julilili42/papers huggingface dataset:
Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates
2018-10-19

We present a framework to model microbial transformations in chemostats and retentostats under transient or quasi-steady state conditions. The model accounts for transformation-induced isotope fractionation and mass-transfer across the cell membrane. It also verifies that the isotope fractionation ε can be evaluated as the difference of substrate-specific isotope ratios between inflow and outflow. We explicitly considered that the dropwise feeding of substrate into the reactor at very low dilution rates leads to transient behavior of concentrations and transformation rates and use this information to validate conditions under which a quasi-steady state treatment is justified. We demonstrate the practicality of the code by modeling a chemostat experiment of atrazine degradation at low dilution/growth rates by the strain Arthrobacter aurescens TC1. Our results shed light on the interplay of processes that control biodegradation and isotope fractionation of contaminants at low (μg/L) concentration levels. With the help of the model, an estimate of the mass-transfer coefficient of atrazine through the cell membrane was achieved (0.0025 s<sup>-1</sup>).
Ultrafast Myoglobin Adsorption into Double‐Shelled Hollow Mesoporous Silica Nanospheres
2018-10-19

Abstract The fabrication of hollow mesoporous materials with hierarchical pore structures, regular shape, and uniform particle size via a simple and efficient approach is a major challenge. In this study, a facile preparation approach of hierarchically structured double‐shelled hollow mesoporous silica nanospheres (HS‐DS‐HMSN) is developed. Treatment of monodisperse nonporous silica spheres with CTAB and F127 as well as N,N ‐dimethylhexadecylamine as a cosurfactant under basic conditions gives access to HS‐DS‐HMSNs of uniform particle size. Such HS‐DS‐HMSN‐type materials show a high monodispersibility in aqueous solution, a double‐shelled structure with hierarchically adjustable pore sizes, perpendicularly aligned mesochannels, and high surface areas as well as large pore volumes. On the basis of structure and morphology evolutions as well as unambiguous and reproducible experimental data, a micelle‐assisted self‐assembly process is proposed as a mechanism of formation, further involving cosurfactant‐expanded micelles and a heterogeneous nucleation deposition. The syntheses of a series of HS‐DS‐HMSNs with distinct particle sizes (162–364 nm) as well as distinct inner (range of thickness/pore size: 18–41 nm/3.1–3.7 nm) and outer shells (18–41 nm/3.7–8.0 nm) verify the feasibility and effectiveness of this approach. Such HS‐DS‐HMSNs show an ultrahigh adsorption rate (≈1.7 mg mg −1 min −1 ) and loading (≈300 mg g −1 ) for myoglobin.
Quechuan terms for internal organs of the torso
2018-10-19

Abstract This article discusses the terminology for the major internal organs of the torso across the Quechuan language family. From both semasiological and onomasiological points of view, differences in the synchronic organization of the semantic field across individual Quechua varieties as well as the diachronic developments that brought them about are described. Particular attention is also paid to semantic reconstruction within the field at the proto-Quechua level, and, with recourse to recent efforts at internal reconstruction, also beyond. Another recurrent theme is the interrelation between lexical data and the conceptions of anatomy and bodily functions encountered in quechua-speaking communities. A major conclusion is that an engagement with such perspectives allows for a considerably richer understanding of lexical organization in synchrony and diachrony than linguistic data alone could provide.
Solar Neutrinos Spectroscopy with Borexino Phase-II
2018-10-19

Solar neutrinos have played a central role in the discovery of the neutrino oscillation mechanism. They still are proving to be a unique tool to help investigate the fusion reactions that power stars and further probe basic neutrino properties. The Borexino neutrino observatory has been operationally acquiring data at Laboratori Nazionali del Gran Sasso in Italy since 2007. Its main goal is the real-time study of low energy neutrinos (solar or originated elsewhere, such as geo-neutrinos). The latest analysis of experimental data, taken during the so-called Borexino Phase-II (2011-present), will be showcased in this talk - yielding new high-precision, simultaneous wide band flux measurements of the four main solar neutrino components belonging to the "pp" fusion chain (pp, pep, 7Be, 8B), as well as upper limits on the remaining two solar neutrino fluxes (CNO and hep).
Smart but evil? Student-teachers perception of educational researchers’ epistemic trustworthiness.
2018-10-19

