bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering privileged topologies of molecular knots with self-assembling models
Authors: Marenda Mattia , Orlandini Enzo , Micheletti Cristian 
Published: July 2018

AbstractDespite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.
Dynamic contrast enhancement and flexible odor codes
Authors: Nizampatnam Srinath , Saha Debajit , Chandak Rishabh , Raman Baranidharan 
Published: July 2018

AbstractSensory stimuli evoke spiking activities patterned across neurons and time that are hypothesized to encode information about their identity. Since the same stimulus can be encountered in a multitude of ways, how stable or flexible are these stimulus-evoked responses? Here we examine this issue in the locust olfactory system. In the antennal lobe, we find that both spatial and temporal features of odor-evoked responses vary in a stimulus-history dependent manner. The response variations are not random, but allow the antennal lobe circuit to enhance the uniqueness of the current stimulus. Nevertheless, information about the odorant identity is conf	ounded due to this contrast enhancement computation. Notably, predictions from a linear logical classifier (OR-of-ANDs) that can decode information distributed in flexible subsets of neurons match results from behavioral experiments. In sum, our results suggest that a trade-off between stability and flexibility in sensory coding can be achieved using a simple computational logic.
Illness uncertainty, anxiety and depression in Chinese patients with glaucoma or cataract
Authors: Zhang Dandan , Fan Zhigang , Gao Xinbo , Huang Wenmin , Yang Qiongman , Li Zhongwen , Lin Mingkai , Xiao Huiming , Ge Jian 
Published: July 2018

AbstractThis study evaluated illness uncertainty, anxiety and depression among glaucoma patients and cataract patients in China. 263 patients with primary glaucoma and 100 patients with age-related cataract were recruited sequentially from Zhongshan Ophthalmic Center between October 2013 and March 2016. All the participants completed questionnaires for socio-demographic information, Mishel Uncertainty in Illness Scale (MUIS) and Hospital Anxiety and Depression Scale (HADS). 25 of the 263 glaucoma patients and 21 of the100 cataract patients finished two copies of the same questionnaires before and after surgery. Statistics were analyzed using SPSS17.0 software. We observed that glaucoma patients had higher MUIS and HADS score than did cataract patients. Multivariate logistic regression analysis indicated risk factors for illness uncertainty, anxiety and depression for glaucoma patients were high HADS score, poor visual acuity (VA) in the better eye and education level respectively. Risk factors for the same parameters of cataract patients were high HADS-A score, poor VA in the better eye and high illness uncertainty respectively. Scores of MUIS and HADS both decreased after surgery, but the change in HADS score among glaucoma patients was not significant. Clinical workers should take these factors into account to improve therapy, especially for glaucoma patients who undergo surgery.
AAV9-mediated Rbm24 overexpression induces fibrosis in the mouse heart
Authors: van den Hoogenhof Maarten M. G. , van der Made Ingeborg , de Groot Nina E. , Damanafshan Amin , van Amersfoorth Shirley C. M. , Zentilin Lorena , Giacca Mauro , Pinto Yigal M. , Creemers Esther E. 
Published: July 2018

AbstractThe RNA-binding protein Rbm24 has recently been identified as a pivotal splicing factor in the developing heart. Loss of Rbm24 in mice disrupts cardiac development by governing a large number of muscle-specific splicing events. Since Rbm24 knockout mice are embryonically lethal, the role of Rbm24 in the adult heart remained unexplored. Here, we used adeno-associated viruses (AAV9) to investigate the effect of increased Rbm24 levels in adult mouse heart. Using high-resolution microarrays, we found 893 differentially expressed genes and 1102 differential splicing events in 714 genes in hearts overexpressing Rbm24. We found splicing differences in cardiac genes, such as PDZ and Lim domain 5, Phospholamban, and Titin, but did not find splicing differences in previously identified embryonic splicing targets of Rbm24, such as skNAC, αNAC, and Coro6. Gene ontology enrichment analysis demonstrated increased expression of extracellular matrix (ECM)-related and immune response genes. Moreover, we found increased expression of Tgfβ-signaling genes, suggesting enhanced Tgfβ-signaling in these hearts. Ultimately, this increased activation of cardiac fibroblasts, as evidenced by robust expression of Periostin in the heart, and induced extensive cardiac fibrosis. These results indicate that Rbm24 may function as a regulator of cardiac fibrosis, potentially through the regulation of TgfβR1 and TgfβR2 expression.
Fine-scale processes shape ecosystem service provision by an Amazonian hyperdominant tree species
Authors: Thomas Evert , Atkinson Rachel , Kettle Chris 
Published: July 2018

