julilili42/papers huggingface dataset:
Lantibiotic production is a burden for the producing staphylococci
2018-05-04

Abstract Lantibiotics are antimicrobial peptides that contain non-proteinogenic amino acids lanthionine and 3-methyllanthionine and are produced by Gram-positive bacteria. Here we addressed the pros and cons of lantibiotic production for its producing strains. Two staphylococcal strains, S. gallinarum Tü3928 and S. epidermidis Tü3298 producing gallidermin and epidermin respectively were selected. In each of these parental strains, the structural genes gdmA and epiA were deleted; all the other biosynthetic genes including the immunity genes were left intact. Comparative analysis of the lantibiotic-producing strains with their non-producing mutants revealed that lantibiotic production is a burden for the cells. The production affected growth, caused release of ATP, lipids and increased the excretion of cytoplasmic proteins (ECP). The epidermin and gallidermin immunity genes were insufficient to protect the cells from their own product. Co-cultivation studies showed that the Δ gdmA mutant has an advantage over the parental strain; the latter was outcompeted. On the one hand, the production of staphylococcal lantibiotics is beneficial by suppressing competitors, but on the other hand they impose a burden on the producing-strains when they accumulate in higher amounts. Our observations explain why antibiotic-producing strains occur as a minority on our skin and other ecological niches, but retain corresponding antibiotic resistance.
Exercise therapy in medical rehabilitation: Study protocol of a national survey at facility and practitioner level with a mixed method design
2018-05-04

The project generates a comprehensive picture of exercise therapy in medical rehabilitation at facility level and inserts further information at the practitioner level into this context. The chosen methodology of a mixed method design combines the perspective of the facility with that of the practitioner, thus allowing for a complex and multifaceted description of the status quo in exercise therapy practice and makes it possible to identify facilitators and barriers for the refinement of exercise therapy in specific everyday rehabilitation. These findings form the basis for the systematic development of quality exercise therapy in rehabilitation, in particular in terms of the refinement, implementation and dissemination of biopsychosocial concepts of exercise therapy.
Writing against neocolonial necropolitics: literary responses by Iraqi/Arab writers to the US ‘War on Terror’
2018-05-04

(2018). Writing against neocolonial necropolitics: literary responses by Iraqi/Arab writers to the US 'War on Terror'. European Journal of English Studies: Vol. 22, GLOBAL RESPONSES TO THE 'WAR ON TERROR', pp. 128-141.
Diagnostics as prevention — a rapid testing-based strategy of sex workers against sexual HIV exposure
2018-05-04

Introduction: German sex workers have illegally established a prevention strategy, which consists of testing potential sexual partners with human immunodeficiency virus (HIV)-specific rapid diagnostic tests (RDTs) prior to engaging in unprotected sexual intercourse eventually performed in case of a negative test result. Based on a recently established modeling approach, the effectiveness of this strategy regarding the risk of HIV exposure was compared with protection provided by condom use. Methods: Based on a literature search, the following assumptions were used for the calculations: an averaged 80% exposure risk reduction with a condom used during sexual intercourse, usage of a well-characterized 4th-generation HIV RDT, and a 10 day post-infection period without any measurable viral load in peripheral blood followed by a seroconversion period of about 3 weeks with 12.3% test sensitivity (antigen-specific) and only afterwards 97.3% (antibody-specific) test sensitivity. Results: In most constellations, the HIV exposure risk in case of RDT-based prevention was lower than with condom use. Conclusions: The RDT-based HIV exposure prevention as established by sex workers is effective in most situations. A notable weakness of the strategy is the RDTs' poor sensitivity in spite of a high transmission risk during the seroconversion stage.
Thiyl Radicals in Biochemically Important Thiols in the Presence of Metal Ions
2018-05-04

This chapter focuses on thiyl radicals associated with transition metal ions some of which are able to stabilize these radicals in biological systems. Of special interest was the reactivity of iron, cobalt, and manganese. Chromium and vanadium toxicity has been found to be related with the generation of thiyl radical intermediates. The chapter examines copper-thiolate reactions in the authors' laboratory. A common feature of ionic sulfur-centered radicals is their intense electronic absorption in the visible wavelength region. Due to this phenomenon pulse radiolysis was extensively used. In general, the measurement of thiyl radicals is monitored by means of electron paramagnetic resonance (EPR) spin trapping. 5,5-Dimethyl-1-pyrroline-N-oxide, the tetramethyl derivative tetramethylpyrroline oxide, and N-t-butyl-α-phenylnitrone are frequently used as spin traps. Direct identification of the various sulfur-centered radicals by EPR is difficult. In the case of the thiyl species the direct detection is possible under special conditions.
Determination of rotation in the pitch degree of freedom for a spherical birefringent particle
2018-05-04