In-service and pre-service teachers are increasingly required to integrate research results into their classroom practice. However, due to their limited methodological background knowledge, they often cannot evaluate scientific evidence firsthand and instead must trust the sources on which they rely. In two experimental studies, we investigated the amount of this so-called epistemic trustworthiness (dimensions expertise, integrity, and benevolence) that student teachers ascribe to the authors of texts who present classical research findings (e.g., learning with worked-out examples) that allegedly were written by either a practitioner, expert, or scientist. Results from the first exploratory study suggest that student teachers view scientists as “smart, but evil” since they rate them as having substantially more expertise than practitioners, while also being less benevolent and lacking in integrity. Moreover, results from the exploratory study suggest that evaluativistic epistemic beliefs (beliefs about the nature of knowledge) predict epistemic trustworthiness. In a preregistered conceptual replication study (Study 2), these effects [will be completed at stage 2].
The non-transcranial TMS-evoked potential is an inherent source of ambiguity in TMS-EEG studies
2018-10-20

Transcranial Magnetic Stimulation (TMS) excites populations of neurons in the stimulated cortex, and the resulting activation may spread to connected brain regions. The distributed cortical response can be recorded with electroencephalography (EEG). Since TMS also stimulates peripheral sensory and motor axons and generates a loud "click" sound, the TMS-evoked EEG potentials (TEPs) reflect not only neural activity induced by transcranial neuronal excitation but also neural activity due to somatosensory and auditory processing. In 17 healthy young individuals, we systematically assessed the contribution of multisensory peripheral stimulation to TEPs using a TMS-compatible EEG system. Real TMS was delivered with a figure-of-eight coil over the left para-median posterior parietal cortex or superior frontal gyrus with the coil being oriented perpendicularly or in parallel to the target gyrus. We also recorded the EEG responses evoked by realistic sham stimulation over the posterior parietal and superior frontal cortex, mimicking the auditory and somatosensory sensations evoked by real TMS. We applied state-of-the-art procedures to attenuate somatosensory and auditory confounds during real TMS, including the placement of a foam layer underneath the coil and auditory noise masking. Despite these precautions, the temporal and spatial features of the cortical potentials evoked by real TMS at the prefrontal and parietal site closely resembled the cortical potentials evoked by realistic sham TMS, both for early and late TEP components. Our findings stress the need to include a peripheral multisensory control stimulation in the design of TMS-EEG studies to enable a dissociation between truly transcranial and non-transcranial components of TEPs.
The severity of human peri‐implantitis lesions correlates with the level of submucosal microbial dysbiosis
2018-10-20

Abstract Aim To cross‐sectionally analyse the submucosal microbiome of peri‐implantitis ( PI ) lesions at different severity levels. Materials and Methods Microbial signatures of 45 submucosal plaque samples from untreated PI lesions obtained from 30 non‐smoking, systemically healthy subjects were assessed by 16s sequencing. Linear mixed models were used to identify taxa with differential abundance by probing depth, after correction for age, gender, and multiple samples per subject. Network analyses were performed to identify groups of taxa with mutual occurrence or exclusion. Subsequently, the effects of peri‐implant probing depth on submucosal microbial dysbiosis were calculated using the microbial dysbiosis index. Results In total, we identified 337 different taxa in the submucosal microbiome of PI. Total abundance of 12 taxa correlated significantly with increasing probing depth; a significant relationship with lower probing depth was found for 16 taxa. Network analysis identified two mutually exclusive complexes associated with shallow pockets and deeper pockets, respectively. Deeper peri‐implant pockets were associated with significantly increased dysbiosis. Conclusion Increases in peri‐implant pocket depth are associated with substantial changes in the submucosal microbiome and increasing levels of dysbiosis.
Functionally distinct assembly of vascular plants colonizing alpine cushions suggests their vulnerability to climate change
2018-10-20

