julilili42/papers huggingface dataset:
The Genome of Staphylococcus epidermidis O47
2020-08-25

The skin colonizing coagulase-negative <i>Staphylococcus epidermidis</i> causes nosocomial infections and is an important opportunistic and highly adaptable pathogen. To gain more insight into this species, we sequenced the genome of the biofilm positive, methicillin susceptible <i>S. epidermidis</i> O47 strain (hereafter O47). This strain belongs to the most frequently isolated sequence type 2. In comparison to the RP62A strain, O47 can be transformed, which makes it a preferred strain for molecular studies. <i>S. epidermidis</i> O47's genome has a single chromosome of about 2.5 million base pairs and no plasmid. Its <i>oriC</i> sequence has the same directionality as <i>S. epidermidis</i> RP62A, <i>S. carnosus</i>, <i>S. haemolyticus</i>, <i>S. saprophyticus</i> and is inverted in comparison to <i>Staphylococcus aureus</i> and <i>S. epidermidis</i> ATCC 12228. A phylogenetic analysis based on all <i>S. epidermidis</i> genomes currently available at GenBank revealed that O47 is closest related to DAR1907. The genome of O47 contains genes for the typical global regulatory systems known in staphylococci. In addition, it contains most of the genes encoding for the typical virulence factors for <i>S. epidermidis</i> but not for <i>S. aureus</i> with the exception of a putative hemolysin III. O47 has the typical <i>S. epidermidis</i> genetic islands and several mobile genetic elements, which include staphylococcal cassette chromosome (SCC) of about 54 kb length and two prophages φO47A and φO47B. However, its genome has no transposons and the smallest number of insertion sequence (IS) elements compared to the other known <i>S. epidermidis</i> genomes. By sequencing and analyzing the genome of O47, we provide the basis for its utilization in genetic and molecular studies of biofilm formation.
Impact of an interprofessional training ward on interprofessional competencies – a quantitative longitudinal study
2020-08-25

Complex learning strategies, like interprofessional training wards in which students work autonomously in interprofessional collaboration, can support the development of interprofessional competencies in terms of knowledge, abilities and attitudes. To assess the short-term and long-term effects of a three to five weeks placement on such an interprofessional training ward on nursing and medical undergraduates, a study with pre-post-follow-up design was conducted from April 2017 until February 2019. Outcome measures were the University of the West of England Interprofessional Questionnaire (UWE-IP), the Interprofessional Socialization and Valuing Scale (ISVS), and the Assessment of Interprofessional Team Collaboration Scale (AITCS) measuring interprofessional competencies, including teamwork, communication, interprofessional learning, collaboration, and socialization. 60 medical and 63 nursing undergraduates of the first 16 interprofessional student teams that were placed on the Heidelberg interprofessional training ward (HIPSTA) between April 2017 and November 2018 were included in the study. Data was analyzed using the linear mixed model analysis for longitudinal comparisons of scores before, directly after and three months after the placement on the interprofessional training ward. Statistically significant positive short-term effects in interprofessional competencies were found in all three questionnaires, with effect sizes up to d = 1.05. Statistically significant positive long-term effects with effect sizes up to d = 0.60 were found in the ISVS and the AITCS concerning socialization and collaboration. These results indicate that interprofessional education in a clinical setting positively influences the participants' perception of interprofessional socialization and teamwork. This may possibly lead to improved interprofessional collaboration in their further career. Strategies to yield a sustainable improvement of attitudes toward interprofessional interaction are still needed.
Gulf of Nuna: Astrochronologic correlation of a Mesoproterozoic oceanic euxinic event
2020-08-25

Abstract The ca. 1.4 Ga Velkerri and Xiamaling Formations, in Australia and the north China craton, respectively, are both carbonaceous shale deposits that record a prominent euxinic interval and were intruded by ca. 1.3 Ga dolerite sills. These similarities raise the possibility that these two units correlate, which would suggest the occurrence of widespread euxinia, organic carbon burial, and source rock deposition. Paleomagnetic data are consistent with Australia and the north China craton being neighbors in the supercontinent Nuna and thus permit deposition in a single large basin, and the putative stratigraphic correlation. However, lack of geochronological data has precluded definitive testing. The Xiamaling Formation has been shown to exhibit depositional control by orbital cycles. Here, we tested the putative correlation with the Velkerri Formation by cyclostratigraphic analysis. The Velkerri Formation exhibits sedimentological cycles that can be interpreted to represent the entire hierarchy of orbital cycles, according to a sedimentation rate that is consistent with Re-Os ages. Comparison of the inferred durations of the euxinic intervals preserved in both the Xiamaling and Velkerri Formations reveals a nearly identical ∼10-m.y.-long oceanic euxinic event. This permits the interpretation that the two hydrocarbon-rich units were deposited and matured in the same basin of Nuna, similar to the Gulf of Mexico during the breakup of Pangea.
Assessment of tobacco heating system 2.4 on osteogenic differentiation of mesenchymal stem cells and primary human osteoblasts compared to conventional cigarettes
2020-08-25