AbstractConspecific distance and density-dependence is a key driver of tree diversity in natural forests, but the extent to which this process may influence ecosystem service provision is largely unknown. Drawing on a dataset of >135,000 trees from the Peruvian Amazon, we assessed its manifestation in biomass accumulation and seed production of Brazil nut (Bertholletia excelsa) which plays a keystone role in carbon sequestration and NTFP harvesting in Amazonia. For the first time, we find both negative and positive effects of conspecific proximity on seed production and above ground biomass at small and large nearest neighbour distances, respectively. Plausible explanations for negative effects at small distances are fine-scale genetic structuring and competition for shared resources, whereas positive effects at large distances are likely due to increasing pollen limitation and suboptimal growth conditions. Finally, findings suggest that most field plots in Amazonia used for estimating carbon storage are too small to account for distance and density-dependent effects and hence may be inadequate for measuring species-centric ecosystem services.
Shear Deformation Dissipates Energy in Biofilaments
Authors: Maghsoodi Ameneh , Perkins Noel 
Published: July 2018

AbstractThermally fluctuating biofilaments possessing porous structures or viscoelastic properties exhibit energy losses from internal friction as well as external friction from drag. Prior models for internal friction account for energy dissipation solely from the dynamic bending of filaments. In this paper, we present a new energy dissipation model that captures the important effects of dynamic shear in addition to bending. Importantly, we highlight that shear-induced friction plays a major role in energy dissipation for shorter filaments and for shorter wavelengths (larger wavenumbers). The new model exhibits coupled shear-bending energy relaxation on two distinct time scales in lieu of a single time scale predicted by bending alone. We employ this model to interpret results from prior experiments on the internal friction of thermally fluctuating chromosomes and the drag-induced friction of thermally fluctuating microtubules. The examples confirm the energy relaxation on two time scales associated with internal friction and on two length scales associated with external friction. Overall, this new model that accounts for shear deformation yields superior estimates of energy dissipation for fluctuating biofilaments.
CINDY2011/DYNAMO Madden-Julian oscillation successfully reproduced in global cloud/cloud-system resolving simulations despite weak tropical wavelet power
Authors: Miyakawa Tomoki , Kikuchi Kazuyoshi 
Published: July 2018

AbstractThe role of tropical atmospheric waves in the propagation mechanism of the Madden-Julian oscillation (MJO), a huge eastward-propagating atmospheric pulse that dominates intraseasonal variation of the tropics and affects the entire globe, has been long discussed but remains unclear. An MJO event observed in a major field campaign is reproduced using a front-running global cloud/cloud-system resolving model with 3.5 km, 7 km, and 14 km meshes. The eastward-migration speed of the MJO convective envelope in the 3.5 km and 14 km simulations agree well with observation, despite weak Kelvin wave signal power calculated by applying a combined Fourier-wavelet transform method. Our results suggest that the eastward propagation of this MJO event was principally controlled by an MJO-scale energy balance, and not by dynamical interaction of embedded tropical waves. The eastward propagation is delayed in the 7 km simulation, which features the highest surface latent heat flux to the west of the convective envelope center. This latent heat flux appears to be caused by prolonged existence of westward-migrating Rossby wave-like cyclonic disturbances near the equator; the embedded waves may not be part of the essential mechanism for the MJO eastward propagation, but can affect it by altering the energy balance.
Structure and nucleic acid binding properties of KOW domains 4 and 6–7 of human transcription elongation factor DSIF
Authors: Zuber Philipp K. , Hahn Lukas , Reinl Anne , Schweimer Kristian , Knauer Stefan H. , Gottesman Max E. , Rösch Paul , Wöhrl Birgitta M. 
Published: July 2018

