bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus phylogenetic analysis and morphological data reveal a new species composition of the genusDrepanocephalusDietz, 1909 (Digenea: Echinostomatidae), parasites of fish-eating birds in the Americas
Authors: Hernández-Cruz E. , Hernández-Orts J.S. , Sereno-Uribe A.L. , Pérez-Ponce de León G. , García-Varela M. 
Published: October 2017

AbstractMembers of the genusDrepanocephalusare endoparasites of fish-eating birds of the families Phalacrocoracidae and Sulidae distributed across the Americas. Currently,Drepanocephaluscontains three species, i.e.D. spathans(type species),D. olivaceusandD. auritus.Two additional species,D. parvicephalusandD. mexicanuswere transferred to the genusPetasiger. In the current study, available DNA sequences ofD. spathans,D. auritusandDrepanocephalussp., were aligned with newly generated sequences ofD. spathansandPetasiger mexicanus. Phylogenetic analyses inferred with three nuclear (LSU, SSU and ITS1, 5.8S, ITS2) and two mitochondrial (cox1,nad1) molecular markers showed that the sequences ofD. spathansandD. auritusare nested together in a single clade with very low genetic divergence, withPetasiger mexicanusas its sister species. Additionally,P. mexicanuswas not a close relative of other members of the genusPetasiger,showing thatP. mexicanusactually belongs to the genusDrepanocephalus,suggesting the need to re-allocatePetasiger mexicanusback into the genusDrepanocephalus, asD. mexicanus.Morphological observations of the newly sampled individuals ofD. spathansshowed that the position of the testes is variable and testes might be contiguous or widely separated, which is one of the main diagnostic traits forD. auritus. Our results suggest thatD. auritusmight be considered a synonym ofD. spathansand, as a result, the latter represents a species with a wide geographic range across the Americas, parasitizing both the Neotropical and the double-crested cormorant in Argentina, Brazil, Paraguay, Venezuela, Colombia, Mexico, USA and Canada.
Cardioprotection induced in a mouse model of neuropathic pain via anterior nucleus of paraventricular thalamus
Authors: Cheng Yi-Fen , Chang Ya-Ting , Chen Wei-Hsin , Shih Hsi-Chien , Chen Yen-Hui , Shyu Bai-Chuang , Chen Chien-Chang 
Published: October 2017

AbstractMyocardial infarction is the leading cause of death worldwide. Restoration of blood flow rescues myocardium but also causes ischemia-reperfusion injury. Here, we show that in a mouse model of chronic neuropathic pain, ischemia-reperfusion injury following myocardial infarction is reduced, and this cardioprotection is induced via an anterior nucleus of paraventricular thalamus (PVA)-dependent parasympathetic pathway. Pharmacological inhibition of extracellular signal-regulated kinase activation in the PVA abolishes neuropathic pain-induced cardioprotection, whereas activation of PVA neurons pharmacologically, or optogenetic stimulation, is sufficient to induce cardioprotection. Furthermore, neuropathic injury and optogenetic stimulation of PVA neurons reduce the heart rate. These results suggest that the parasympathetic nerve is responsible for this unexpected cardioprotective effect of chronic neuropathic pain in mice.
Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder
Authors: Huppke Peter , Weissbach Susann , Church Joseph A. , Schnur Rhonda , Krusen Martina , Dreha-Kulaczewski Steffi , Kühn-Velten W. Nikolaus , Wolf Annika , Huppke Brenda , Millan Francisca , Begtrup Amber , Almusafri Fatima , Thiele Holger , Altmüller Janine , Nürnberg Peter , Müller Michael , Gärtner Jutta 
Published: October 2017

AbstractTranscription factor NRF2, encoded by NFE2L2, is the master regulator of defense against stress in mammalian cells. Somatic mutations of NFE2L2 leading to NRF2 accumulation promote cell survival and drug resistance in cancer cells. Here we show that the same mutations as inborn de novo mutations cause an early onset multisystem disorder with failure to thrive, immunodeficiency and neurological symptoms. NRF2 accumulation leads to widespread misregulation of gene expression and an imbalance in cytosolic redox balance. The unique combination of white matter lesions, hypohomocysteinaemia and increased G-6-P-dehydrogenase activity will facilitate early diagnosis and therapeutic intervention of this novel disorder.
3D integrated superconducting qubits
Authors: Rosenberg D. , Kim D. , Das R. , Yost D. , Gustavsson S. , Hover D. , Krantz P. , Melville A. , Racz L. , Samach G. O. , Weber S. J. , Yan F. , Yoder J. L. , Kerman A. J. , Oliver W. D. 
Published: October 2017