A three dimensional rigid spherical microscopic object can rotate in either the pitch, yaw or roll fashion. Among these, yaw motion has been conventionally studied using the intensity of the scattered light from birefringent microspheres through crossed polarizers. So far, however, there is no way to study the pitch rotational motion in spherical microspheres. Here we suggest a new method towards the study of such pitch motion in birefringent microspheres under crossed polarizers by measuring the 2-fold asymmetry in the scattered signal using video microscopy. We show a simple example of pitch rotation determination using video microscopy for a microsphere attached with a kinesin molecule while moving along a microtubule. It can also be extended to optical tweezers.
Current Challenges in Plant Eco-Metabolomics
2018-05-06

The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
P II -like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response
2018-05-07

Significance Life on Earth depends on photosynthetic CO 2 fixation to form organic carbon. This process evolved in cyanobacteria and was later conveyed to eukaryotes, giving rise to plastids in algae and plants. To cope with low atmospheric CO 2 concentrations that developed over the course of evolution, cyanobacteria evolved a CO 2 -concentrating mechanism (CCM), which elevates CO 2 levels in the vicinity of RubisCO, the key enzyme of CO 2 fixation. Here we describe a conserved cyclic AMP receptor protein, SbtB, which participates in the sensing of fluctuating C i levels to regulate the cyanobacterial CCM system. SbtB represents a new principle of C i sensing, which is important for acclimation to varying C i regimes in the ecological niches of cyanobacteria.
Statistics of Natural Communication Signals Observed in the Wild Identify Important Yet Neglected Stimulus Regimes in Weakly Electric Fish
2018-05-07

Sensory systems evolve in the ecological niches that each species is occupying. Accordingly, encoding of natural stimuli by sensory neurons is expected to be adapted to the statistics of these stimuli. For a direct quantification of sensory scenes, we tracked natural communication behavior of male and female weakly electric fish, <i>Apteronotus rostratus</i>, in their Neotropical rainforest habitat with high spatiotemporal resolution over several days. In the context of courtship, we observed large quantities of electrocommunication signals. Echo responses, acknowledgment signals, and their synchronizing role in spawning demonstrated the behavioral relevance of these signals. In both courtship and aggressive contexts, we observed robust behavioral responses in stimulus regimes that have so far been neglected in electrophysiological studies of this well characterized sensory system and that are well beyond the range of known best frequency and amplitude tuning of the electroreceptor afferents' firing rate modulation. Our results emphasize the importance of quantifying sensory scenes derived from freely behaving animals in their natural habitats for understanding the function and evolution of neural systems.<b>SIGNIFICANCE STATEMENT</b> The processing mechanisms of sensory systems have evolved in the context of the natural lives of organisms. To understand the functioning of sensory systems therefore requires probing them in the stimulus regimes in which they evolved. We took advantage of the continuously generated electric fields of weakly electric fish to explore electrosensory stimulus statistics in their natural Neotropical habitat. Unexpectedly, many of the electrocommunication signals recorded during courtship, spawning, and aggression had much smaller amplitudes or higher frequencies than stimuli used so far in neurophysiological characterizations of the electrosensory system. Our results demonstrate that quantifying sensory scenes derived from freely behaving animals in their natural habitats is essential to avoid biases in the choice of stimuli used to probe brain function.
Evolution of the Optical Gap in the Acene Series: Undecacene
2018-05-08

Abstract Undecacene, the largest member of the acene family, was photogenerated in a polymer matrix under cryogenic conditions from a precursor with two α‐diketone bridges. The electronic absorption of undecacene extends into the NIR region, but the spectrum is dominated by two strong absorptions in the UV/Vis range. The HOMO–LUMO transition is continuously shifted to lower energies as the number of rings of the acene increases ( E vs. 1/ N , N =number of rings), which is in line with the strong electron correlation calculated by DFT/MRCI.
Impact of Cognitive Abilities and Prior Knowledge on Complex Problem Solving Performance – Empirical Results and a Plea for Ecologically Valid Microworlds
2018-05-08

