julilili42/papers huggingface dataset:
Human cerebrospinal fluid induces neuronal excitability changes in resected human neocortical and hippocampal brain slices
2019-08-08

Abstract Human cerebrospinal fluid (hCSF) have proven advantageous over conventional medium when culturing both rodent and human brain tissue. Increased excitability and synchronicity, similar to the active state exclusively recorded in vivo , reported in rodent slice and cell-cultures with hCSF as recording medium, indicates properties of the hCSF not matched by the artificial cerebrospinal fluid (aCSF) commonly used for electrophysiological recording. To evaluate the possible importance of using hCSF as electrophysiological recording medium of human brain tissue, we compared the general excitability in ex vivo human brain tissue slice cultures during perfusion with hCSF and aCSF. For measuring the general activity from a majority of neurons within neocortical and hippocampal human ex vivo slices we used a microelectrode array (MEA) recording technique with 252 electrodes covering an area of 3.2 x 3.2 mm 2 and a second CMOS-based MEA with 4225 electrodes on a 2 x 2 mm 2 area for detailed mapping of action potential waveforms. We found that hCSF increase the number of active neurons and the firing rate of the neurons in the slices as well as increasing the numbers of bursts while leaving the duration of the bursts unchanged. Interestingly, not only an increase in the overall activity in the slices was observed, but a reconfiguration of the network functionality could be detected with specific activation and inactivation of subpopulations of neuronal ensembles. In conclusion, hCSF is an important component to consider for future human tissue studies, especially for experiments designed to mimic the in vivo situation.
Pyridinylimidazoles as GSK3β inhibitors: the impact of tautomerism on compound activity via water networks
2019-08-08

Data related to publication: Heider et al.: Pyridinylimidazoles as GSK3β inhibitors: the impact of tautomerism on compound activity via water networks. The files include: 1) Output conformations of the QM Tautomer &amp; Conformation Predictor of Maestro (Schrödinger, LLC, New York, NY, 2018) of the compounds <strong>1</strong>, <strong>3a</strong>, <strong>3b</strong>, <strong>3c</strong>, <strong>3d</strong>, <strong>3e</strong>, <strong>3f</strong>, <strong>3g</strong>, <strong>3h</strong>, <strong>3j</strong>, <strong>3k</strong>, <strong>3l</strong>, <strong>3m</strong>, <strong>6f</strong> and <strong>6g</strong> [.mae and .sdf files]. 2) Movies of the MD simulations of compounds <strong>3a</strong>, <strong>3j</strong>, <strong>4a</strong>, <strong>4b</strong>, <strong>6b</strong>, <strong>6g</strong> (6GN1) and movies (*_2) of <strong>3a</strong>, <strong>3j</strong>, <strong>6b</strong>, <strong>6g</strong> (4PTC) [.mpg files] . 3) Raw Desmond trajectory files of the MD simulations of the compounds <strong>3a</strong>, <strong>3j</strong>, <strong>4a</strong>, <strong>4b</strong>, <strong>6b</strong>, <strong>6g</strong> [out.cms and the full trj files]. <br>
CEST MR‐Fingerprinting: Practical considerations and insights for acquisition schedule design and improved reconstruction
2019-08-09

Purpose To understand the influence of various acquisition parameters on the ability of CEST MR‐Fingerprinting (MRF) to discriminate different chemical exchange parameters and to provide tools for optimal acquisition schedule design and parameter map reconstruction. Methods Numerical simulations were conducted using a parallel computing implementation of the Bloch‐McConnell equations, examining the effect of TR, TE, flip‐angle, water and , saturation‐pulse duration, power, and frequency on the discrimination ability of CEST‐MRF. A modified Euclidean distance matching metric was evaluated and compared to traditional dot product matching. L‐Arginine phantoms of various concentrations and pH were scanned at 4.7T and the results compared to numerical findings. Results Simulations for dot product matching demonstrated that the optimal flip‐angle and saturation times are and 1100 ms, respectively. The optimal maximal saturation power was 3.4 μT for concentrated solutes with a slow exchange rate, and 5.2 μT for dilute solutes with medium‐to‐fast exchange rates. Using the Euclidean distance matching metric, much lower maximum saturation powers were required (1.6 and 2.4 μT, respectively), with a slightly longer saturation time (1500 ms) and flip‐angle. For both matching metrics, the discrimination ability increased with the repetition time. The experimental results were in agreement with simulations, demonstrating that more than a 50% reduction in scan‐time can be achieved by Euclidean distance‐based matching. Conclusions Optimization of the CEST‐MRF acquisition schedule is critical for obtaining the best exchange parameter accuracy. The use of Euclidean distance‐based matching of signal trajectories simultaneously improved the discrimination ability and reduced the scan time and maximal saturation power required.
Gross national income and antibiotic resistance in invasive isolates: analysis of the top-ranked antibiotic-resistant bacteria on the 2017 WHO priority list
2019-08-09