AbstractThe human transcription elongation factor DSIF is highly conserved throughout all kingdoms of life and plays multiple roles during transcription. DSIF is a heterodimer, consisting of Spt4 and Spt5 that interacts with RNA polymerase II (RNAP II). DSIF binds to the elongation complex and induces promoter-proximal pausing of RNAP II. Human Spt5 consists of a NusG N-terminal (NGN) domain motif, which is followed by several KOW domains. We determined the solution structures of the human Spt5 KOW4 and the C-terminal domain by nuclear magnetic resonance spectroscopy. In addition to the typical KOW fold, the solution structure of KOW4 revealed an N-terminal four-stranded β-sheet, previously designated as the KOW3-KOW4 linker. In solution, the C-terminus of Spt5 consists of two β-barrel folds typical for KOW domains, designated KOW6 and KOW7. We also analysed the nucleic acid and RNAP II binding properties of the KOW domains. KOW4 variants interacted with nucleic acids, preferentially single stranded RNA, whereas no nucleic acid binding could be detected for KOW6-7. Weak binding of KOW4 to the RNAP II stalk, which is comprised of Rpb4/7, was also detected, consistent with transient interactions between Spt5 and these RNAP II subunits.
Regional differences in thermal adaptation of a cold-water fish Rhynchocypris oxycephalus revealed by thermal tolerance and transcriptomic responses
Authors: Yu Dan , Zhang Zhi , Shen Zhongyuan , Zhang Chen , Liu Huanzhang 
Published: July 2018

AbstractUnderstanding how populations adapt to different thermal environments is an important issue for biodiversity conservation in the context of recent global warming. To test the hypothesis that populations from southern region are more sensitive to climate change than northern region in cold-water species, we determined the thermal tolerance of two geographical populations of a cold-water fish, Rhynchocypris oxycephalus: the Hangzhou population from southern region and the Gaizhou population from northern region, then compared their transcriptomic responses between a control and a high temperature treatment. The results showed that the thermal tolerance range and thermal tolerance polygon area of Hangzhou population were narrower than the Gaizhou population, indicating populations from southern region were possibly more vulnerable. Further transcriptomic analysis revealed that the Gaizhou population expressed more temperature responding genes than the Hangzhou population (583 VS. 484), corresponding with their higher thermal tolerance, while some of these genes (e.g. heat shock protein) showed higher expression in the Hangzhou population under control condition, suggesting individuals from southern region possibly have already responded to the present higher environmental temperature pressure. Therefore, these results confirm the prediction that populations from southern region are more sensitive to global warming, and will be important for their future conservation.
Pre-exposure prophylaxis (PrEP) for MSM in low HIV incidence places: should high risk individuals be targeted?
Authors: Wong Ngai Sze , Kwan Tsz Ho , Tsang Owen T. Y. , Lee Man Po , Yam Wing Cheong , Lam Wilson , Leung Wai Shing , Chan Jacky M. C. , Ho Kai Man , Lee Shui Shan 
Published: July 2018

AbstractPre-exposure prophylaxis (PrEP) targeting high-risk men who have sex with men (MSM) has been shown to be a cost-effective HIV control measure. However, the approach could be a challenge in low HIV incidence places with a low proportion of high-risk MSM. To examine the impact of PrEP in such setting in Asia, we developed an epidemic model and conducted cost-effectiveness analysis using empirical multicentre clinical and HIV sequence data from HIV-infected MSM in Hong Kong, in conjunction with behavioural data of local MSM. Without PrEP, the HIV incidence (per 100 person-years) would increase from 1.1 to 1.6 between 2011 and 2021. PrEP could avert 3–63% of total new infections in a five-year period (2017–2021), the variability of which depends on the implementation strategies and combination with test-and-treat. However, under current market drug price in 2016, the incremental cost per quality-adjusted life-year gained (QALYG) of PrEP (USD1583136/QALYG) is almost 3 times higher than test-and-treat intervention alone (USD396874/QALYG). Assuming 93% fall of PrEP drug price and in combination with test-and-treat, putting 30% of MSM on non-targeting PrEP would be more feasible, cost-effective (USD268915/QALYG), and could avert more new infections (40%). PrEP could contribute to HIV epidemic control in a low incidence place.
The antioxidant activities of alkalic-extractable polysaccharides from Coprinus comatus on alcohol-induced liver injury in mice
Authors: Zhao Huajie , Zhang Jianjun , Liu Xinchao , Yang Qihang , Dong Yuhan , Jia Le 
Published: July 2018