Species colonizing tight cushions of T. caespitosum are competitively strong graminoids and herbaceous perennials from alpine grasslands. Since climate change in the Himalayas favours these species, highly specialized subnival cushion plants may face intense competition and a greater risk of decline in the future.
The PRIDE database and related tools and resources in 2019: improving support for quantification data
2018-10-22

This FAIRsharing record describes: The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories.
Micrometeorological impacts of offshore wind farms as seen in observations and simulations
2018-10-22

In Europe, offshore wind farms have a capacity of 16 GW, with 71% installed at the North Sea. These wind farms represent an additional source of turbulence and may influence the stratification of the marine boundary layer. We present aircraft measurements and simulations showing an impact on temperature and humidity at hub height in the order of 0.5 K and 0.5 g kg&lt;sup&gt;-1&lt;/sup&gt; even 60 km downwind of a wind farm cluster. We extend these simulations to explore a realistic future scenario, suggesting wakes in potential temperature and water vapor propagating more than 100 km downwind. Furthermore, such impacts of wind farms are only observed in case of a strong stable stratification at rotor height, allowing wind farms to mix warmer air downward.
Phase I study of domatinostat (4SC‐202), a class I histone deacetylase inhibitor in patients with advanced hematological malignancies
2018-10-22

Abstract Objectives Domatinostat (4 SC ‐202) is a selective class I histone deacetylase inhibitor ( HDAC i). This phase I study investigated safety, tolerability, pharmacokinetics ( PK ), pharmacodynamics, and antitumor activity in patients with advanced hematological malignancies. Methods Domatinostat was administered orally once ( QD ) or twice daily ( BID ) on days 1‐14 with 7 days off or continuously days 1‐21 in a 3 + 3 design at 7 dose levels from 25 to 400 mg total daily dose ( TDD ). Twenty‐four patients were treated with domatinostat. Results No formal maximum tolerated dose ( MTD ) was determined. One dose‐limiting toxicity ( DLT , grade 4 hypercalcemia) occurred during 200 mg BID continuous treatment. Six patients were reported with ≥ grade 3 treatment‐related adverse events ( TRAE ; grade 3 hematological in three patients, grade 3 and grade 4 liver enzyme increase in 2 patients, grade 4 pulmonary embolism, and grade 4 hypercalcemia in one patient each). Higher grade hepatic TRAE occurred in the 200 mg BID continuous treatment cohort. Out of 24 patients, 1 achieved a complete response, 1 achieved a partial response, and 18 had stable disease as best response. Conclusion Administration of domatinostat was safe, well tolerated with signs of antitumor activity. Four hundred milligram TDD in a 200 mg BID schedule (14 + 7) is the recommended phase II dose for monotherapy.
Modelling the brain response to arbitrary visual stimulation patterns for a flexible high-speed Brain-Computer Interface
2018-10-22

Visual evoked potentials (VEPs) can be measured in the EEG as response to a visual stimulus. Commonly, VEPs are displayed by averaging multiple responses to a certain stimulus or a classifier is trained to identify the response to a certain stimulus. While the traditional approach is limited to a set of predefined stimulation patterns, we present a method that models the general process of VEP generation and thereby can be used to predict arbitrary visual stimulation patterns from EEG and predict how the brain responds to arbitrary stimulation patterns. We demonstrate how this method can be used to model single-flash VEPs, steady state VEPs (SSVEPs) or VEPs to complex stimulation patterns. It is further shown that this method can also be used for a high-speed BCI in an online scenario where it achieved an average information transfer rate (ITR) of 108.1 bit/min. Furthermore, in an offline analysis, we show the flexibility of the method allowing to modulate a virtually unlimited amount of targets with any desired trial duration resulting in a theoretically possible ITR of more than 470 bit/min.
Acquiring Clinical Knowledge from an Online Video Platform: A Randomized Controlled Experiment on the Relevance of Integrating Anatomical Information and Clinical Practice
2018-10-22