THS was significantly less harmful to osteoprogenitor cells during osteogenesis than conventional CS. Additional studies are required to confirm whether THS is a better alternative for smokers to improve delays in bone healing following fracture.
Determination of hydrocarbon sources in major rivers and estuaries of peninsular Malaysia using aliphatic hydrocarbons and hopanes as biomarkers
2020-08-25

In this study, levels and sources of aliphatic hydrocarbons and hopanes in surface sediments collected from rivers and estuaries of Peninsular Malaysia were assessed. The concentrations of total n-alkanes ranged from 21.19 to 364.54, and the concentrations of hopanes ranged from 0.23 to 2.45 mg kg−1 dry weight. Evaluation of aliphatic diagnostic indices including Carbon Preference Index (CPI), low molecular weight/high molecular weight ratio (LMW/HMW), terrigenous to aquatic ratio (TAR), carbon preference index (CPI), average chain length (ACL) and pristine to phytane indicate mostly petrogenic input especially in estuaries, which is indicative of anthropogenic activities in the study areas. The results also indicate biogenic origin n-alkanes masked by the anthropogenic features in some stations. The hopane ratios indicate hopanes from the Prai and Malacca Rivers were similar to Middle East Crude Oil (MECO), indicating MECO as one of the sources of petroleum hydrocarbons.
Stability of topological neutron stars
2020-08-25

Tensor-multi-scalar theories (TMST) are among the most natural generalizations of Einstein's theory, they are mathematically self-consistent and free from pathologies. They pass through all the known observations but contrary to standard scalar-tensor theories, TMST offer extremely rich spectrum of solutions and allow for large deviations from general relativity. One of the most interesting objects in these theories are the topological neutron stars. The main goal in the present paper is to study their radial stability since many branches of solutions can exist even for a fixed value of the topological charge. It turns out that only one of these branches is stable for each value of the topological charge while all the rest are unstable. The stable branch is exactly the one that spans from small to large neutron star masses having as well moderate values of the radii in agreement with the observations. As expected, it becomes unstable at the maximum of the mass. The frequencies of the radial modes are examined and it turns out that in most cases the mode frequencies are larger than the general relativistic ones and they increase with the increase of the topological charge. All this shows that the topological neutron stars are viable astrophysical objects that should be explored further in order to determine their observational manifestations.
Does the brain encode the gaze of others as beams emitted by their eyes?
2020-08-25

With great interest we read the recent report of Guterstam et al. (1) in which they show that the direction of someone’s gaze can be decoded from blood oxygen level-dependent (BOLD) activity in areas MT+ (middle temporal complex) (and temporo-parietal junction). In preceding publications, they presented evidence that the observation of directed gaze evokes motion adaptation (2) and the experience of physical interactions with the environment as if the gaze were pushing the targeted objects (3). The authors suggested that these behavioral effects originate in a cognitive representation of another person’s gaze as a force-carrying beam emanating from the eyes, traversing space and operating on the ... [↵][1]1To whom correspondence may be addressed. Email: marius.goerner{at}uni-tuebingen.de. [1]: #xref-corresp-1-1
Do Political Attitudes Matter for Epistemic Decisions of Scientists?
2020-08-25

Abstract The epistemic attitudes of scientists, such as epistemic tolerance and authoritarianism, play important roles in the discourse about rivaling theories. Epistemic tolerance stands for the mental attitude of an epistemic agent, e.g., a scientist, who is open to opposing views, while epistemic authoritarianism represents the tendency to uncritically accept views of authorities. Another relevant epistemic factor when it comes to the epistemic decisions of scientists is the skepticism towards the scientific method. However, the question is whether these epistemic attitudes are influenced by their sociopolitical counterparts, such as the researcher’s degree of conservatism. To empirically investigate the interplay between epistemic and sociopolitical attitudes of scientists, we conducted a survey with researchers ( N = 655) across different disciplines. We propose scales for measuring epistemic tolerance and epistemic authoritarianism, as well as a scale for detecting the participants' readiness to question the scientific method. Furthermore, we investigate the relationship between epistemic tolerance and epistemic authoritarianism on the one hand, and career stage and sociopolitical views on the other hand. Interestingly, our study found only small correlations between the participants' degree of conservatism and their epistemic attitudes. This suggests that political views, against common argumentation, actually do not play an important role in one’s scientific decisions. Moreover, social scientists scored higher on the epistemic tolerance and lower on the epistemic authoritarianism scale than natural scientists. Finally, the results indicate that natural scientists question the scientific method less than social scientists.
Virtual Histology of Cortical Thickness and Shared Neurobiology in 6 Psychiatric Disorders
2020-08-26

