cap dolostone accumulated is not directly coupled to the timescale of the Snowball Earth deglaciation.
Poly (ADP-Ribose) Polymerase-1 (PARP1) Deficiency and Pharmacological Inhibition by Pirenzepine Protects From Cisplatin-Induced Ototoxicity Without Affecting Antitumor Efficacy
2019-09-10

Cisplatin remains an indispensable drug for the systemic treatment of many solid tumors. However, a major dose-limiting side-effect is ototoxicity. In some scenarios, such as treatment of germ cell tumors or adjuvant therapy of non-small cell lung cancer, cisplatin cannot be replaced without undue loss of efficacy. Inhibition of polyadenosine diphosphate-ribose polymerase-1 (PARP1), is presently being evaluated as a novel anti-neoplastic principle. Of note, cisplatin-induced PARP1 activation has been related to inner ear cell death. Thus, PARP1 inhibition may exert a protective effect on the inner ear without compromising the antitumor activity of cisplatin. Here, we evaluated PARP1 deficiency and PARP1 pharmacological inhibition as a means to protect the auditory hair cells from cisplatin-mediated ototoxicity. We demonstrate that cisplatin-induced loss of sensory hair cells in the organ of Corti is attenuated in PARP1-deficient cochleae. The PARP inhibitor pirenzepine and its metabolite LS-75 mimicked the protective effect observed in PARP1-deficient cochleae. Moreover, the cytotoxic potential of cisplatin was unchanged by PARP inhibition in two different cancer cell lines. Taken together, the results from our study suggest that the negative side-effects of cisplatin anti-cancer treatment could be alleviated by a PARP inhibition adjunctive therapy.
Origins of Iodine-Rich W6I12 Cluster Compounds and the Soluble Compound W6I22
2019-09-10

In search of iodine-rich compounds with an octahedral tungsten cluster, we explored the treatment of β-W<sub>6</sub>I<sub>12</sub>, the most stable tungsten iodide cluster compound, with liquid iodine. The most iodine-rich compound obtained from these reactions was W<sub>6</sub>I<sub>22</sub>, whose crystal structure adopts two closely related modifications. The remarkable connectivity of [W<sub>6</sub>I<sub>8</sub>]<sup>4+</sup> clusters in the structure of W<sub>6</sub>I<sub>22</sub> makes this compound the first example of a soluble binary octahedral tungsten iodide cluster, as demonstrated by dissolution experiments in several solvents. Differential scanning calorimetry showed that the thermolysis of triclinic α-W<sub>6</sub>I<sub>22</sub> proceeds via a phase transformation into monoclinic β-W<sub>6</sub>I<sub>22</sub>, followed by the formation of W<sub>6</sub>I<sub>18</sub> and W<sub>6</sub>I<sub>16</sub> with release of iodine. A corresponding ambient-pressure study by combined differential thermal analysis and thermal gravimetry revealed the transformation of β-W<sub>6</sub>I<sub>22</sub> into W<sub>6</sub>I<sub>14</sub> and β-W<sub>6</sub>I<sub>12</sub>, which finally decomposes into the elements. On the basis of this simple example, we demonstrate how a complete reaction sequence, including preparation and subsequent phase transformations, can be monitored and analyzed by thermal scanning methods. Moreover, a reaction cycle is reported that relates a whole series of binary tungsten iodides. Syntheses of the new compounds α- and β-W<sub>6</sub>I<sub>22</sub>, and W<sub>6</sub>I<sub>14</sub> are reported, and their crystal structures, as determined by X-ray diffraction techniques, are presented.
Senescence induces pro-apoptotic features in tumor cells enabling targeted senolysis by type I immune-mediators and subsequent phagocytic clearance
2019-09-10