Basic subjects in medical education, such as anatomy, are often taught through teaching formats that do not always sufficiently demonstrate the relevance of this basic information for clinical practice. Accordingly, it is a recent trend in anatomy education to link anatomical information more explicitly to clinical practice. This article presents an online video platform (Tuebingen’s Sectio Chirurgica [TSC]) as one means of explicitly integrating preclinical anatomical knowledge and clinical application. The purpose of the study presented here was to examine the effects of videos through which medical students were educated about Anterior Cruciate Ligament reconstruction. A TSC video about this surgical procedure was compared to a video with a traditional lecture providing the identical information. Participants ( n = 114) perceived the TSC video to be superior in comprehensibility of the presentation ( P = 0.003) and conceivability of the surgical procedure ( P = 0.027), and to be more entertaining ( P &lt; 0.001). Moreover, participants in the TSC condition acquired more clinical knowledge than in the lecture condition ( P = 0.043) but did not differ in their acquisition of anatomical knowledge. Mediation analyses indicated that the effect on the acquisition of clinical knowledge was mediated by comprehensibility, conceivability, and entertainment. These findings are discussed regarding their implications for medical education in terms of contributing to the general trend of linking preclinical anatomical knowledge to clinical application. A discussion about the limitations of the study and suggestions for future research are also provided.
Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance
2018-10-22

The data show that the rifin/stevor and var gene families represent the most diverse compartments of the P. falciparum genome but that the majority of var genes are inherited without alterations within their respective parental chromosomal context. Furthermore, MS genotyping with 54 MS can successfully distinguish between two sibling progeny of a natural P. falciparum cross and thus can be used to investigate identity by descent in field isolates.
Erratum for Nguyen et al., “Toll-Like Receptor 2 and Lipoprotein-Like Lipoproteins Enhance Staphylococcus aureus Invasion in Epithelial Cells”
2018-10-22

Volume 86, no. 8, e00343-18, 2018, [https://doi.org/10.1128/IAI.00343-18][1]. Page 1: This article was published on 23 July 2018 with Francesca Barletta's name incorrectly appearing as “Francesca Barletta Solari” in the byline. The byline was updated in the version posted on 15 August 2018. [1
Mental Training for Better Achievement: Effects of Verbal Suggestions and Evaluation (of Effectiveness) on Cognitive Performance
2018-10-22

<b>Objective:</b> There is only some literature regarding the influence of verbal suggestions on cognitive performance in healthy volunteers. For example, the performance in a knowledge test was enhanced when participants were told that they had subliminally received the correct answer. However, enhancing cognitive performance only via verbal suggestions without prior conditioning phases has not yet been examined. The goal of our study was therefore to investigate the effects of a mental training based on verbal suggestions compared to a control training on cognitive performance in a student population using a balanced-placebo-design. <b>Methods:</b> In total, 103 participants were randomly assigned either to listening to a 20 min audio-taped mental training or to a 20 min philosophy lecture (control training) via headphones. Participants were individually tested before and after the training concerning their cognitive performance. Information about the type of training were varied in both intervention conditions ("You are part of our experimental condition and you will receive an effective mental training" or "You are part of our control group and you will receive the control condition"). At the end of the assessment, participants were asked what kind of training they believed they had received and how effective they would rate the received training. <b>Results:</b> Overall, the cognitive performance improved in all participants, <i>F</i> <sub>(1, 99)</sub> = 490.01, <i>p</i> < 0.001. Contrary to our hypotheses, we found no interaction of the type of training and type of instruction on the cognitive performance. Participants who rated the received training as being effective at the end of the experiment (regardless if it was the mental or the control training), have before experienced a greater improvement in their cognitive performance [<i>F</i> <sub>(2,100)</sub> = 7.26, <i>p</i> = 0.001] and showed higher scores in the ability to absorb [<i>F</i> <sub>(2, 99)</sub> = 3.75, <i>p</i> = 0.027]. <b>Conclusion:</b> The subjects' own experiences in the task might have influenced the rating of the training rather than the actual training or the information they receive regarding the type of training. This finding underlines the relevance of enhancing the subjective beliefs and self-efficacy in situations where cognitive attention processes are important and of individually tailoring mental trainings.
Spectral theory for structured perturbations of linear operators
2018-10-22