AbstractAs the field of quantum computing advances from the few-qubit stage to larger-scale processors, qubit addressability and extensibility will necessitate the use of 3D integration and packaging. While 3D integration is well-developed for commercial electronics, relatively little work has been performed to determine its compatibility with high-coherence solid-state qubits. Of particular concern, qubit coherence times can be suppressed by the requisite processing steps and close proximity of another chip. In this work, we use a flip-chip process to bond a chip with superconducting flux qubits to another chip containing structures for qubit readout and control. We demonstrate that high qubit coherence (T1, T2,echo > 20 μs) is maintained in a flip-chip geometry in the presence of galvanic, capacitive, and inductive coupling between the chips.
A Bivariate Hypothesis Testing Approach for Mapping the Trait-Influential Gene
Authors: Saunders Garrett , Fu Guifang , Stevens John R. 
Published: October 2017

AbstractThe linkage disequilibrium (LD) based quantitative trait loci (QTL) model involves two indispensable hypothesis tests: the test of whether or not a QTL exists, and the test of the LD strength between the QTaL and the observed marker. The advantage of this two-test framework is to test whether there is an influential QTL around the observed marker instead of just having a QTL by random chance. There exist unsolved, open statistical questions about the inaccurate asymptotic distributions of the test statistics. We propose a bivariate null kernel (BNK) hypothesis testing method, which characterizes the joint distribution of the two test statistics in two-dimensional space. The power of this BNK approach is verified by three different simulation designs and one whole genome dataset. It solves a few challenging open statistical questions, closely separates the confounding between ‘linkage’ and ‘QTL effect’, makes a fine genome division, provides a comprehensive understanding of the entire genome, overcomes limitations of traditional QTL approaches, and connects traditional QTL mapping with the newest genotyping technologies. The proposed approach contributes to both the genetics literature and the statistics literature, and has a potential to be extended to broader fields where a bivariate test is needed.
Transient postnatal overfeeding causes liver stress-induced premature senescence in adult mice
Authors: Yzydorczyk Catherine , Li Na , Chehade Hassib , Mosig Dolores , Bidho Mickael , Keshavjee Basile , Armengaud Jean Baptiste , Nardou Katya , Siddeek Benazir , Benahmed Mohamed , Vergely Catherine , Simeoni Umberto 
Published: October 2017

AbstractUnbalanced nutrition early in life is increasingly recognized as an important factor in the development of chronic, non-communicable diseases at adulthood, including metabolic diseases. We aimed to determine whether transient postnatal overfeeding (OF) leads to liver stress-induced premature senescence (SIPS) of hepatocytes in association with liver structure and hepatic function alterations. Litters sizes of male C57BL/6 mice were adjusted to 9 pups (normal feeding, NF) or reduced to 3 pups during the lactation period to induce transient postnatal OF. Compared to the NF group, seven-month-old adult mice transiently overfed during the postnatal period were overweight and developed glucose intolerance and insulin resistance. Their livers showed microsteatosis and fibrosis, while hepatic insulin signaling and glucose transporter protein expressions were altered. Increased hepatic oxidative stress (OS) was observed, with increased superoxide anion production, glucose-6-phosphate dehydrogenase protein expression, oxidative DNA damage and decreased levels of antioxidant defense markers, such as superoxide dismutase and catalase proteins. Hepatocyte senescence was characterized by increased p21WAF, p53, Acp53, p16INK4a and decreased pRb/Rb and Sirtuin-1 (SIRT-1) protein expression levels. Transient postnatal OF induces liver OS at adulthood, associated with hepatocyte SIPS and alterations in liver structure and hepatic functions, which could be mediated by a SIRT-1 deficiency.
Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin’s Favourite Orchids
Authors: Pérez-Escobar Oscar Alejandro , Chomicki Guillaume , Condamine Fabien L. , de Vos Jurriaan M. , Martins Aline C. , Smidt Eric C. , Klitgård Bente , Gerlach Günter , Heinrichs Jochen 
Published: October 2017