In this study, shared neurobiologic processes were associated with differences in cortical thickness across multiple psychiatric disorders. These processes implicate a common role of prenatal development and postnatal functioning of the cerebral cortex in these disorders.
Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37–Viruses That Cause Highly Contagious Eye Infections
2020-08-26

Coxsackievirus A24 variant (CVA24v) and human adenovirus 37 (HAdV-37) are leading causative agents of the severe and highly contagious ocular infections acute hemorrhagic conjunctivitis and epidemic keratoconjunctivitis, respectively. Currently, neither vaccines nor antiviral agents are available for treating these diseases, which affect millions of individuals worldwide. CVA24v and HAdV-37 utilize sialic acid as attachment receptors facilitating entry into host cells. Previously, we and others have shown that derivatives based on sialic acid are effective in preventing HAdV-37 binding and infection of cells. Here, we designed and synthesized novel pentavalent sialic acid conjugates and studied their inhibitory effect against CVA24v and HAdV-37 binding and infection of human corneal epithelial cells. The pentavalent conjugates are the first reported inhibitors of CVA24v infection and proved efficient in blocking HAdV-37 binding. Taken together, the pentavalent conjugates presented here form a basis for the development of general inhibitors of these highly contagious ocular pathogens.
Fibrinolysis shut down in COVID-19 patients: Report on two severe cases with potential diagnostic and clinical relevance
2020-08-26

•To date most reports on COVID-19 associated coagulopathy focused an increased activation of the plasmatic coagulation system.•Using a novel method to assess clot lysis we observed abnormalities in fibrinolysis in COVID-19 infection.•Our finding suggests that fibrinolysis system may contribute to the procoagulatory status in COVID-19 patients.
Evidence for periodic accretion–ejection in LS I +61°303
2020-08-26

ABSTRACT The stellar binary system LS I +61°303, composed of a compact object in an eccentric orbit around a B0 Ve star, emits from radio up to γ-ray energies. The orbital modulation of radio spectral index, X-ray, and GeV γ-ray data suggests the presence of two peaks. This two-peaked profile is in line with the accretion theory predicting two accretion–ejection events for LS I +61°303 along the 26.5 d orbit. However, the existing multiwavelength data are not simultaneous. In this paper, we report the results of a campaign covering radio, X-ray, and γ-ray observations of the system along one single orbit. Our results confirm the two predicted events along the orbit and in addition show that the positions of radio and γ-ray peaks are coincident with X-ray dips as expected for radio and γ-ray emitting ejections depleting the X-ray emitting accretion flow. We discuss future observing strategies for a systematic study of the accretion–ejection physical processes in LS I +61°303.
Surgical Outcomes After Neoadjuvant Chemoradiation Followed by Curative Surgery in Patients With Esophageal Cancer
2020-08-26

Objective: To assess the impact of surgical technique in regard to morbidity and mortality after neoadjuvant treatment for esophageal cancer. Background: The SAKK trial 75/08 was a multicenter phase III trial (NCT01107639) comparing induction chemotherapy followed by chemoradiation and surgery in patients with locally advanced esophageal cancer. Methods: Patients in the control arm received induction chemotherapy with cisplatin and docetaxel, followed by concomitant chemoradiation therapy with cisplatin, docetaxel, and 45Gy. In the experimental arm, the same regimen was used with addition of cetuximab. After completion of neoadjuvant treatment, patients underwent esophagectomy. The experimental arm received adjuvant cetuximab. Surgical outcomes and complications were prospectively recorded and analyzed. Results: Total of 259 patients underwent esophagectomy. Overall complication rate was 56% and reoperation rate was 15% with no difference in complication rates for transthoracic versus transhiatal resections (56% vs 54%, P = 0.77), nor for video assisted thoracic surgeries (VATS) versus open transthoracic resections (67% vs 55%, P = 0.32). There was a trend to higher overall complication rates in squamous cell carcinoma versus adenocarcinoma (65% vs 51%, P = 0.035), and a significant difference in ARDS in squamous cell carcinoma with 14% versus 2% in adenocarcinoma ( P = 0.0002). For patients with involved lymph nodes, a lymph node ratio of ≥0.1 was an independent predictor of PFS (HR 2.5, P = 0.01) and OS (HR 2.2, P = 0.03). Conclusions: This trial showed no difference in surgical complication rates between transthoracic and transhiatal resections. For patients with involved lymph nodes, lymph node ratio was an independent predictor of progression free survival and overall survival.
On Compact RAC Drawings
2020-08-26