Abstract Objectives To assess the association between country income status and national prevalence of invasive infections caused by the top-ranked bacteria on the WHO priority list: carbapenem-resistant (CR) Acinetobacter spp., Klebsiella spp. and Pseudomonas aeruginosa; third-generation cephalosporin-resistant (3GCR) Escherichia coli and Klebsiella spp.; and MRSA and vancomycin-resistant Enterococcus faecium (VR E. faecium). Methods Active surveillance systems providing yearly prevalence data from 2012 onwards for the selected bacteria were included. The gross national income (GNI) per capita was used as the indicator for income status of each country and was log transformed to account for non-linearity. The association between antibiotic prevalence data and GNI per capita was investigated individually for each bacterium through linear regression. Results Surveillance data were available from 67 countries: 38 (57%) were high income, 16 (24%) upper-middle income, 11 (16%) lower-middle income and two (3%) low income countries. The regression showed significant inverse association (P&lt;0.0001) between resistance prevalence of invasive infections and GNI per capita. The highest rate of increase per unit decrease in log GNI per capita was observed in 3GCR Klebsiella spp. (22.5%, 95% CI 18.2%–26.7%), CR Acinetobacter spp. (19.2% 95% CI 11.3%–27.1%) and 3GCR E. coli (15.3%, 95% CI 11.6%–19.1%). The rate of increase per unit decrease in log GNI per capita was lower in MRSA (9.5%, 95% CI 5.2%–13.7%). Conclusions The prevalence of invasive infections caused by the WHO top-ranked antibiotic-resistant bacteria is inversely associated with GNI per capita at the global level. Public health interventions designed to limit the burden of antimicrobial resistance should also consider determinants of poverty and inequality, especially in lower-middle income and low income countries.
MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels
2019-08-09

Abstract The mechanisms behind carbon dioxide (CO 2 ) dependency in non-autotrophic bacterial isolates are unclear. Here we show that the Staphylococcus aureus mpsAB operon, known to play a role in membrane potential generation, is crucial for growth at atmospheric CO 2 levels. The genes mpsAB can complement an Escherichia coli carbonic anhydrase (CA) mutant, and CA from E. coli can complement the S. aureus delta- mpsABC mutant. In comparison with the wild type, S. aureus mps mutants produce less hemolytic toxin and are less virulent in animal models of infection. Homologs of mpsA and mpsB are widespread among bacteria and are often found adjacent to each other on the genome. We propose that MpsAB represents a dissolved inorganic carbon transporter, or bicarbonate concentrating system, possibly acting as a sodium bicarbonate cotransporter.
Patients’ Experiences of Diabetes Self-Management Education According to Health-Literacy Levels
2019-08-09

Diabetes self-management is an important part of patient care for those with diabetes. The purpose of this study was to explore patients’ experiences with diabetes self-management education and how these experiences differed by health-literacy levels. A descriptive qualitative design was conducted. In 2016, 20 patients with diabetes who took a formal diabetes self-management course at a university hospital in South Korea were interviewed. A conventional content analysis was conducted. Patients with low health-literacy misunderstood diabetes management, showed passive attitudes towards seeking information, and had difficulty obtaining detailed information. Patients with high health-literacy wanted systematic, in-depth, individualized counselling on lifestyle modifications and medications. Patients’ experiences with diabetes self-management education revealed differences in their health-literacy dimensions. In addition to practising health-literacy precautions, the content and delivery of diabetes self-management education need to be accommodated according to patients’ health-literacy levels to obtain better outcomes.
The time to relapse correlates with the histopathological growth pattern in nodular lymphocyte predominant Hodgkin lymphoma
2019-08-09