AbstractEnvironmental sex determination (ESD) − a change in sexual function during an individual life span driven by environmental cues − is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.
Squeezing giant spin states via geometric phase control in cavity-assisted Raman transitions
Authors: Xia Keyu 
Published: October 2017

AbstractSqueezing ensemble of spins provides a way to surpass the standard quantum limit in quantum metrology and test the fundamental physics as well, and therefore attracts broad interest. Here we propose an experimentally accessible protocol to squeeze a giant ensemble of spins via the geometric phase control (GPC). Using the cavity-assisted Raman transition (CART) in a double Λ-type system, we realize an effective Dicke model. Under the condition of vanishing effective spin transition frequency, we find a particular evolution time where the cavity decouples from the spins and the spin ensemble is squeezed considerably. Our scheme combines the CART and the GPC, and has the potential to improve the sensitivity in quantum metrology with spins by about two orders.
Geometry Optimization with Machine Trained Topological Atoms
Authors: Zielinski François , Maxwell Peter I. , Fletcher Timothy L. , Davie Stuart J. , Di Pasquale Nicodemo , Cardamone Salvatore , Mills Matthew J. L. , Popelier Paul L. A. 
Published: October 2017

AbstractThe geometry optimization of a water molecule with a novel type of energy function called FFLUX is presented, which bypasses the traditional bonded potentials. Instead, topologically-partitioned atomic energies are trained by the machine learning method kriging to predict their IQA atomic energies for a previously unseen molecular geometry. Proof-of-concept that FFLUX’s architecture is suitable for geometry optimization is rigorously demonstrated. It is found that accurate kriging models can optimize 2000 distorted geometries to within 0.28 kJ mol−1of the correspondingab initioenergy, and 50% of those to within 0.05 kJ mol−1. Kriging models are robust enough to optimize the molecular geometry to sub-noise accuracy, when two thirds of the geometric inputs are outside the training range of that model. Finally, the individual components of the potential energy are analyzed, and chemical intuition is reflected in the independent behavior of the three energy terms$${E}_{{\rm{intra}}}^{{\rm{A}}}$$EintraA(intra-atomic),$${V}_{{\rm{cl}}}^{\text{AA}\text{'}}$$VclAA'(electrostatic) and$${V}_{{\rm{x}}}^{\text{AA}\text{'}}$$VxAA'(exchange), in contrast to standard force fields.
Associative visual learning by tethered bees in a controlled visual environment
Authors: Buatois Alexis , Pichot Cécile , Schultheiss Patrick , Sandoz Jean-Christophe , Lazzari Claudio R. , Chittka Lars , Avarguès-Weber Aurore , Giurfa Martin 
Published: October 2017

AbstractFree-flying honeybees exhibit remarkable cognitive capacities but the neural underpinnings of these capacities cannot be studied in flying insects. Conversely, immobilized bees are accessible to neurobiological investigation but display poor visual learning. To overcome this limitation, we aimed at establishing a controlled visual environment in which tethered bees walking on a spherical treadmill learn to discriminate visual stimuli video projected in front of them. Freely flying bees trained to walk into a miniature Y-maze displaying these stimuli in a dark environment learned the visual discrimination efficiently when one of them (CS+) was paired with sucrose and the other with quinine solution (CS−). Adapting this discrimination to the treadmill paradigm with a tethered, walking bee was successful as bees exhibited robust discrimination and preferred the CS+ to the CS− after training. As learning was better in the maze, movement freedom, active vision and behavioral context might be important for visual learning. The nature of the punishment associated with the CS− also affects learning as quinine and distilled water enhanced the proportion of learners. Thus, visual learning is amenable to a controlled environment in which tethered bees learn visual stimuli, a result that is important for future neurobiological studies in virtual reality.
Difference in intracellular temperature rise between matured and precursor brown adipocytes in response to uncoupler and β-adrenergic agonist stimuli
Authors: Tsuji Toshikazu , Ikado Kumiko , Koizumi Hideki , Uchiyama Seiichi , Kajimoto Kazuaki 
Published: October 2017

