julilili42/papers huggingface dataset:
Diversity and Ecological Correlates of Red Fluorescence in Marine Fishes
2016-11-07

Marine environments at depths below -10 to -25 m are almost devoid of ambient red sunlight because water quickly attenuates long wavelengths. This stenospectral light environment presents unique opportunities for organisms that can transform ambient blue-green light into red light by fluorescence. Numerous marine fish species display intricate patterns of fluorescence. Because color vision is a key component of fish sensory ecology, several putative visual functions of red fluorescence have been proposed but are difficult to test experimentally. Here, we follow a comparative approach to assess the consistency between the phylogenetic distribution of red fluorescence with its presumed functions. We collected and analyzed the largest data set of red fluorescence in fishes to date, consisting of confirmed cases in 272 primarily diurnal fish species from 49 out of 90 surveyed fish families and 12 out of 21 surveyed fish orders, contrasted to 393 fish species with confirmed absence of red fluorescence. Based on a priori hypotheses on adaptive function, we compare the prevalence of red fluorescence among pre-defined sets of species based on ecological or biological characteristics while controlling for shared ancestry. When comparing between species, we find no evidence that red fluorescence is more prevalent in deep-water species, contrasting with our recent finding that fluorescence brightness increases with depth within species. There is also no evidence for a role in group-driven communication. Phylogenetic patterns are consistent, however, with three other predictions. First, fluorescence with a rather patchy distribution across the body occurred significantly more often among sit-and-wait predators or otherwise sedentary fish than in more mobile species, consistent with background matching for camouflage. Second, small, predatory fishes tended to show red fluorescent irides disproportionally often consistent with a proposed function in prey localization. Finally, sexually dimorphic species showed fluorescent fins more often, as predicted if relevant in sexual communication. From these findings, we derive predictions for experimental investigations of the presumed functions of red fluorescence.
Total Synthesis of Lingzhiol and its Analogues through the Wittig Reaction of an Oxocyclopentane Carboxylate
2016-11-07

Abstract The biosynthesis of polycyclic natural product lingzhiol ( 1 ) through an intramolecular Friedel–Crafts alkylation reaction of an aryl‐substituted cyclopentane epoxide ( 22 ) was attempted. The synthesis of this endocyclic epoxide involved the alkylation of cyclopentane carboxylate 14 with alkyl iodide 25 to afford ketoester 26 . Subsequent Wittig olefination led to exocyclic alkene exo ‐ 15 in good yield. Epoxidation, opening of the epoxide to generate allyl alcohol 29 , and a second epoxidation reaction afforded compounds 22 and 31 . However, presumably owing to stereoelectronic effects, the cyclization of these substrates into polycycles 17 and 32 , respectively, was unsuccessful. Nevertheless, the Wittig reaction to afford exo ‐ 15 allowed us to converge with the previously reported route of Qin et al., which featured the cyclization of spiro epoxide 16 . Thus, lingzhiol is now available in only nine steps. Various analogues of lingzhiol were also prepared, including desoxy derivative 37 , quinone 38 , mono‐methoxy‐deoxy derivative 39 , and ketone 40 .
Do KV7.1 channels contribute to control of arterial vascular tone?
2016-11-07

Background and Purpose K V 7.1 voltage‐gated potassium channels are expressed in vascular smooth muscle cells (VSMC) of diverse arteries, including mesenteric arteries. Based on pharmacological evidence using R‐L3 (K V 7.1 channel opener), HMR1556, chromanol 293B (K V 7.1 channel blockers), stimulation of these channels has been suggested to evoke profound relaxation in various vascular beds of rats. However, the specificity of these drugs in vivo is uncertain. Experimental Approach We used Kcnq1 −/− mice and pharmacological tools to determine whether K V 7.1 channels play a role in the regulation of arterial tone. Key Results R‐L3 produced similar concentration‐dependent relaxations (EC 50 ~ 1.4 μM) of arteries from wild‐type ( Kcnq1 +/+ ) and Kcnq1 −/− mice, pre‐contracted with either phenylephrine or 60 mM KCl. This relaxation was not affected by 10 μM chromanol 293B, 10 μM HMR1556 or 30 μM XE991 (pan‐K V 7 channel blocker). The anti‐contractile effects of the perivascular adipose tissue (PVAT) were normal in Kcnq1 −/− arteries. Chromanol 293B and HMR1556 did not affect the anti‐contractile effects of (PVAT). Isolated VSMCs from Kcnq1 −/− mice exhibited normal peak K V currents. The K V 7.2–5 channel opener retigabine caused similar relaxations in Kcnq1 −/− and wild‐type vessels. Conclusion and Implications We conclude that K V 7.1 channels were apparently not involved in the control of arterial tone by α 1 ‐adrenoceptor agonists and PVAT. In addition, R‐L3 is an inappropriate pharmacological tool for studying the function of native vascular K V 7.1 channels in mice.
Influence of social contact patterns and demographic factors on influenza simulation results
2016-11-07