We present new bounds for the required area of Right Angle Crossing (RAC) drawings for complete graphs, i.e. drawings where any two crossing edges are perpendicular to each other. First, we improve upon results by Didimo et al. [Walter Didimo et al., 2011] and Di Giacomo et al. [Emilio Di Giacomo et al., 2011] by showing how to compute a RAC drawing with three bends per edge in cubic area. We also show that quadratic area can be achieved when allowing eight bends per edge in general or with three bends per edge for p-partite graphs. As a counterpart, we prove that in general quadratic area is not sufficient for RAC drawings with three bends per edge.
Benjamini–Schramm convergence and zeta functions
2020-08-26

Abstract The equivalence of Benjamini–Schramm convergence and zeta-convergence, known for graphs, is proven for sequences of compact Riemann surfaces. A program is initialized, to extend this connection to arbitrary locally homogeneous spaces.
Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations
2020-08-27

The objective of our study was to test whether limited microbial degradation at low pesticide concentrations could explain the discrepancy between overall degradability demonstrated in laboratory tests and their actual persistence in the environment. Studies on pesticide degradation are often performed using unrealistically high application rates seldom found in natural environments. Nevertheless, biodegradation rates determined for higher pesticide doses cannot necessarily be extrapolated to lower concentrations. In this context, we wanted to (i) compare the kinetics of pesticide degradation at different concentrations in arable land and (ii) clarify whether there is a concentration threshold below which the expression of the functional genes involved in the degradation pathway is inhibited without further pesticide degradation taking place. We set up an incubation experiment for four weeks using 14C-ring labeled 2-methyl-4-chlorophenoxyacetic acid (MCPA) as a model compound in concentrations from 30 to 20,000 μg kg<sup>-1</sup> soil. To quantify the abundance of putative microorganisms involved in MCPA degradation and their degradation activity, tfdA gene copy numbers (DNA) and transcripts (mRNA) were determined by quantitative real-time PCR. Mineralization dynamics of MCPA derived-C were analyzed by monitoring 14CO<sub>2</sub> production and 14C assimilation by soil microorganisms. We identified two different concentration thresholds for growth and activity with respect to MCPA degradation using tfdA gene and mRNA transcript abundance as growth and activity indices, respectively. The tfdA gene expression started to increase between 1,000 and 5,000 μg MCPA kg<sup>-1</sup> dry soil, but an actual increase in tfdA sequences could only be determined at a concentration of 20,000 μg. Accordingly, we observed a clear shift from catabolic to anabolic utilization of MCPA-derived C in the concentration range of 1,000 to 5,000 μg kg<sup>-1</sup>. Concentrations ≥1,000 μg kg<sup>-1</sup> were mainly associated with delayed mineralization, while concentrations ≤1,000 μg kg<sup>-1</sup> showed rapid absolute dissipation. The persistence of pesticides at low concentrations cannot, therefore, be explained by the absence of functional gene expression. Nevertheless, significant differences in the degradation kinetics of MCPA between low and high pesticide concentrations illustrate the need for studies investigating pesticide degradation at environmentally relevant concentrations.
Rapid adaptive evolution to drought in a subset of plant traits in a large‐scale climate change experiment
2020-08-27

Abstract Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, −30%) for 10 years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species Biscutella didyma consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non‐evolving traits may indicate potential constraints to full adaptation.
Epidemiological insights from a large-scale investigation of intestinal helminths in Medieval Europe
2020-08-27

Helminth infections are among the World Health Organization's top neglected diseases with significant impact in many Less Economically Developed Countries. Despite no longer being endemic in Europe, the widespread presence of helminth eggs in archaeological deposits indicates that helminths represented a considerable burden in past European populations. Prevalence of infection is a key epidemiological feature that would influence the elimination of endemic intestinal helminths, for example, low prevalence rates may have made it easier to eliminate these infections in Europe without the use of modern anthelminthic drugs. To determine historical prevalence rates we analysed 589 grave samples from 7 European sites dated between 680 and 1700 CE, identifying two soil transmitted nematodes (Ascaris spp. and Trichuris trichiura) at all locations, and two food derived cestodes (Diphyllobothrium latum and Taenia spp.) at 4 sites. The rates of nematode infection in the medieval populations (1.5 to 25.6% for T. trichiura; 9.3-42.9% for Ascaris spp.) were comparable to those reported within modern endemically infected populations. There was some evidence of higher levels of nematode infection in younger individuals but not at all sites. The genetic diversity of T. trichiura ITS-1 in single graves was variable but much lower than with communal medieval latrine deposits. The prevalence of food derived cestodes was much lower (1.0-9.9%) than the prevalence of nematodes. Interestingly, sites that contained Taenia spp. eggs also contained D. latum which may reflect local culinary practices. These data demonstrate the importance of helminth infections in Medieval Europe and provide a baseline for studies on the epidemiology of infection in historical and modern contexts. Since the prevalence of medieval STH infections mirror those in modern endemic countries the factors affecting STH decline in Europe may also inform modern intervention campaigns.