Hydration and self-​aggregation of a neutral cosolute from dielectric relaxation spectroscopy and MD simulations: the case of 1,​3-​dimethylurea

The influence of the amphiphile 1,3-dimethylurea (1,3-DMU) on the dynamic properties of water was studied using dielec. relaxation spectroscopy. The expt. provided evidence for substantial retardation of water reorientation in the hydration shell of 1,3-DMU, leading to a sep. slow-water relaxation in addn. to contributions from bulk-like and fast water as well as from the solute. From the amplitudes of the resolved water modes effective hydration nos. were calcd., showing that each 1,3-DMU mol. effectively freezes the reorientation of 1-2 water mols. Addnl., a significant amt. of solvent mols., decreasing from ~39 at infinite diln. to ~3 close to the soly. limit, is retarded by a factor of ~1.4 to 2.3, depending on concn. The marked increase of the solute amplitude indicates pronounced parallel dipole alignment between 1,3-DMU and its strongly bound H2O mols. Mol. dynamics (MD) simulations of selected solns. revealed a notable slowdown of water rotation for those solvent mols. surrounding the Me groups of 1,3-DMU and strong binding of ~2H2O by the hydrophilic carbonyl group, corroborating thus the exptl. results. Addnl., the simulations revealed 1,3-DMU self-aggregates of substantial lifetime

Authentisches Lernen mit Atemalkoholsensoren im Physikunterricht: Physikalische Grundlagen, Visualisierungen und Experimente

Authentisches Lernen ist ein Ansatz, bei dem der Realitätsbezug und die Lebensnä­he besonders wichtig sind. Sie sollen Schülerinnen und Schüler motivieren, sich mit der Anwendung physikalischer Inhalte auseinander zu setzen. Außerdem wird an­genommen, dass sie sich positiv auf den Wissenserwerb und die Wissensanwen­dung auswirken. Eine Möglichkeit für die Umsetzung authentischen Lernens ist das Einbinden von Geräten aus dem Alltag in den Unterricht. Eine didaktische He­raus­forderung ist dabei, die oftmals komplizierten physikalischen Sachverhalte schü­lergerecht zu veranschaulichen ohne Einbußen in der Realitätsnähe, im Kontext­bezug und in der Authentizität hinnehmen zu müssen.In diesem Beitrag geht es um Atemalkoholmessgeräte aus Halbleiterma­terialien. Da­zu werden ihre fachlichen und messtechnischen Grundlagen beschrieben. Disku­tiert werden anschließend die beiden physikdidaktischen Themen: Authen­tisches Lernen und Visualisierungen. Bezüglich des authentischen Lernens werden cha­rakteristische Merkmale aufgezeigt. Hinsichtlich der Visualisierungen werden die lernförderliche Darstellung physikalischer Sachverhalte und das Herstellen authen­tischer Anwendungsbezüge beschrieben und jeweils durch Beispiele kon­kreti­siert. Zuletzt werden einige Experimente vorgestellt, mit denen entweder interessante Kontexte zum Thema Alkohol im Alltag behandelt oder fachliche Grundlagen er­schlossen werden können

Authentisches Lernen mit Atemalkoholsensoren im Physikunterricht: Physikalische Grundlagen, Visualisierungen und Experimente

Authentisches Lernen ist ein Ansatz, bei dem der Realitätsbezug und die Lebensnä­he besonders wichtig sind. Sie sollen Schülerinnen und Schüler motivieren, sich mit der Anwendung physikalischer Inhalte auseinander zu setzen. Außerdem wird an­genommen, dass sie sich positiv auf den Wissenserwerb und die Wissensanwen­dung auswirken. Eine Möglichkeit für die Umsetzung authentischen Lernens ist das Einbinden von Geräten aus dem Alltag in den Unterricht. Eine didaktische He­raus­forderung ist dabei, die oftmals komplizierten physikalischen Sachverhalte schü­lergerecht zu veranschaulichen ohne Einbußen in der Realitätsnähe, im Kontext­bezug und in der Authentizität hinnehmen zu müssen.In diesem Beitrag geht es um Atemalkoholmessgeräte aus Halbleiterma­terialien. Da­zu werden ihre fachlichen und messtechnischen Grundlagen beschrieben. Disku­tiert werden anschließend die beiden physikdidaktischen Themen: Authen­tisches Lernen und Visualisierungen. Bezüglich des authentischen Lernens werden cha­rakteristische Merkmale aufgezeigt. Hinsichtlich der Visualisierungen werden die lernförderliche Darstellung physikalischer Sachverhalte und das Herstellen authen­tischer Anwendungsbezüge beschrieben und jeweils durch Beispiele kon­kreti­siert. Zuletzt werden einige Experimente vorgestellt, mit denen entweder interessante Kontexte zum Thema Alkohol im Alltag behandelt oder fachliche Grundlagen er­schlossen werden können

Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data

IntroductionMicrobes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amplicon sequencing is typically applied to assess microbial communities, metagenomics and total RNA sequencing (herein summarized as omics-based methods) can provide a more holistic picture of microbial biodiversity at sufficient sequencing depths. Despite this advantage, amplicon sequencing and omics-based methods have not yet been compared for taxonomy-based environmental assessments with machine learning.MethodsIn this study, we applied 16S and ITS-2 sequencing, metagenomics, and total RNA sequencing to samples from a stream mesocosm experiment that investigated the impacts of two aquatic stressors, insecticide and increased fine sediment deposition, on stream biodiversity. We processed the data using similarity clustering and denoising (only applicable to amplicon sequencing) as well as multiple taxonomic levels, data types, feature selection, and machine learning algorithms and evaluated the stressor prediction performance of each generated model for a total of 1,536 evaluated combinations of taxonomic datasets and data-processing methods.ResultsSequencing and data-processing methods had a substantial impact on stressor prediction. While omics-based methods detected a higher diversity of taxa than amplicon sequencing, 16S sequencing outperformed all other sequencing methods in terms of stressor prediction based on the Matthews Correlation Coefficient. However, even the highest observed performance for 16S sequencing was still only moderate. Omics-based methods performed poorly overall, but this was likely due to insufficient sequencing depth. Data types had no impact on performance while feature selection significantly improved performance for omics-based methods but not for amplicon sequencing.DiscussionWe conclude that amplicon sequencing might be a better candidate for machine-learning-based environmental stressor prediction than omics-based methods, but the latter require further research at higher sequencing depths to confirm this conclusion. More sampling could improve stressor prediction performance, and while this was not possible in the context of our study, thousands of sampling sites are monitored for routine environmental assessments, providing an ideal framework to further refine the approach for possible implementation in environmental diagnostics

Acquired von Willebrand syndrome and factor VIII in patients with moderate to severe mitral regurgitation undergoing transcatheter mitral valve repair

Background and Hypothesis: The acquired von Willebrand syndrome (AvWS), which predisposes to bleeding events, is often related to valvular heart diseases. We investigated possible implications of AvWS and factor VIII levels in patients with moderate to severe mitral regurgitation (MR) undergoing transcatheter mitral valve repair (TMVR). Methods and Results: 123 patients with moderate to severe MR were prospectively enrolled. Complete measurements of von Willebrand Factor activity (vWFAct), von Willebrand Factor antigen (vWFAg), and factor VIII expression before and 4 weeks after TMVR were available in 85 patients. At baseline, seven patients had a history of gastrointestinal bleeding, two patients suffered bleeding events during their hospital stay, and one patient had a bleeding 4 weeks after TMVR. Even though vWFAct, vWFAct/vWFAg ratio and vWFAg values did not change after TMVR, we observed a significantly lower vWFAct/vWFAg ratio in patients with primary MR as compared to patients with secondary MR both at baseline (p = 0.022) and 4 weeks following the TMVR procedure (p = 0.003). Additionally, patients with a mean mitral valve gradient ≥4 mmHg after TMVR had significantly lower vWFAct/vWFAg ratios as compared to patients with a mean mitral valve gradient <4 mmHg (p = 0.001). Conclusions: MR of primary etiology was associated with lower vWFAct/vWFAg ratio, hinting toward HMWM loss due to shear stress caused by eccentric regurgitation jets. In addition, morphological changes leading to postprocedural transmitral gradients ≥4 mmHg were related to lower vWFAct/vWFAg ratio 4 weeks after the procedure. Alterations of the vWFAct/vWFAg ratio in turn did not translate into a greater risk for bleeding events

Soteriological Specifics in Paul, James, John, and Peter

Topic The ideas of New Testament authors seem to stand in contradiction to each other: some appear to focus on justification by faith, whereas others seems to proclaim that works need to be performed in order to be saved. It is therefore very difficult to deduce relevant practical implications from the doctrine of salvation because it is often explained in a rather superficial and dissatisfactory way. Purpose The development of the interpretation of the doctrine of salvation is outlined in a chapter about church history. In the following chapter relevant Bible text passages in Paul, James, John, and Peter about the doctrine of salvation are examined carefully. Because the doctrine of salvation has some practical and theological consequences, the implications of it will be discussed in another chapter before coming to a final conclusion. Sources Throughout each period of time during church history, there appeared to be two groups of scholars and theologians who tried to convince church members of their opinion. One group tried to emphasize righteousness by faith; the other group stressed the importance of deeds (as New Testament authors appear to do also). But this study indicates that Bible authors actually wrote about the same topic from different points of view. They focused on different aspects that contribute to the whole picture. They did not contradict each other. Conclusions A closer study reveals no theological differences among the different writers’ points of view and approaches concerning the doctrine of salvation. Some of them tried to focus on justification and sanctification in their correct chronological order, some focused on the truthfulness of faith that presents itself through appropriate works, and others emphasized the importance of both aspects to show that they are inseparable

BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems

DNA metabarcoding workflows produce hundreds to ten-thousands of Operational Taxonomic Units (OTUs) or Exact Sequence Variants (ESVs) per analysis. In most workflows, a taxonomic assignment to these generated sequences is needed. This is typically done using publicly available databases. Especially, yet not exclusively, for Eumetazoan metabarcoding, the Barcode of Life Data system (BOLD) is the most comprehensive and curated reference barcode database and, therefore, typically the first choice for taxonomic assignment. While an application programme interface (API) exists to query data in large batches, no information on the many and important unpublished data are obtained through the API. The alternative approach using the BOLD identification engine on the website provides full access, yet it is restricted to 100 sequences at once. We developed a small platform-independent and graphical user interface (GUI) software package, BOLDigger, which aims to solve this problem by automating the process of sending successive requests of up to 100 sequences without surpassing the capacities of BOLD. BOLDigger can be used to download the results of the identification engine, as well as metadata for the obtained hits. For the selection of the best fitting hit, three different methods are implemented. A new approach, combining a threshold-based approach with the metadata information, was implemented to make use of the metadata

Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics

DNA metabarcoding is an efficient tool to characterize invertebrate species composition in environmental samples. Most metabarcoding protocols for invertebrate bulk samples start with sample homogenization, followed by DNA extraction, amplification of a specific marker region and sequencing on a high-throughput sequencer.Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist. Giving the amount of research done to validate almost all laboratory steps of metabarcoding workflows it is surprising that there is no clear recommendation for the basis of almost all metabarcoding studies: the homogenization of samples itself.For homogenization, different devices are used that can be divided into two major categories: bead mills and blenders. While bead-mills accelerate small, hard particles in a closed container or tube to break down specimens into small tissue fragments, blenders work with a rapidly rotating blades that reliably slice specimens as well as other substrate of the sample. Both methods are currently used in metabarcoding studies and have downsides to consider.Bead-mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large scale studies. Blenders on the other hand offer the opportunity to be cleaned and can handle larger sample volumes in shorter time, with an increased risk of cross-contamination.We here aimed to develop a fast, robust, cheap and reliable sample homogenization protocol that overcomes the above-mentioned limitations of both methods, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six sorted Malaise trap insect samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 technical replicates of each sample and many negative controls per sample (Fig. 1) to quantify impacts of i) insufficient homogenization and ii) possible sources of cross-contamination.Our results show that homogenization is sufficient after 3 minutes of homogenization. Rinsing the blender with water is sufficient in most cases but leads to low read-numbers in some of the negative controls. These could be further reduced by rinsing the blender with self-made drain-safe sterilization solution based on bleach but far less corrosive than pure bleach. Our results suggest that rinsing 1-2 times for 20 seconds is sufficient to avoid any cross-contamination.The improvements of the protocol in terms of speed, ease of handling, overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenization after sampling in particular for large-scale and regulatory metabarcoding biodiversity assessments and monitoring programs

The Interplay of Methyl-Group Distribution and Hydration Pattern of Isomeric Amphiphilic Osmolytes

The intermol. interactions and dynamics of aq. 1,​1-​dimethyurea (1,​1-​DMU) solns. were studied by examg. the concn. dependence of the solvent and solute relaxations detected by dielec. spectroscopy. Mol. dynamics simulations were carried out to facilitate interpretation of the dielec. data and to get a deeper insight into the behavior of the system components at the microscopic level. In particular, the simulations allowed for explaining the main differences between the dielec. spectra of aq. solns. of 1,​1-​DMU and of its structural isomer 1,​3-​DMU. Similar to the previously studied compds. urea and 1,​3-​DMU, 1,​1-​DMU forms rather stable hydrates. This is evidenced by an effective solute dipole moment that significantly exceeds the value of a neat 1,​1-​DMU mol., indicating pronounced parallel alignment of the solute dipole with two to three H2O moments. The MD simulations revealed that the involved water mols. form strong hydrogen bonds with the carbonyl group. However, in contrast to 1,​3-​DMU, it was not possible to resolve a "slow-​water" mode in the dielec. spectra, suggesting rather different hydration-​shell dynamics for 1,​1-​DMU as confirmed by the simulations. In contrast to aq. urea and 1,​3-​DMU, addn. of 1,​1-​DMU to water leads to a weak decrease of the static permittivity. This is explained by the emergence of antiparallel dipole-​dipole correlations among 1,​1-​DMU hydrates with rising concn

An explanation for the charge on water's surface, by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994. Comment

Gray-Weale and Beattie's rationalization of the neg. charge obsd. on the surface of water in terms of accumulation of OH- is based on the supposedly uniquely large dielec. decrement of hydroxide solns. [A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994]. We challenge this rationalization and point to another ion, namely fluoride, which has a comparable dielec. decrement and size and which is repelled from the surface of water