AbstractThe aim of this work was to provide a preliminary characterization of alkalic-extractable polysaccharides (ALPS) from Coprinus comatus, to explore its in vivo antioxidant activities and protective effects on alcohol-induced liver injury. ALPS showed strong antioxidant and anti-inflammatory abilities and markedly low serum enzyme activities, hepatic and serum lipid levels, as well as low hepatic lipid peroxidation levels; moreover, ALPS improved the alcohol metabolism system. These results were also confirmed by an analysis of histopathological section observations. ALPS, in both α- and β-configurations, as analysed by fourier-transform infrared (FT-IR) and nuclear magnetic resonance (NMR), was mainly composed of rhamnose (Rha), fucose (Fuc), ribose (Rib), xylose (Xyl), mannose (Man), galactose (Gal) and glucose (Glu) with mass percentages of 0.52%, 1.02%, 0.80%, 0.92%, 3.05%, 2.96% and 90.73%, respectively. These results may offer support for the use of ALPS as a functional food or natural drug source that can prevent and treat alcohol-induced liver injury.
Fitting mathematical models of biochemical pathways to steady state perturbation response data without simulating perturbation experiments
Authors: Santra Tapesh 
Published: July 2018

AbstractFitting Ordinary Differential Equation (ODE) models of signal transduction networks (STNs) to experimental data is a challenging problem. Computational parameter fitting algorithms simulate a model many times with different sets of parameter values until the simulated STN behaviour match closely with experimental data. This process can be slow when the model is fitted to measurements of STN responses to numerous perturbations, since this requires simulating the model as many times as the number of perturbations for each set of parameter values. Here, I propose an approach that avoids simulating perturbation experiments when fitting ODE models to steady state perturbation response (SSPR) data. Instead of fitting the model directly to SSPR data, it finds model parameters which provides a close match between the scaled Jacobian matrices (SJM) of the model, which are numerically calculated using the model’s rate equations and estimated from SSPR data using modular response analysis (MRA). The numerical estimation of SJM of an ODE model does not require simulating perturbation experiments, saving significant computation time. The effectiveness of this approach is demonstrated by fitting ODE models of the Mitogen Activated Protein Kinase (MAPK) pathway using simulated and real SSPR data.
Bacterial diversity among the fruit bodies of ectomycorrhizal and saprophytic fungi and their corresponding hyphosphere soils
Authors: Liu Yaping , Sun Qibiao , Li Jing , Lian Bin 
Published: July 2018

AbstractMacro-fungi play important roles in the soil elemental cycle in terrestrial ecosystems. Many researchers have focused on the interactions between mycorrhizal fungi and host plants, whilst comparatively few studies aim to characterise the relationships between macro-fungi and bacteria in situ. In this study, we detected endophytic bacteria within fruit bodies of ectomycorrhizal and saprophytic fungi (SAF) using high-throughput sequencing technology, as well as bacterial diversity in the corresponding hyphosphere soils below the fruit bodies. Bacteria such as Helicobacter, Escherichia-Shigella, and Bacillus were found to dominate within fruit bodies, indicating that they were crucial in the development of macro-fungi. The bacterial richness in the hyphosphere soils of ectomycorrhizal fungi (EcMF) was higher than that of SAF and significant difference in the composition of bacterial communities was observed. There were more Verrucomicrobia and Bacteroides in the hyphosphere soils of EcMF, and comparatively more Actinobacteria and Chloroflexi in the hyphosphere of SAF. The results indicated that the two types of macro-fungi can enrich, and shape the bacteria compatible with their respective ecological functions. This study will be beneficial to the further understanding of interactions between macro-fungi and relevant bacteria.
Surgical Occlusion Setup in Correction of Skeletal Class III Deformity Using Surgery-First Approach: Guidelines, Characteristics and Accuracy
Authors: Liao Yu-Fang , Lo Shu Hsien 
Published: July 2018