AbstractBrown adipocytes function to maintain body temperature by heat production. However, direct measurement of heat production at a single cell level remains difficult. Here we developed a method to measure the temperature within primary cultured brown adipocytes using a cationic fluorescent polymeric thermometer. Placement of the thermometer within a matured brown adipocyte and a precursor cell enabled the detection of heat production following uncoupler treatment. The increase in the intracellular temperature due to stimulation with a mitochondrial uncoupler was higher in matured brown adipocytes than in precursor cells. Stimulation with a β-adrenergic receptor (β-AR) agonist, norepinephrine, raised the intracellular temperature of matured brown adipocytes to a level comparable to that observed after stimulation with a β3-AR-specific agonist, CL316.243. In contrast, neither β-AR agonist induced an intracellular temperature increase in precursor cells. Further, pretreatment of brown adipocytes with a β3-AR antagonist inhibited the norepinephrine-stimulated elevation of temperature. These results demonstrate that our novel method successfully determined the difference in intracellular temperature increase between matured brown adipocytes and precursor cells in response to stimulation by an uncoupler and β-AR agonists.
Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition
Authors: Chan Kiat Hwa , Xue Bo , Robinson Robert C. , Hauser Charlotte A. E. 
Published: October 2017

AbstractSelf-assembly of small biomolecules is a prevalent phenomenon that is increasingly being recognised to hold the key to building complex structures from simple monomeric units. Small peptides, in particular ultrashort peptides containing up to seven amino acids, for which our laboratory has found many biomedical applications, exhibit immense potential in this regard. For next-generation applications, more intricate control is required over the self-assembly processes. We seek to find out how subtle moiety variation of peptides can affect self-assembly and nanostructure formation. To this end, we have selected a library of 54 tripeptides, derived from systematic moiety variations from seven tripeptides. Our study reveals that subtle structural changes in the tripeptides can exert profound effects on self-assembly, nanostructure formation, hydrogelation, and even phase transition of peptide nanostructures. By comparing the X-ray crystal structures of two tripeptides, acetylated leucine-leucine-glutamic acid (Ac-LLE) and acetylated tyrosine-leucine-aspartic acid (Ac-YLD), we obtained valuable insights into the structural factors that can influence the formation of supramolecular peptide structures. We believe that our results have major implications on the understanding of the factors that affect peptide self-assembly. In addition, our findings can potentially assist current computational efforts to predict and design self-assembling peptide systems for diverse biomedical applications.
Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane
Authors: Chiaradia Laura , Lefebvre Cyril , Parra Julien , Marcoux Julien , Burlet-Schiltz Odile , Etienne Gilles , Tropis Maryelle , Daffé Mamadou 
Published: October 2017

AbstractThe mycobacterial envelope is unique, containing the so-called mycomembrane (MM) composed of very-long chain fatty acids, mycolic acids (MA). Presently, the molecular composition of the MM remains unproven, due to the diversity of methods used for determining its composition. The plasma membranes (PM) and the native MM-containing cell walls (MMCW) of two rapid-growing mycobacterial species, Mycobacterium aurum and M. smegmatis, were isolated from their cell lysates by differential ultracentrifugation. Transmission electron microscopy and biochemical analyses demonstrated that the two membranes were virtually pure. Bottom-up quantitative proteomics study indicated a different distribution of more than 2,100 proteins between the PM and MMCW. Among these, the mannosyltransferase PimB, galactofuranosyltransferase GlfT2, Cytochrome p450 and ABC transporter YjfF, were most abundant in the PM, which also contain lipoglycans, phospholipids, including phosphatidylinositol mannosides, and only a tiny amount of other glycolipids. Antigen85 complex proteins, porins and the putative transporters MCE protein family were mostly found in MMCW fraction that contains MA esterifying arabinogalactan, constituting the inner leaflet of MM. Glycolipids, phospholipids and lipoglycans, together with proteins, presumably composed the outer leaflet of the MM, a lipid composition that differs from that deduced from the widely used extraction method of mycobacterial cells with dioctylsulfosuccinate sodium.
ADAR1 polymorphisms are related to severity of liver fibrosis in HIV/HCV-coinfected patients
Authors: Medrano Luz M. , Berenguer Juan , Jiménez-Sousa María A. , Aldámiz-Echevarria Teresa , Tejerina Francisco , Diez Cristina , Vigón Lorena , Fernández-Rodríguez Amanda , Resino Salvador 
Published: October 2017