The original aim of complex problem solving (CPS) research was to bring the cognitive demands of complex real-life problems into the lab in order to investigate problem solving behavior and performance under controlled conditions. Up until now, the validity of psychometric intelligence constructs has been scrutinized with regard to its importance for CPS performance. At the same time, different CPS measurement approaches competing for the title of the best way to assess CPS have been developed. In the first part of the paper, we investigate the predictability of CPS performance on the basis of the Berlin Intelligence Structure Model and Cattell's investment theory as well as an elaborated knowledge taxonomy. In the first study, 137 students managed a simulated shirt factory (<i>Tailorshop</i>; i.e., a complex real life-oriented system) twice, while in the second study, 152 students completed a forestry scenario (<i>FSYS</i>; i.e., a complex artificial world system). The results indicate that reasoning - specifically numerical reasoning (Studies 1 and 2) and figural reasoning (Study 2) - are the only relevant predictors among the intelligence constructs. We discuss the results with reference to the Brunswik symmetry principle. Path models suggest that reasoning and prior knowledge influence problem solving performance in the <i>Tailorshop</i> scenario mainly indirectly. In addition, different types of system-specific knowledge independently contribute to predicting CPS performance. The results of Study 2 indicate that working memory capacity, assessed as an additional predictor, has no incremental validity beyond reasoning. We conclude that (1) cognitive abilities and prior knowledge are substantial predictors of CPS performance, and (2) in contrast to former and recent interpretations, there is insufficient evidence to consider CPS a unique ability construct. In the second part of the paper, we discuss our results in light of recent CPS research, which predominantly utilizes the minimally complex systems (MCS) measurement approach. We suggest ecologically valid microworlds as an indispensable tool for future CPS research and applications.
A Systematic Review and Meta-Analysis of the Relationship Between Brain Data and the Outcome in Disorders of Consciousness
2018-05-08

A systematic search revealed 68 empirical studies of neurophysiological [EEG, event-related brain potential (ERP), fMRI, PET] variables as potential outcome predictors in patients with Disorders of Consciousness (diagnoses Unresponsive Wakefulness Syndrome [UWS] and Minimally Conscious State [MCS]). Data of 47 publications could be presented in a quantitative manner and systematically reviewed. Insufficient power and the lack of an appropriate description of patient selection each characterized about a half of all publications. In more than 80% studies, neurologists who evaluated the patients' outcomes were familiar with the results of neurophysiological tests conducted before, and may, therefore, have been influenced by this knowledge. In most subsamples of datasets, effect size significantly correlated with its standard error, indicating publication bias toward positive results. Neurophysiological data predicted the transition from UWS to MCS substantially better than they predicted the recovery of consciousness (i.e., the transition from UWS or MCS to exit-MCS). A meta-analysis was carried out for predictor groups including at least three independent studies with N > 10 per predictor per improvement criterion (i.e., transition to MCS versus recovery). Oscillatory EEG responses were the only predictor group whose effect attained significance for both improvement criteria. Other perspective variables, whose true prognostic value should be explored in future studies, are sleep spindles in the EEG and the somatosensory cortical response N20. Contrary to what could be expected on the basis of neuroscience theory, the poorest prognostic effects were shown for fMRI responses to stimulation and for the ERP component P300. The meta-analytic results should be regarded as preliminary given the presence of numerous biases in the data.
Pericytes/vessel-associated mural cells (VAMCs) are the major source of key epithelial-mesenchymal transition (EMT) factors SLUG and TWIST in human glioma
2018-05-08

Epithelial-to-mesenchymal transition (EMT) is supposed to be responsible for increased invasion and metastases in epithelial cancer cells. The activation of EMT genes has further been proposed to be important in the process of malignant transformation of primary CNS tumors. Since the cellular source and clinical impact of EMT factors in primary CNS tumors still remain unclear, we aimed at deciphering their distribution <i>in vivo</i> and clinico-pathological relevance in human gliomas. We investigated 350 glioma patients for the expression of the key EMT factors SLUG and TWIST by immunohistochemistry and immunofluorescence related to morpho-genetic alterations such as <i>EGFR</i>-amplification, <i>IDH-1</i> (R132H) mutation and 1p/19q LOH. Furthermore, transcriptional cluster and survival analyses were performed. Our data illustrate that SLUG and TWIST are overexpressed in gliomas showing vascular proliferation such as pilocytic astrocytomas and glioblastomas. EMT factors are exclusively expressed by non-neoplastic pericytes/vessel-associated mural cells (VAMCs). They are not associated with patient survival but correlate with pericytic/VAMC genes in glioblastoma cluster analysis. In summary, the upregulation of EMT genes in pilocytic astrocytomas and glioblastomas reflects the level of activation of pericytes/VAMCs in newly formed blood vessels. Our results underscore that the negative prognostic potential of the EMT signature in the group of diffuse gliomas of WHO grade II-IV does most likely not derive from glioma cells but rather reflects the degree of proliferating mural cells thereby constituting a potential target for future alternative treatment approaches.
Constrained Magnetostratigraphic Dating of a Continental Middle Miocene Section in the Arid Central Asia
2018-05-08