Abstract Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) can present with different histopathological growth patterns. The impact of these histopathological growth patterns on relapse characteristics is unknown. We therefore analyzed paired biopsies obtained at initial diagnosis and relapse from 33 NLPHL patients who had received first‐line treatment within German Hodgkin Study Group (GHSG) trial protocols, and from a second cohort of 41 relapsed NLPHL patients who had been treated outside GHSG studies. Among the 33 GHSG patients, 21 patients presented with a typical growth pattern at initial diagnosis, whereas 12 patients had a variant histology. The histopathological growth patterns at initial diagnosis and at relapse were consistent in 67% of cases. A variant histology at initial diagnosis was associated with a shorter median time to lymphoma recurrence (2.8 vs 5.2 years; P = .0219). A similar tendency towards a shorter median time to lymphoma recurrence was observed for patients presenting with a variant histology at relapse, irrespective of the growth pattern at initial diagnosis. Results obtained from the 41 NLPHL patients who had been treated outside GHSG studies were comparable (median time to lymphoma recurrence for variant histology vs typical growth pattern at initial diagnosis: 1.5 vs 7.0 years). In conclusion, the histopathological growth pattern remains consistent at relapse in the majority of NLPHL cases, and has major impact on the time of relapse.
Association of CAG Repeats With Long-term Progression in Huntington Disease
2019-08-12

Results of this study suggest that succinct summary measures of function and brain loss characterize HD progression across a wide disease span. CAG repeat length strongly predicts their decline rate. This work aids our understanding of the age and CAG repeat length-dependent association between changes in the brain and clinical manifestations of HD.
miRNAs in Plant Development
2019-08-12

Abstract Since the discovery of the first microRNA (miRNA) in Caenorhabditis elegans about 25 years ago, small RNAs have emerged as key players in the broad regulation of gene expression in most developmental processes in both plants and animals. miRNAs are small (20–24 nt) noncoding RNA molecules involved in post‐transcriptional regulation of gene expression. miRNAs regulate gene expression by cleavage of the target transcript and/or through translational repression. The former appears to be a more prevalent mechanism in plants whereas the later appears to be predominant in animals. The level of miRNA‐target sequence complementarity typically dictates whether mRNA repression or transcript cleavage occurs. This article will focus on our current understanding of the roles of miRNAs in plant development with a key focus on developmentally important miRNAs of the model plant, Arabidopsis thaliana , their modes of action, and the networks to which they belong. This article will also briefly discuss conservation of microRNAs across other plant species and directions for future research on miRNA.
14 True “Nos” in Physics
2019-08-12

Novel Research in Sciences 14 True “Nos” in Physics Otto E Rossler* Faculty of Science, University of Tübingen, Germany *Corresponding author:Otto E Rossler, Faculty of Science, university of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany Submission: August 09, 2019; Published: August 12, 2019 Volume1 Issue5August, 2019
Iron Lung: How Rice Roots Induce Iron Redox Changes in the Rhizosphere and Create Niches for Microaerophilic Fe(II)-Oxidizing Bacteria
2019-08-13

Although water-logged rice paddies are characterized by anoxic conditions, radial oxygen loss (ROL) from rice roots temporarily oxygenates the soil rhizosphere. ROL not only triggers the abiotic oxidation of ferrous iron (Fe(II)) but also provides the electron acceptor for microaerophilic Fe(II)-oxidizing bacteria (microFeOx). Both processes contribute to the formation of ferric (Fe(III)) iron plaque on root surfaces. Redox interactions at single roots have been studied intensively. However, temporally resolved spatial changes of ROL in the entire rhizosphere and the impact on redoximorphic biogeochemistry are currently poorly understood. Here, we show how ROL spatiotemporally evolves and correlates with Fe-redox transformations. Applying noninvasive measurements in a transparent artificial soil, we were able to visualize opposing O<sub>2</sub> and Fe(II) gradients that extend from the root surface 10-25 mm into the rhizosphere. The microoxic zone expanded exponentially in size throughout the entire rhizosphere creating niches for microFeOx. Following iron mineral formation and pH, we show that root-related ROL induces iron redox transformations on and around roots and correlates with rhizosphere acidification. These findings highlight the dynamic nature of roots in the rice plant rhizosphere, and our approach spatiotemporally resolved their impact on iron redox chemistry and microbial niche formation in the rice plant rhizosphere.
Scalar fields and parametrized spherically symmetric black holes: Can one hear the shape of space-time?
2019-08-13