AbstractThe aims of this study were to establish guidelines for the surgical occlusion setup of surgery-first orthognathic surgery, and evaluate the resulting characteristics and accuracy. Skeletal Class III patients (N = 53) underwent Le Fort I osteotomy and bilateral sagittal split osteotomy. Study models before orthognathic surgery were set according to the guidelines. Occlusion was measured and computer-aided surgical simulation was used to evaluate the characteristics and accuracy of the surgical occlusion. The mean age of participants was 25 ± 6 years with 24 males and 29 females. The occlusion was set as positive overjet (4.4 ± 2.0 mm) and overbite (1.4 ± 1.8 mm), Class II or I molar relation, and posterior cross bite (overjet: 4.9 ± 2.0 mm and 4.4 ±1.9 mm, respectively for the right and left second molars) and open bite (overbite: −2.0 ± 1.6 mm and −1.9 ± 1.3 mm, respectively for the right and left second molars). Normal jaw relationship and symmetry were noted after virtual surgery. None of the patients required new occlusal setup. Our data contribute the use of the surgery-first approach for skeletal Class III patients by establishing guidelines for a surgical occlusion setup in three dimensions.
Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) and Tandem Repeat Sequence Typing (TRST), helpful tools for subtyping Staphylococcus lugdunensis
Authors: Dahyot Sandrine , Lebeurre Jérémie , Argemi Xavier , François Patrice , Lemée Ludovic , Prévost Gilles , Pestel-Caron Martine 
Published: July 2018

AbstractStaphylococcus lugdunensis is an emergent virulent coagulase-negative Staphylococcus that is increasingly responsible for severe infections. In an attempt to generate informative sequence data for subtyping S. lugdunensis, we selected and sequenced seven polymorphic variable number of tandem repeats (VNTRs) to develop two new methods: a classic length-based multiple-locus VNTR analysis (MLVA) method and a tandem repeat sequence typing (TRST) method. We assessed their performances compared to two existing methods, multilocus sequence typing (MLST) and multivirulence-locus sequence typing (MVLST) for 128 isolates from diverse clinical settings and geographical origins. The clustering achieved by the four methods was highly congruent, with MLVA discriminating within clonal complexes as defined by MLST. Indeed, MLVA was highly discriminant compared to MLST and MVLST in terms of number of genotypes as well as diversity indexes. Sequencing of the seven VNTRs showed that they were stable, and analysis of sequence polymorphisms provided superior discriminatory power. The typeability, reproducibility, and epidemiological concordance of these new methods were excellent. Of note, no link between clustering and clinical settings was identified. This study demonstrates that MLVA and TRST provide valuable information for molecular epidemiological study of S. lugdunensis, and represent promising tools to distinguish between strains of homogenous lineages in this clonal species.
The human phrenic nerve serves as a morphological conduit for autonomic nerves and innervates the caval body of the diaphragm
Authors: Verlinden Thomas J. M. , van Dijk Paul , Herrler Andreas , de Gier - de Vries Corrie , Lamers Wouter H. , Köhler S. Eleonore 
Published: July 2018

AbstractCommunicating fibres between the phrenic nerve and sympathetic nervous system may exist, but have not been characterized histologically and immunohistochemically, even though increased sympathetic activity due to phrenic nerve stimulation for central sleep apnoea may entail morbidity and mortality. We, therefore, conducted a histological study of the phrenic nerve to establish the presence of catecholaminergic fibres throughout their course. The entire phrenic nerves of 35 formalin-fixed human cadavers were analysed morphometrically and immunohistochemically. Furthermore, the right abdominal phrenic nerve was serially sectioned and reconstructed. The phrenic nerve contained 3 ± 2 fascicles in the neck that merged to form a single fascicle in the thorax and split again into 3 ± 3 fascicles above the diaphragm. All phrenic nerves contained catecholaminergic fibres, which were distributed homogenously or present as distinct areas within a fascicle or as separate fascicles. The phrenicoabdominal branch of the right phrenic nerve is a branch of the celiac plexus and, therefore, better termed the “phrenic branch of the celiac plexus”. The wall of the inferior caval vein in the diaphragm contained longitudinal strands of myocardium and atrial natriuretic peptide-positive paraganglia (“caval bodies”) that where innervated by the right phrenic nerve.