AbstractThe adenosine deaminase acting on RNA (ADAR1) gene is an interferon-stimulated gene involved in liver injury protection. Our aim was to analyze the association of polymorphisms within this gene with the severity of liver disease in European HIV/HCV-coinfected patients. We performed a cross-sectional study in 220 patients that underwent a liver biopsy. Five SNPs in the ADAR1 gene (rs1127326, rs1127317, rs1127314, rs1127313, rs2229857) were genotyped by GoldenGate assay. The outcome variables were fibrosis stage and necroinflammatory activity grade by METAVIR-score, aspartate aminotransferase to platelet ratio index (APRI), FIB-4 index, and fibrosis progression rate (FPR). In multivariate analysis, fibrosis progression rate (FPR) (aAMRs = 0.97) decreased in a dose-dependent manner with the presence of rs2229857_T, rs1127313_G, rs1127314_G and rs1127317_G; while rs1127326_T allele had only significant associations with FIB-4 (aAMRs ≤ 0.63) and FPR (aAMRs ≤ 0.97). Moreover, carriers of rs2229857_T, rs1127314_G, rs1127317_G, and rs1127326_T alleles were protected against advanced fibrosis (F ≥ 3) (adjusted ORs (aORs) ≤ 0.44), APRI ≥ 1.5 (aORs ≤ 0.33), and FPR ≥ 0.075 (aORs ≤ 0.45). rs1127313_G carriers showed lower odds of having F ≥ 3 (aORs = 0.39), FIB4 ≥ 3.25 (aOR = 0.22) and FPR ≥ 0.075 (aORs = 0.44). In conclusion, ADAR1 polymorphisms protected against severe liver disease in HIV/HCV-coinfected patients. These results could be used to improve therapeutic decision-making in clinical practice.
Stochastic resonance improves vision in the severely impaired
Authors: Itzcovich Elena , Riani Massimo , Sannita Walter G. 
Published: October 2017

AbstractWe verified whether a stochastic resonance paradigm (SR), with random interference (“noise”) added in optimal amounts, improves the detection of sub-threshold visual information by subjects with retinal disorder and impaired vision as it does in the normally sighted. Six levels of dynamic, zero-mean Gaussian noise were added to each pixel of images (13 contrast levels) in which alphabet characters were displayed against a uniform gray background. Images were presented with contrast below the subjective threshold to 14 visually impaired subjects (age: 22–53 yrs.). The fraction of recognized letters varied between 0 and 0.3 at baseline and increased in all subjects when noise was added in optimal amounts; peak recognition ranged between 0.2 and 0.8 at noise sigmas between 6 and 30 grey scale values (GSV) and decreased in all subjects at noise levels with sigma above 30 GSV. The results replicate in the visually impaired the facilitation of visual information processing with images presented in SR paradigms that has been documented in sighted subjects. The effect was obtained with low-level image manipulation and application appears readily possible: it would enhance the efficiency of today vision-improving aids and help in the development of the visual prostheses hopefully available in the future.
MDSCs are induced after experimental blunt chest trauma and subsequently alter antigen-specific T cell responses
Authors: Hüsecken Yvonne , Muche Sylvia , Kustermann Monika , Klingspor Malena , Palmer Annette , Braumüller Sonja , Huber-Lang Markus , Debatin Klaus-Michael , Strauss Gudrun 
Published: October 2017

AbstractSevere blunt chest trauma (TxT) induces a strong inflammatory response with posttraumatic immune suppression pointing to an impaired adaptive immune response. Since CD11b+Gr-1+-expressing myeloid-derived suppressor cells (MDSCs) are induced after inflammation and suppress T cell responses, MDSC induction and their impact on T cell functions was analysed in an experimental TxT model. MDSCs were induced preferentially in the lung until 24 hours after TxT. Although MDSC numbers were only faintly increased in the spleen, splenic MDSCs isolated after TxT strongly inhibited alloantigen-induced T cell proliferation in vitro. Suppressive activity correlated with increased expression of arginase-1 and iNOS. MDSCs also prevented antigen-induced T cell expansion in vivo, since staphylococcus enterotoxin B (SEB)-induced proliferation of vβ8+ T cells was impaired in TxT mice in the presence of CD11b+Gr-1+ cells. Surprisingly, MDSCs were not involved in shifting T cells into Th2 cells, characterized by the secretion of cytokines impairing cell-mediated immunity and promoting immunosuppression. Instead, the presence of CD11b+Gr-1+ cells was required for efficient IL-2, IFN-γ and TNFα production after antigenic stimulation, indicating, that elevation of MDSCs early after traumatic injuries might contribute to restrict the initial inflammatory response by alleviating T cell expansion, however, without impeding Th1 functions.