In this work we study whether parametrized spherically symmetric black hole solutions in metric theories of gravity can appear to be isospectral when studying perturbations. From a theory agnostic point of view, the test scalar field wave equation is the ideal starting point to approach the quasi-normal mode spectrum in alternative black hole solutions. We use a parametrization for the metric proposed by Rezzolla and Zhidenko, as well as the the higher order WKB method in the determination of the quasi-normal mode spectra. We look for possible degeneracies in a tractable subset of the parameter space with respect to the Schwarzschild quasi-normal modes. Considering the frequencies and damping times of the expected observationally most relevant quasi-normal modes, we find such degeneracies. We explicitly demonstrate that the leading Schwarzschild quasi-normal modes can be approximated by alternative black hole solutions when their mass is treated as free parameter. In practice, we conclude that the mass has to be known with extremely high precision in order to restrict the leading terms in the metric expansion to currently known limits coming from the PPN expansion. Possible limitations of using the quasi-normal mode ringdown to investigate black hole space-times are being discussed.
MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer
2019-08-13

Colorectal cancer (CRC) is characterized by the aberrant activation of cellular signalling pathways, which are frequently caused by genetic alterations. Among those affected pathways, Wnt signalling plays an essential role for tumorigenesis and maintenance of cancer stem cells. However, it is unclear how other oncogenic pathways converge on Wnt signalling to modulate stem cell homeostasis in CRC.
Indirect CE‐UV detection for the characterization of organic and inorganic ions of a broad mobility and pKa range in engine coolants
2019-08-13

Abstract An alternative CE‐(indirect ultraviolet) method for the analysis of inorganic and organic anions in ethylene glycol‐based engine coolants is presented using a BGE with 4 mM pyromellitic acid and 3.4 mM 1,6‐hexamethylene diamine, pH 3. Baseline separation of six inorganic (e.g. nitrite, nitrate, and sulfate) and five organic anions (e.g. acetic and glycolic acid) was achieved. Quantification of 8 out of 11 specified anions was possible in stressed engine coolant samples after simple aqueous dilution. LODs between 0.8 and 15.1 mg/L with RSD values of peak areas between 2.6 and 11.9% were obtained. Some limitations due to matrix effects can be overcome with slight adaptations of the BGE. The flexibility of the method is vital regarding the increasing demands for the composition of engine coolants for pollution reduction.
A QCD analysis for nuclear PDFs at NNLO
2019-08-13

A new QCD analysis for nuclear parton distribution functions (nPDFs) at next-to-leading order (NLO) and next-to-next-to-leading order (NNLO) is presented. The framework of the analysis, including the form of the parameterization as well as the included DIS data sets, are discussed. The results of this QCD analysis are compared to the existing nPDF sets and to the fitted data. The presented framework is based on an open-source tool, xFitter, which has been modified to be applicable also for a nuclear PDF analysis. The required modifications are covered as well. Finally, an outlook for the next developments of the QCD analysis for nuclear PDFs is given.
Dysfunction of Torr causes a Harlequin-type ichthyosis-like phenotype in Drosophila melanogaster
2019-08-13

