bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMDA antagonists for treating the non-motor symptoms in Parkinson’s disease
Authors: Vanle Brigitte , Olcott William , Jimenez Jaime , Bashmi Luma , Danovitch Itai , IsHak Waguih William 
Published: June 2018

AbstractAmong patients with Parkinson’s disease (PD), depression is prevalent and disabling, impacting both health outcomes and quality of life. There is a critical need for alternative pharmacological methods to treat PD depression, as mainstream antidepressant drugs are largely ineffective in this population. Currently, there are no recommendations for the optimal treatment of PD neuropsychiatric symptoms. Given the dual antidepressant and anti-dyskinetic effects of ketamine and other N-methyl-D-aspartate (NMDA) antagonists for PD, this review aims to examine the current evidence of NMDA antagonists for treating neuropsychiatric symptoms, including memantine, amantadine, ketamine, dizoclopine, and d-cycloserine. A comprehensive literature search was conducted using the PubMed database. We also searched the following databases up to March 1, 2018: Ovid MEDLINE, PsycINFO, CINAHL, Google Scholar, Cochrane Central Register of Controlled Trials, and Cochrane Database of Systematic Reviews. The following keywords were used: NMDA antagonist and Parkinson’s disease. Two authors independently reviewed the articles identified from the search using specific selection criteria, focusing on studies of mood, psychiatric condition, depression, cognition, and quality of life, and the consensus was reached on the 20 studies included. There is a preliminary evidence that NMDA antagonists may modulate psychiatric symptoms in PD. However, current evidence of psychiatric symptom-modifying effects is inconclusive and requires that further trials be conducted in PD. The repurposing of old NMDA antagonists, such as ketamine for depression and newer therapies, such as rapastinel, suggests that there is an emerging place for modulating the glutamatergic system for treating non-motor symptoms in PD.
A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process
Authors: Schumacher Paolo , Demarsy Emilie , Waridel Patrice , Petrolati Laure Allenbach , Trevisan Martine , Fankhauser Christian 
Published: June 2018

AbstractPhototropins are light-activated protein kinases, which contribute to photosynthesis optimization both through enhancement of photon absorption when light is limiting and avoidance responses in high light. This duality is in part endowed by the presence of phototropins with different photosensitivity (phot1 and phot2). Here we show that phot1, which senses low light to promote positive phototropism (growth towards the light), also limits the response in high light. This response depends in part on phot1-mediated phosphorylation of Phytochrome Kinase Substrate 4 (PKS4). This light-regulated phosphorylation switch changes PKS4 from a phototropism enhancer in low light to a factor limiting the process in high light. In such conditions phot1 and PKS4 phosphorylation prevent phototropic responses to shallow light gradients and limit phototropism in a natural high light environment. Hence, by modifying PKS4 activity in high light the phot1-PKS4 regulon enables appropriate physiological adaptations over a range of light intensities.
The synaptic receptor Lrp4 promotes peripheral nerve regeneration
Authors: Gribble Katherine D. , Walker Lauren J. , Saint-Amant Louis , Kuwada John Y. , Granato Michael 
Published: June 2018

AbstractEarly during PNS regeneration, regenerating axons emerge from the proximal nerve stump, yet whether they extend simultaneously or whether pioneering axons establish a path for follower axons remains unknown. Moreover, the molecular mechanisms underlying robust regeneration are incompletely understood. Using live imaging, we demonstrate that in zebrafish pioneering axons establish a regenerative path for follower axons. We find this process requires the synaptic receptor lrp4, and in lrp4 mutants pioneers are unaffected while follower axons frequently stall at the injury gap, providing evidence for molecular diversity between pioneering and follower axons in regeneration. We demonstrate that Lrp4 promotes regeneration through an axon extrinsic mechanism and independent of membrane anchoring and MuSK co-receptor signaling essential for synaptic development. Finally, we show that Lrp4 coordinates the realignment of denervated Schwann cells with regenerating axons, consistent with a model by which Lrp4 is repurposed to promote sustained peripheral nerve regeneration via axon-glia interactions.
A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes
Authors: Ohmann Alexander , Li Chen-Yu , Maffeo Christopher , Al Nahas Kareem , Baumann Kevin N. , Göpfrich Kerstin , Yoo Jejoong , Keyser Ulrich F. , Aksimentiev Aleksei 
Published: June 2018