We characterize the spectrum (and its parts) of operators which can be represented as " G=A+BC“ for a "simpler" operator A and a structured perturbation BC . The interest in this kind of perturbations is motivated, e.g., by perturbations of the domain of an operator A but also arises in the theory of closed-loop systems in control theory. In many cases our results yield the spectral values of G as zeros of a " characteristic equation ".
Genome-Wide and Abdominal MRI Data Provide Evidence That a Genetically Determined Favorable Adiposity Phenotype Is Characterized by Lower Ectopic Liver Fat and Lower Risk of Type 2 Diabetes, Heart Disease, and Hypertension
2018-10-23

Recent genetic studies have identified alleles associated with opposite effects on adiposity and risk of type 2 diabetes. We aimed to identify more of these variants and test the hypothesis that such favorable adiposity alleles are associated with higher subcutaneous fat and lower ectopic fat. We combined MRI data with genome-wide association studies of body fat percentage (%) and metabolic traits. We report 14 alleles, including 7 newly characterized alleles, associated with higher adiposity but a favorable metabolic profile. Consistent with previous studies, individuals carrying more favorable adiposity alleles had higher body fat % and higher BMI but lower risk of type 2 diabetes, heart disease, and hypertension. These individuals also had higher subcutaneous fat but lower liver fat and a lower visceral-to-subcutaneous adipose tissue ratio. Individual alleles associated with higher body fat % but lower liver fat and lower risk of type 2 diabetes included those in PPARG, GRB14, and IRS1, whereas the allele in ANKRD55 was paradoxically associated with higher visceral fat but lower risk of type 2 diabetes. Most identified favorable adiposity alleles are associated with higher subcutaneous and lower liver fat, a mechanism consistent with the beneficial effects of storing excess triglycerides in metabolically low-risk depots.
Variable training but not sleep improves consolidation of motor adaptation
2018-10-23

Abstract How motor memory consolidates still remains elusive. Consolidation of motor skills has been shown to depend on periods of sleep. Conversely, motor adaptation during tasks not dependent on the hippocampus may not depend on sleep. Some research suggests that the training schedule affects the sleep dependency of motor adaptation tasks. Here, we investigated whether sleep differentially affects memory consolidation that depends on the training schedule. Healthy men were trained with their dominant, right hand on a force-field adaptation task and re-tested after an 11-h consolidation period involving overnight sleep (Sleep) or daytime wakefulness (Wake). Retesting included a transfer test of the non-dominant hand. Half of the subjects in each group adapted to different force-field magnitudes during training with low inter-trial force variability (Sleep-Blocked; Wake-Blocked), and the other half were trained with a high-variability schedule (Sleep-Random; Wake-Random). EEG was recorded during task execution and overnight polysomnography. Consolidation was comparable between Wake and Sleep groups, although performance changes over sleep correlated with sleep spindles nesting in slow-wave upstates. Higher training variability improved retest performance, including transfer learning, and these improvements correlated with higher alpha power in contralateral parietal areas. These enhanced consolidation effects might be fostered by feedback rather than feedforward mechanisms.