Abstract Prevention of desiccation is a constant challenge for terrestrial organisms. Land insects have an extracellular coat, the cuticle, that plays a major role in protection against exaggerated water loss. Here, we report that the ABC transporter Torr - a human ABCA12 paralog - contributes to the waterproof barrier function of the cuticle in the fruit fly Drosophila melanogaster . We show that the reduction or elimination of Torr function provokes rapid desiccation. Torr is also involved in defining the inward barrier against xenobiotics penetration. Consistently, the amounts of cuticular hydrocarbons that are involved in cuticle impermeability decrease markedly when Torr activity is reduced. GFP-tagged Torr localises to membrane nano-protrusions within the cuticle, likely pore canals. This suggests that Torr is mediating the transport of cuticular hydrocarbons (CHC) through the pore canals to the cuticle surface. The envelope, which is the outermost cuticle layer constituting the main barrier, is unaffected in torr mutant larvae. This contrasts with the function of Snu, another ABC transporter needed for the construction of the cuticular inward and outward barriers, that nevertheless is implicated in CHC deposition. Hence, Torr and Snu have overlapping and independent roles to establish cuticular resistance against transpiration and xenobiotic penetration. The torr deficient phenotype parallels the phenotype of Harlequin ichthyosis caused by mutations in the human abca12 gene. Thus, it seems that the cellular and molecular mechanisms of lipid barrier assembly in the skin are conserved in vertebrates in invertebrates. Author Summary As in humans, lipids on the surface of the skin of insects protect the organism against excessive water loss and penetration of potentially harmful substances. During evolution, a greasy surface was indeed an essential trait for adaptation to life outside a watery environment. Here, we show that the membrane-gate transporter Torr is needed for the deposition of barrier lipids on the skin surface in the fruit fly Drosophila melanogaster through extracellular nano-tubes, called pore canals. In principle, the involvement of Torr parallels the scenario in humans, where the membrane-gate transporter ABCA12 is implicated in the construction of the lipid-based stratum corneum of the skin. In both cases, mutations in the genes coding for the respective transporter cause rapid water-loss and are lethal soon after birth. We conclude that the interaction between the organism and the environment obviously implies an analogous mechanism of barrier formation and function in vertebrates and invertebrates.
Circular RNA ZFR accelerates non-small cell lung cancer progression by acting as a miR-101-3p sponge to enhance CUL4B expression
2019-08-13

Non-small-cell lung carcinoma (NSCLC) is the most common type of lung cancer. Circular RNA ZFR (circZFR) is an identified circular RNA (circRNA) that is correlated with cancer progression. However, the role of circZFR in NSCLC remains unknown. In the present study, we aimed to investigate the function of circZFR in NSCLC and the underlying mechanism. The expression patterns of circZFR were determined using qRT-PCR in NSCLC samples and cell lines. The subcellular distribution of circZFR in NSCLC cells was analyzed by fluorescence <i>in situ</i> hybridization (FISH). Cell proliferation was examined utilizing the CCK-8 assay. Cell migration and invasion were evaluated using the Transwell assay. We used the bioinformatics software TargetScan and miRanda to predict circRNA–miRNA and miRNA–mRNA interactions. Our results showed that circZFR expressions were significantly upregulated in NSCLC tissues and cell lines. Knockdown of circZFR significantly inhibited the cell proliferation, migration and invasion of NSCLC cells <i>in vitro</i>. Furthermore, we demonstrated that circZFR acted as a sponge to absorb microRNA-101-3p (miR-101-3p) and promoted cullin 4B (CUL4B) expression. Collectively, our results demonstrated that circZFR exhibited a carcinogenic role by sponging miR-101-3p and regulating CUL4B expression in NSCLC. These findings provided evidence for understanding the role of circZFR in NSCLC tumourigenesis.
Is there a Central Andean Linguistic Area? A View from the Perspective of the “Minor” Languages
2019-08-14

In this article, I reconsider the evidence for a Central Andean linguistic area. I suggest that there is no evidence for a clear-cut linguistic area comprising the entire Central Andes narrowly defined, and that perceived homogeneity is partially due to an overemphasis on the largest and surviving Central Andean language families, Quechuan and Aymaran. I show that none of the other Central Andean languages known sufficiently well match their typological profile to a high degree. I make a contribution to a more adequate picture by discussing some typological aspects tentatively recoverable for the extinct and poorly documented languages of the North-Central Andes. These suggest that the North was the site of linguistic traits contrasting with those of Quechuan and Aymaran.