AbstractMimicking enzyme function and increasing performance of naturally evolved proteins is one of the most challenging and intriguing aims of nanoscience. Here, we employ DNA nanotechnology to design a synthetic enzyme that substantially outperforms its biological archetypes. Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal pore that connects the membrane’s inner and outer leaflets. The membrane insertion catalyzes spontaneous transport of lipid molecules between the bilayer leaflets, rapidly equilibrating the lipid composition. Through a combination of microscopic simulations and fluorescence microscopy we find the lipid transport rate catalyzed by the DNA nanostructure exceeds 107 molecules per second, which is three orders of magnitude higher than the rate of lipid transport catalyzed by biological enzymes. Furthermore, we show that our DNA-based enzyme can control the composition of human cell membranes, which opens new avenues for applications of membrane-interacting DNA systems in medicine.
Tailoring exciton and excimer emission in an exfoliated ultrathin 2D metal-organic framework
Authors: Liao Wei-Ming , Zhang Jian-Hua , Yin Shao-Yun , Lin He , Zhang Xingmin , Wang Jihong , Wang Hai-Ping , Wu Kai , Wang Zheng , Fan Ya-Nan , Pan Mei , Su Cheng-Yong 
Published: June 2018

AbstractTwo-dimensional (2D) metal–organic frameworks have exhibited a range of fascinating attributes, of interest to numerous fields. Here, a calcium-based metal-organic framework with a 2D layered structure has been designed. Dual emissions relating to intralayer excimers and interlayer trapped excitons are produced, showing excitation-dependent shifting tendency, characteristic of a low dimensional semiconductor nature. Furthermore, the layer stacking by weak van der Waals forces among dynamically coordinated DMF molecules enables exfoliation and morphology transformation, which can be achieved by ultrasound in different ratios of DMF/H2O solvents, or grinding under appropriate humidity conditions, leading to nano samples including ultrathin nanosheets with single or few coordination layers. The cutting down of layer numbers engenders suppression of interlayer exciton-related emission, resulting in modulation of the overall emitting color and optical memory states. This provides a rare prototypical model with switchable dual-channel emissions based on 2D-MOFs, in which the interlayer excitation channel can be reversibly tuned on/off by top-down exfoliation and morphology transformation.
Oak genome reveals facets of long lifespan
Authors: Plomion Christophe , Aury Jean-Marc , Amselem Joëlle , Leroy Thibault , Murat Florent , Duplessis Sébastien , Faye Sébastien , Francillonne Nicolas , Labadie Karine , Le Provost Grégoire , Lesur Isabelle , Bartholomé Jérôme , Faivre-Rampant Patricia , Kohler Annegret , Leplé Jean-Charles , Chantret Nathalie , Chen Jun , Diévart Anne , Alaeitabar Tina , Barbe Valérie , Belser Caroline , Bergès Hélène , Bodénès Catherine , Bogeat-Triboulot Marie-Béatrice , Bouffaud Marie-Lara , Brachi Benjamin , Chancerel Emilie , Cohen David , Couloux Arnaud , Da Silva Corinne , Dossat Carole , Ehrenmann François , Gaspin Christine , Grima-Pettenati Jacqueline , Guichoux Erwan , Hecker Arnaud , Herrmann Sylvie , Hugueney Philippe , Hummel Irène , Klopp Christophe , Lalanne Céline , Lascoux Martin , Lasserre Eric , Lemainque Arnaud , Desprez-Loustau Marie-Laure , Luyten Isabelle , Madoui Mohammed-Amin , Mangenot Sophie , Marchal Clémence , Maumus Florian , Mercier Jonathan , Michotey Célia , Panaud Olivier , Picault Nathalie , Rouhier Nicolas , Rué Olivier , Rustenholz Camille , Salin Franck , Soler Marçal , Tarkka Mika , Velt Amandine , Zanne Amy E. , Martin Francis , Wincker Patrick , Quesneville Hadi , Kremer Antoine , Salse Jérôme 
Published: June 2018

AbstractOaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
A local and scalable lattice renormalization method for ballistic quantum computation
Authors: Herr Daniel , Paler Alexandru , Devitt Simon J. , Nori Franco 
Published: June 2018

AbstractA recent proposal has shown that it is possible to perform linear-optics quantum computation using a ballistic generation of the lattice. Yet, due to the probabilistic generation of its cluster state, it is not possible to use the fault-tolerant Raussendorf lattice, which requires a lower failure rate during the entanglement-generation process. Previous work in this area showed proof-of-principle linear-optics quantum computation, while this paper presents an approach to it which is more practical, satisfying several key constraints. We develop a classical measurement scheme that purifies a large faulty lattice to a smaller lattice with entanglement faults below threshold. A single application of this method can reduce the entanglement error rate to 7% for an input failure rate of 25%. Thus, we can show that it is possible to achieve fault tolerance for ballistic methods.
The Small Molecule Inhibitor QLT-0267 Decreases the Production of Fibrin-Induced Inflammatory Cytokines and Prevents Post-Surgical Peritoneal Adhesions
Authors: Fang Cheng-Chung , Chou Tzung-Hsin , Huang Jenq-Wen , Lee Chien-Chang , Chen Shyr-Chyr 
Published: June 2018

AbstractPeritoneal adhesions develop after abdominal surgery, trauma or intraperitoneal infections, and have important consequences. The deposition of peritoneal fibrin is a common pathophysiological pathway for the formation of adhesions. Here, we aimed to examine the effects of fibrin-induced cytokine production on peritoneal mesothelial cells (PMCs), and to block the effects of fibrin using an integrin-linked kinase (ILK) inhibitor, QLT-0267. PMCs were cultured from the enzymatic disaggregation of rat omentum. After the PMCs were covered with fibrin, the expression of IL-1β, IL-6, TNFα and VEGF-A increased. This increase in cytokine production was attenuated by QLT-0267, which acted via the inhibition of both the ILK and focal adhesion kinase (FAK) pathways, and subsequently via the GSK-3β pathway. We found that QLT-0267 decreased both the severity of peritoneal adhesion and the serum levels of IL-6 in our post-surgical adhesion mouse model. In conclusion, our study provides novel evidence that fibrin-induced cytokine production may involve in the mechanism of peritoneal adhesion formation. Furthermore, the use of the small molecule inhibitor QLT-0267 is a new strategy in preventing peritoneal adhesion in patients undergoing abdominal surgery.
Accuracy and Precision of Tidal Wetland Soil Carbon Mapping in the Conterminous United States
Authors: Holmquist James R. , Windham-Myers Lisamarie , Bliss Norman , Crooks Stephen , Morris James T. , Megonigal J. Patrick , Troxler Tiffany , Weller Donald , Callaway John , Drexler Judith , Ferner Matthew C. , Gonneea Meagan E. , Kroeger Kevin D. , Schile-Beers Lisa , Woo Isa , Buffington Kevin , Breithaupt Joshua , Boyd Brandon M. , Brown Lauren N. , Dix Nicole , Hice Lyndie , Horton Benjamin P. , MacDonald Glen M. , Moyer Ryan P. , Reay William , Shaw Timothy , Smith Erik , Smoak Joseph M. , Sommerfield Christopher , Thorne Karen , Velinsky David , Watson Elizabeth , Grimes Kristin Wilson , Woodrey Mark 
Published: June 2018