Contact matrix and demography strongly influence the age-dependent incidence of influenza and the success of vaccination. Projecting simulation results from one country to another can, therefore, lead to erroneous results.
Influence of C60 co-deposition on the growth kinetics of diindenoperylene–From rapid roughening to layer-by-layer growth in blended organic films
2016-11-07

We investigated the growth of the two phase-separating materials diindenoperylene (DIP) and buckminsterfullerene C60 with different mixing ratio in real-time and in situ by X-ray scattering experiments. We found that at room temperature, mixtures with an excess of DIP show a growth mode which is very close to the perfect layer-by-layer limit with DIP crystallites forming over the entire film thickness. An unexpected increase in the island size is observed for these mixtures as a function of film thickness. On the other hand, equimolar and C60 dominated mixtures grow with poor crystallinity but form very smooth films. Additionally, it is observed that higher substrate temperatures lead to an increase in the length scale of phase separation with film thickness.
Multiparametric Functional MRI: A Tool to Uncover Subtle Changes following Allogeneic Renal Transplantation
2016-11-07

Multiparametric functional MRI is suited to detect renal allograft rejection in an experimental murine model and allows to characterize effects of immunosuppressive therapy alleviating acute rejection processes in allogeneic transplantation.
A fresh look at IBS—opportunities for systems medicine approaches
2016-11-07

Abstract Neuro GUT is a EU ‐funded initial training network ( ITN ) of 14 research projects in neurogastroenterology that have employed an equal number of early‐stage researchers. Neurogut trainees have—among other activities—attended an international conference on irritable bowel syndrome ( IBS ) in Bologna in 2016 and were asked to critically review and evaluate the current knowledge on IBS for their respective research activities, and to state what they were missing. Most appreciated were the topics brain imaging of gut activity, the role of the gut microbiota, the pharmacology of gut functions, the IBS ‐ IBD interrelation, the new Rome IV criteria, the role of gas, and the placebo response in functional disorders. Missed were more detailed coverage of high‐resolution manometry, functional brain imaging, advanced “systems medicine” approaches and bioinformatics technology, better sub‐classification of IBS patients, and the development of disease biomarkers, extended at the molecular (genetic/epigenetic, proteonomic) level. They summarize that despite excellent specialized research, there is a gap open that should be filled with systems medicine. For this, it would be necessary that medical research learns even more from the data sciences and other basic disciplines, for example, information technology and system biology, and also welcomes a change in paradigm that enhances open sharing of data, information, and resources.
Rapidly rotating neutron stars with a massive scalar field—structure and universal relations
2016-11-08

We construct rapidly rotating neutron star models in scalar-tensor theories with a massive scalar field. The fact that the scalar field has nonzero mass leads to very interesting results since the allowed range of values of the coupling parameters is significantly broadened. These deviations from pure general relativity can be very large for values of the parameters that are in agreement with the observations. The rapid rotation can magnify the differences several times compared to the static case. The universal relations between the normalized moment of inertia and quadrupole moment are also investigated both for the slowly and rapidly rotating cases. The results show that these relations are still EOS independent up to a large extend and the deviations from pure general relativity can be large. This places the massive scalar-tensor theories amongst the few alternative theories of gravity that can be tested via the universal -Love- relations.
The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems
2016-11-08

Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.
Why does MP2 work?
2016-11-08

We show analytically and numerically that the performance of second order Møller-Plesset (MP) perturbation theory (PT), coupled-cluster (CC) theory, and other perturbation theory approaches can be rationalized by analyzing the wavefunctions of these methods. While rather large deviations for the individual contributions of configurations to the electron correlation energy are found for MP wavefunctions, they profit from an advantageous and robust error cancellation: The absolute contribution to the correlation energy is generally underestimated for the critical excitations with small energy denominators and all other doubly excited configurations where the two excited electrons are coupled to a singlet. This is balanced by an overestimation of the contribution of triplet-coupled double excitations to the correlation energy. The even better performance of spin-component-scaled-MP2 theory is explained by a similar error compensation effect. The wavefunction analysis for the lowest singlet states of H2O, CH2, CO, and Cu+ shows the predicted trends for MP methods, rapid but biased convergence of CC theory as well as the substantial potential of linearized CC, or retaining the excitation-degree (RE)-PT.
A travel time‐based approach to model kinetic sorption in highly heterogeneous porous media via reactive hydrofacies
2016-11-08