The induction of senescence in cancer cells is becoming a relevant strategy in tumor treatment. This can be achieved using therapeutic compounds (TIS u2013 therapy induced senescence) or modulation of the immune system. The cytokines IFNy and TNF can induce senescence in tumor cells in vitro and in vivo via TH1 cell treatment in mice (CIS u2013 cytokine induced senescence). Here we show that CIS induction leads to pro-apoptotic features in murine cancer cells. While the majority of CIS cancer cells remain viable, show SA-u00df-Gal activity and cease proliferation, the cells accumulate the following features commonly associated with early apoptotic events. Amongst others, the surface localization of negatively charged phospholipids increases under CIS treatment leading to a loss of the original membrane composition. This is accompanied by the increased protein levels of pro-apoptotic proteins (e.g. BID) as well as mitochondrial outer membrane permeabilization (MOMP) and Cytochrome c release. While CIS cancer cells do show an increase in Caspase 3 activity in comparison to non-senescent cancer cells we suspect that the increased levels of the anti-apoptotic protein Bcl-2 in CIS cancer cells counteracts a possible death induction in favor of senescence. Furthermore, we show that CIS acquired vulnerabilities make the cancer cells susceptible to secondary apoptosis (senolysis) by immune mediators. Following senescence with senolysis allowed phagocytosis by macrophages, while non-senescent cancer cells were not cleared. Therefore, senolysis is required for the clearance of senescent tumor cells. Up to date it is not clear whether senescent cancer cells cause harm and should be deleted or whether they are protective by inducing tumor specific immune responses. These findings may allow to answer this Question.
An Insight into Professional Identity Formation: Qualitative Analyses of Two Reflection Interventions During the Dissection Course
2019-09-11

The professional behavior of future doctors is increasingly important in medical education. One of the first subjects in the curriculum to address this issue is gross anatomy. The Tuebingen Medical Faculty implemented a learning portfolio and a seminar on medical professionalism during the dissection course. The aims of this research project are to get an overview of how students form a professional identity in the dissection course and to compare the content of both their oral and written reflections on the course. A qualitative analysis was conducted of the oral and written reflections on the dissection laboratory experience. This study was conducted during winter term 2013/2014 with a cohort of 163 participants in the regular dissection course. Written reflection texts (from n = 96 students) and audio recordings from four oral reflection seminar discussions (with n = 11 students) were transcribed and deductively categorized with Mayring’s qualitative content analysis method. Both qualitative analyses show that students reflected on many topics relevant to professional development, including empathy, respect, altruism, compassion, teamwork, and self‐regulation. Quantitative analysis reveals that students who attended the oral reflection wrote significantly more in their written reflection than students who did not. There is, however, no difference in the reflection categories. Reflection content from students corresponds with categories derived from existing competency frameworks. Both the seminar (oral reflections) and the learning portfolio (written reflections) present excellent opportunities to foster professional development during anatomy education; the key is using them in conjunction with the dissection course.
Detrimental Effect of Type I IFNs During Acute Lung Infection With Pseudomonas aeruginosa Is Mediated Through the Stimulation of Neutrophil NETosis
2019-09-11

<i>Pseudomonas aeruginosa</i> is an opportunistic multidrug-resistant pathogen, able to grow in biofilms. It causes life-threatening complications in diseases characterized by the up-regulation of type I interferon (IFN) signaling, such as cancer or viral infections. Since type I IFNs regulate multiple functions of neutrophils, which constitute the first line of anti-bacterial host defense, in this work we aimed to study how interferon-activated neutrophils influence the course of <i>P. aeruginosa</i> infection of the lung. In lungs of infected IFN-sufficient WT mice, significantly elevated bacteria load was observed, accompanied by the prominent lung tissue damage. At the same time IFN-deficient animals seem to be partly resistant to the infection. Lung neutrophils from such IFN-deficient animals release significantly lower amounts of neutrophil extracellular traps (NETs) and reactive oxygen species (ROS), as compared to WT neutrophils. Of note, such IFN-deficient neutrophils show significantly decreased capacity to stimulate biofilm formation by <i>P. aeruginosa</i>. Reduced biofilm production impairs in turn the survival of bacteria in a lung tissue. In line with that, treatment of neutrophils with recombinant IFN-β enhances their NETosis and stimulates biofilm formation by <i>Pseudomonas</i> after co-incubation with such neutrophils. Possibly, bacteria utilizes neutrophil-derived NETs as a scaffold for released biofilms. In agreement with this, <i>in vivo</i> treatment with ROS-scavengers, NETs disruption or usage of the bacterial strains unable to bind DNA, suppress neutrophil-mediated biofilm formation in the lungs. Together, our findings indicate that the excessive activation of neutrophils by type I IFNs leads to their boosted NETosis that in turn triggers biofilm formation by <i>P. aeruginosa</i> and supports its persistence in the infected lung. Targeting these mechanisms could offer a new therapeutic approach to prevent persistent bacterial infections in patients with diseases associated with the up-regulation of type I IFNs.