AbstractTidal wetlands produce long-term soil organic carbon (C) stocks. Thus for carbon accounting purposes, we need accurate and precise information on the magnitude and spatial distribution of those stocks. We assembled and analyzed an unprecedented soil core dataset, and tested three strategies for mapping carbon stocks: applying the average value from the synthesis to mapped tidal wetlands, applying models fit using empirical data and applied using soil, vegetation and salinity maps, and relying on independently generated soil carbon maps. Soil carbon stocks were far lower on average and varied less spatially and with depth than stocks calculated from available soils maps. Further, variation in carbon density was not well-predicted based on climate, salinity, vegetation, or soil classes. Instead, the assembled dataset showed that carbon density across the conterminous united states (CONUS) was normally distributed, with a predictable range of observations. We identified the simplest strategy, applying mean carbon density (27.0 kg C m−3), as the best performing strategy, and conservatively estimated that the top meter of CONUS tidal wetland soil contains 0.72 petagrams C. This strategy could provide standardization in CONUS tidal carbon accounting until such a time as modeling and mapping advancements can quantitatively improve accuracy and precision.
The role of irradiance and C-use strategies in tropical macroalgae photosynthetic response to ocean acidification
Authors: Zweng Regina C. , Koch Marguerite S. , Bowes George 
Published: June 2018

AbstractFleshy macroalgae may increase photosynthesis with greater CO2 availability under ocean acidification (OA) and outcompete calcifying macroalgae important for tropical reef accretion. Macroalgae use energy-dependent carbon concentrating mechanisms (CCMs) to take up HCO3−, the dominant inorganic carbon for marine photosynthesis, but carbon-use strategies may depend on the pCO2, pH and irradiance. We examined photosynthesis in eight tropical macroalgae across a range of irradiances (0–1200 μmol photon m−2 s−1), pH levels (7.5–8.5) and CO2 concentrations (3–43 μmol kg−1). Species-specific CCM strategies were assessed using inhibitors and δ13C isotope signatures. Our results indicate that the log of irradiance is a predictor of the photosynthetic response to elevated pCO2 (R2 > 0.95). All species utilized HCO3−, exhibited diverse C-use pathways and demonstrated facultative HCO3− use. All fleshy species had positive photosynthetic responses to OA, in contrast to a split amongst calcifiers. We suggest that shifts in photosynthetically-driven tropical macroalgal changes due to OA will most likely occur in moderate to high-irradiance environments when CCMs are ineffective at meeting the C-demands of photosynthesis. Further, facultative use of HCO3− allows greater access to CO2 for photosynthesis under OA conditions, particularly amongst fleshy macroalgae, which could contribute to enhance fleshy species dominance over calcifiers.
CSF-1/CSF-1R axis is associated with epithelial/mesenchymal hybrid phenotype in epithelial-like inflammatory breast cancer
Authors: Kai Kazuharu , Iwamoto Takayuki , Zhang Dongwei , Shen Li , Takahashi Yuko , Rao Arvind , Thompson Alastair , Sen Subrata , Ueno Naoto T. 
Published: June 2018