Abstract We present a semianalytical model for the transport of solutes being subject to sorption in porous aquifers. We couple a travel time‐based model of advective transport with a spherical diffusion model of kinetic sorption in nonuniform material mixtures. The model is formulated in the Laplace domain and transformed to the time domain by numerical inversion. By this, three‐dimensional transport of solutes undergoing mass transfer between aqueous and solid phases can be simulated very efficiently. The model addresses both hydraulic and reactive heterogeneity of porous aquifers by means of hydrofacies, which function as homogeneous but nonuniform subunits. The total exposure time to each of these subunits controls the magnitude of sorption effects, whereas the particular sequence of facies through which the solute passes is irrelevant. We apply the model to simulate the transport of phenanthrene in a fluvio‐glacial aquifer, for which the hydrofacies distribution is known at high resolution, the lithological composition of each facies has been analyzed, and sorption properties of the lithological components are available. Taking the fully resolved hydrofacies model as reference, we evaluate different approximations referring to lower information levels, reflecting shortcomings in typical modeling projects. The most important feature for a good description of both the main breakthrough and tailing of phenanthrene is the nonuniformity of the porous medium. While spatial heterogeneity of chemical properties might be neglected without introducing a large error, an approximation of the facies' composition in terms of a uniform substitute material considerably compromises the quality of the modeling result.
Selective p38α MAP kinase/MAPK14 inhibition in enzymatically modified LDL‐stimulated human monocytes: implications for atherosclerosis
2016-11-08

ABSTRACT The first ATP‐competitive p38a MAPK/MAPK14 inhibitor with excellent in vivo efficacy and selectivity, skepinone‐L, is now available. We investigated the impact of selective p38a MAPK/MAPK14 inhibition on enzymatically modified LDL (eLDL) stimulated human monocytes with its implications for atherosclerosis. Among the different p38 MAPK isoforms, p38a/MAPK14 was the predominantly expressed and activated isoform in isolated human peripheral blood monocytes. Moreover, eLDL colocalized with macrophages positive for p38a MAPK/ MAPK14 in human carotid endarterectomy specimens. Using the human leukemia cell line THP‐1 and/or primary monocyte‐derived macrophages, skepinone‐L inhibited eLDL‐induced activation of the p38 MAPK pathway, inhibited eLDL induced expression of both cluster of differentiation 36 (CD36) and ATP‐binding cassette, subfamily A, member 1 (ABCA1), without a net effect on foam cell formation, had a cell‐and time‐dependent effect on eLDLtriggered apoptosis, and inhibited eLDL‐stimulated secretion of IL‐8 and MIP‐1b/CCL4 (macrophage inflammatory protein‐1b/chemokine, CC motif, ligand 4). Inhibition of a key signaling molecule of the p38 MAPK pathway, p38a MAPK/MAPK14, by selective inhibitors like skepinone‐L, conclusively facilitates elucidation of the impact of the complex network of p38 MAPK signaling on atherogenesis and might provide a promising therapeutic tool to prevent inflammatory cascades in atherosclerosis.—Cheng, F., Twardowski, L., Fehr, S., Aner, C., Schaeffeler, E., Joos, T., Knorpp, T., Dorweiler, B., Laufer, S., Schwab, M., Torzewski, M. Selective p38a MAP kinase/MAPK14 inhibition in enzymatically modified LDL‐stimulated human monocytes: implications for atherosclerosis. FASEB J. 31, 674–686 (2017). www.fasebj.org
Comparison of the Catalytic Performance and Carbon Monoxide Sensing Behavior of Pd‐SnO2 Core@Shell Nanocomposites
2016-11-08

Abstract The catalytic activity of Pd‐SnO 2 core@shell nanocomposites in the oxidation of CO and their CO‐sensing behavior were compared. For this purpose, Pd particles were placed on the inside and the outside of SnO 2 hollow spheres, as demonstrated by electron tomography, X‐ray photoelectron spectroscopy, and X‐ray absorption spectroscopy. Both the sensing and catalytic effect were studied in a systematic manner on such nanocomposites, and striking differences in the catalytic performance of the nanocomposites in CO oxidation and CO and H 2 sensing were found. At low temperatures, SnO 2 @Pd was found to be a good sensor, and the light‐off temperature was significantly lower than that of Pd@SnO 2 . Above the ignition temperature, CO was probably rapidly removed from the gas so that the sensing effect disappeared. This demonstrated that understanding of the sensing and catalytic behavior can help in unraveling the functional properties of core@shell and Pd‐SnO 2 nanocomposites in more detail.
Molecular Signatures of Primary Human Spermatogonial Progenitors and Its Neighboring Peritubular Stromal Compartment
2016-11-08