The Neogene succession of the Aktau Mountains in the Ili Basin, southeast Kazakhstan, is a terrestrial archive well suited for researching the role of Central Asia in Miocene climate evolution. We present an integrated approach for dating the well-exposed Bastau Formation, based on magnetostratigraphy and constraints from cyclostratigraphy and biostratigraphy. Stepwise demagnetization yielded characteristic remanence directions that are consistent with those expected for the Miocene in Central Asia. The reddish-colored alluvial floodplain deposits and gray lacustrine deposits show partly complex magnetic behavior with magnetite and hematite as the main magnetic carriers, with variable demagnetization behavior and non-dipolar normal and reverse polarity directions. The observed magnetic properties are best explained by depositional variability and magneto-mineralogical alteration effects of both dissolution and neo-formation of magnetite, including significant secondary magnetization. The mean of reverse polarity directions is flatter than the expected Middle Miocene Earth magnetic field, which is an indicator for the existence of inclination shallowing that supports a primary origin. Detailed rock magnetic analyses are used to analyze the nature of the characteristic remanent magnetization and to discriminate primary and secondary remanence directions in order to obtain a reliable magnetostratigraphic result. The proposed age of 15.3–13.9 Ma for the Bastau Formation corresponds to the known biostratigraphic setting, matches with typical sedimentation rates of foreland basins in Central Asia, and coincides with spectral analysis of geochemical proxies of that section. The resulting age model serves as a robust framework for paleoclimate reconstruction of Neogene climate dynamics in Central Asia.
YB-1 Expression and Phosphorylation Regulate Tumorigenicity and Invasiveness in Melanoma by Influencing EMT
2018-05-09

Abstract Cutaneous melanoma represents one of the most aggressive human tumor entities possessing a high tendency to metastasize. Cancer cells frequently exploit a highly conserved developmental program, the epithelial-to-mesenchymal transition (EMT), to gain migratory and invasive properties promoting their metastatic spread. Cytoplasmic localization of the oncogenic transcription and translation factor Y-box binding protein 1 (YB-1) is a powerful inducer of EMT in breast carcinoma cells. Interestingly, EMT-like processes have also been observed in cutaneous melanoma despite its neural crest origin. Here, increased expression of YB-1 negatively affects patient survival in malignant melanoma and promotes melanoma cell tumorigenicity both in vitro and in vivo. Intriguingly, this effect seems to be mainly mediated by cytoplasmic YB-1 that does not exhibit phosphorylation at serine-102 (S102). Moreover, S102 unphosphorylated YB-1 enhances the migratory and invasive potential of human melanoma cells in two-dimensional (2D) and three-dimensional (3D) culture systems and facilitates acquisition of a mesenchymal-like invasive phenotype in the chick embryo model. Collectively, these data demonstrate that the cytoplasmic activity of YB-1 stimulates tumorigenicity and metastatic potential of melanoma cells by promoting EMT-like properties. Implications: This study reveals for the first time that YB-1 efficiently drives tumorigenicity and invasiveness of melanoma cells in its S102 unphosphorylated cytoplasmic state and that YB-1 expression represents a negative prognostic factor in primary melanoma patients. Mol Cancer Res; 16(7); 1149–60. ©2018 AACR.
Disruption of circumstellar discs by large-scale stellar magnetic fields
2018-05-09

Spectropolarimetric surveys reveal that 8-10\\\\% of OBA stars harbor\\nlarge-scale magnetic fields, but thus far no such fields have been detected in\\nany classical Be stars. Motivated by this, we present here MHD simulations for\\nhow a pre-existing Keplerian disc -- like that inferred to form from decretion\\nof material from rapidly rotating Be stars -- can be disrupted by a\\nrotation-aligned stellar dipole field. For characteristic stellar and disc\\nparameters of a near-critically rotating B2e star, we find that a polar surface\\nfield strength of just 10 G can significantly disrupt the disc, while a field\\nof 100 G, near the observational upper limit inferred for most Be stars,\\ncompletely destroys the disc over just a few days. Our parameter study shows\\nthat the efficacy of this magnetic disruption of a disc scales with the\\ncharacteristic plasma beta {(defined as the ratio between thermal and magnetic\\npressure)} in the disc, but is surprisingly insensitive to other variations,\\ne.g. in stellar rotation speed, or the mass loss rate of the star's radiatively\\ndriven wind. The disc disruption seen here for even a modest field strength\\nsuggests that the presumed formation of such Be discs by decretion of material\\nfrom the star would likely be strongly inhibited by such fields; this provides\\nan attractive explanation for why no large-scale fields are detected from such\\nBe stars.\\n