AbstractInflammatory breast cancer (IBC) is a rare subtype of breast cancer, accounting for 8–10% of breast cancer-associated deaths in the US. Clinical hallmarks of IBC include tumor emboli in lymphatic vessels and E-cadherin overexpression, which supports a type of metastasis referred to as cell cluster-based metastasis, prevalent in IBC. In contrast, we previously reported epithelial-to-mesenchymal transition (EMT)-based progression of IBC, utilizing in vivo xenografts and in vitro Matrigel culture models. To address these two contradictory concepts of IBC metastasis, we used Matrigel culture to induce EMT in a panel of IBC cells. Results revealed Matrigel culture induced vimentin expression in SUM149 and SUM190 IBC cells at the transcriptional and protein levels while maintaining the expression of E-cadherin, a phenomenon referred to as partial EMT. Transcriptional profiling revealed that expression of colony-stimulating factor 1 (CSF-1) was induced in Matrigel culture. When the receptor tyrosine kinase of CSF-1 (CSF-1R) was inhibited by CSF-1R inhibitor BLZ945, the partial EMT was reversed in a dose-dependent manner, indicating that the CSF-1/CSF-1R axis plays a key role in controlling partial EMT. This observation may help reconcile the two contradictory theories of IBC metastasis, EMT vs cell cluster-based metastasis.
Nationwide survey on the organ-specific prevalence and its interaction with sarcoidosis in Japan
Authors: Hattori Takeshi , Konno Satoshi , Shijubo Noriharu , Yamaguchi Tetsuo , Sugiyama Yukihiko , Honma Sakae , Inase Naohiko , Ito Yoichi M. , Nishimura Masaharu 
Published: June 2018

AbstractPrevious studies attempted to characterize the subjects with sarcoidosis according to differences in sex, age, and the presence of specific organ involvement. However, significant interactions among these factors precluded a clear conclusion based on simple comparison. This study aimed to clarify the age- and sex-stratified prevalence of specific organ involvement and the heterogenous nature of sarcoidosis. Using the data of 9,965 patients who were newly registered into a database at the Ministry of Health, Labour and Welfare, Japan between 2002 and 2011, we evaluated the age- and sex-specific prevalence of the eye, lung, and skin involvement of sarcoidosis. We also attempted corresponding analysis considering multiple factors. As compared with several decades ago, the monophasic age distribution in men became biphasic, and the biphasic distribution in women, monophasic. The prevalence of pulmonary and cutaneous lesions was significantly associated with age, whereas the prevalence of ocular involvement showed a biphasic pattern. The prevalence of bilateral hilar lymphadenopathy was significantly higher, whereas the prevalence of diffuse lung shadow was significantly lower, in subjects with ocular involvement than those without ocular involvement. Corresponding analysis visually clarified the complex interactions among factors. Our results contribute to a better understanding of the heterogeneous features of sarcoidosis.
Immune interconnectivity of anatomically distant tumors as a potential mediator of systemic responses to local therapy
Authors: Walker Rachel , Poleszczuk Jan , Pilon-Thomas Shari , Kim Sungjune , Anderson Alexander A. R. A. , Czerniecki Brian J. , Harrison Louis B. , Moros Eduardo G. , Enderling Heiko 
Published: June 2018

AbstractComplex interactions occur between tumor and host immune system at each site in the metastatic setting, the outcome of which can determine behavior ranging from dormancy to rapid growth. An additional layer of complexity arises from the understanding that cytotoxic T cells can traffic through the host circulatory system. Coupling mathematical models of local tumor-immune dynamics and systemic T cell trafficking allows us to simulate the evolution of tumor and immune cell populations in anatomically distant sites following local therapy and thus computationally evaluate immune interconnectivity. Results suggest that the presence of a secondary site may either inhibit or promote growth of the primary, depending on the capacity for immune recruitment of each tumor and the resulting systemic redistribution of T cells. Treatment such as surgical resection and radiotherapy can be simulated to estimate both the decrease in tumor volume at the local treatment-targeted site, and the change in overall tumor burden and tumor growth trajectories across all sites. Qualitatively similar responses of distant tumors to local therapy (positive and negative abscopal effects) to those reported in the clinical setting were observed. Such findings may facilitate an improved understanding of general disease kinetics in the metastatic setting: if metastatic sites are interconnected through the immune system, truly local therapy does not exist.
Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
Authors: Reyes Elisabeth , Nadot Sophie , von Balthazar Maria , Schönenberger Jürg , Sauquet Hervé 
Published: June 2018

AbstractAncestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.