In-depth understanding of human spermatogenesis requires studying specific molecular signatures and interactions of spermatogonia with other testicular cell populations, for which isolation of pure populations of different cell types is crucial. Here, we describe a technique to simultaneously enrich pure, multiple testicular cell populations, including spermatogonia, endothelial (TECs), and perivascular mesenchymal stem/stromal cells (TMSCs), from testicular tissue by flow cytometry using a combination of defined markers. Immunohistochemical studies, multicolor staining, and cell sorting followed by multiplex quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that spermatogonia were highly enriched in the CD49f<sup>+</sup>CD49a<sup>-</sup>HLA-ABC<sup>-</sup>SSEA-4<sup>+</sup> fraction of primary testicular cells. In contrast to spermatogonia, TMSCs and TECs were highly enriched in the CD49f<sup>+</sup>CD49a<sup>+</sup>HLA-ABC<sup>+</sup>CD144<sup>-</sup> and CD49f<sup>+</sup>CD49a<sup>+</sup>HLA-ABC<sup>+</sup>CD144<sup>+</sup>subsets, respectively. The delineation was confirmed by the expression of specific stromal and endothelial key markers as well as by the differentiation and angiogenic capacity of the sorted populations. In this article, for the first time, we performed transcriptome profiling of highly enriched, freshly isolated human spermatogonia and compared their expression profile with that of TMSCs. Our RNA sequencing data favor the hypothesis that TMSCs are candidate niche components for spermatogonia. The composite genotype and phenotype of defined testicular cell populations combined with a robust isolation procedure from small biopsies contributes to a better understanding of cellular interactions and for the establishment of efficient culture techniques to maintain spermatogonial progenitors.
Ultrasound for patients in a high HIV/tuberculosis prevalence setting: a needs assessment and review of focused applications for Sub-Saharan Africa
2016-11-09

Ultrasound is increasingly used in point-of-care applications and has great potential to support the diagnosis of infectious diseases, especially in resource-limited settings. A cross-sectional study was performed involving 100 Malawian patients with a clinical indication for ultrasound. Furthermore, the literature on point-of-care ultrasound (POCUS) in Sub-Saharan Africa was reviewed to establish its applicability, most frequent indications, findings, and implications for treatment, and therefore relevance in POCUS curricula, with a main focus on infectious diseases. In Malawi, the main indications for ultrasound were weight loss, abdominal pain, and shortness of breath. Abnormal findings were observed in 77% of patients, the most common being enlarged abdominal lymph nodes (n=17), pericardial effusion (n=15), splenic microabscesses (n=15), and pleural effusion (n=14). POCUS led to a change in treatment in 72% of patients. The literature on the various POCUS applications used in Malawi was reviewed, including focused assessment with sonography for HIV-associated TB (FASH), heart, liver, kidney, deep venous thrombosis (DVT), and gynaecology. Based on disease prevalence, impact of POCUS on treatment, and technical difficulty, it is proposed that FASH, heart, and DVT are the most relevant POCUS applications in comparable Sub-Saharan African settings and should be incorporated in POCUS curricula.
Controlled stem cell amplification by HOXB4 depends on its unique proline-rich region near the N terminus
2016-11-09

Key Points The conserved proline-rich region is essential for HOXB4 to amplify long-term hematopoietic stem cells without loss of homeostasis. Loss of this region increases leukemogenicity of HOXB4, altering its DNA-binding properties.
New Evidence from Linguistic Phylogenetics Identifies Limits to Punctuational Change
2016-11-09

Since the early 1970s, biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium. We replicate this result for branch lengths, but find no support for punctuated equilibrium using a different, automated measure of linguistic divergence and a much larger data set. With the automated measure, segments of trees containing more nodes show no greater divergence from an outgroup than segments containing fewer nodes.
Chiral and deconfinement phase transition in the Hamiltonian approach to QCD in Coulomb gauge
2016-11-09

The chiral and deconfinement phase transitions are investigated within the variational Hamiltonian approach to QCD in Coulomb gauge. The temperature is introduced by compactifying a spatial dimension. Thereby the whole temperature dependence is encoded in the vacuum state on the spatial manifold . The chiral quark condensate and the dual quark condensate (dressed Polyakov loop) are calculated as function of the temperature. From their inflection points the pseudo-critical temperatures for the chiral and deconfinement crossover transitions are determined. Using the zero-temperature quark and gluon propagators obtained within the variational approach as input, we find and , respectively, for the chiral and deconfinement transition.