bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modular design of molecular qubits to implement universal quantum gates
Authors: Ferrando-Soria Jesús , Moreno Pineda Eufemio , Chiesa Alessandro , Fernandez Antonio , Magee Samantha A. , Carretta Stefano , Santini Paolo , Vitorica-Yrezabal Iñigo J. , Tuna Floriana , Timco Grigore A. , McInnes Eric J.L. , Winpenny Richard E.P. 
Published: April 2016

AbstractThe physical implementation of quantum information processing relies on individual modules—qubits—and operations that modify such modules either individually or in groups—quantum gates. Two examples of gates that entangle pairs of qubits are the controlled NOT-gate (CNOT) gate, which flips the state of one qubit depending on the state of another, and the "Equation missing"gate that brings a two-qubit product state into a superposition involving partially swapping the qubit states. Here we show that through supramolecular chemistry a single simple module, molecular {Cr7Ni} rings, which act as the qubits, can be assembled into structures suitable for either the CNOT or "Equation missing"gate by choice of linker, and we characterize these structures by electron spin resonance spectroscopy. We introduce two schemes for implementing such gates with these supramolecular assemblies and perform detailed simulations, based on the measured parameters including decoherence, to demonstrate how the gates would operate.
Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling
Authors: Yang Bao-Jun , Han Xin-Xin , Yin Lin-Lin , Xing Mei-Qing , Xu Zhi-Hong , Xue Hong-Wei 
Published: April 2016

AbstractThe plant hormone auxin is perceived by the nuclear F-box protein TIR1 receptor family and regulates gene expression through degradation of Aux/IAA transcriptional repressors. Several studies have revealed the importance of the proteasome in auxin signalling, but details on how the proteolytic machinery is regulated and how this relates to degradation of Aux/IAA proteins remains unclear. Here we show that an Arabidopsis homologue of the proteasome inhibitor PI31, which we name PROTEASOME REGULATOR1 (PTRE1), is a positive regulator of the 26S proteasome. Loss-of-function ptre1 mutants are insensitive to auxin-mediated suppression of proteasome activity, show diminished auxin-induced degradation of Aux/IAA proteins and display auxin-related phenotypes. We found that auxin alters the subcellular localization of PTRE1, suggesting this may be part of the mechanism by which it reduces proteasome activity. Based on these results, we propose that auxin regulates proteasome activity via PTRE1 to fine-tune the homoeostasis of Aux/IAA repressor proteins thus modifying auxin activity.
Thiol reductive stress induces cellulose-anchored biofilm formation in Mycobacterium tuberculosis
Authors: Trivedi Abhishek , Mavi Parminder Singh , Bhatt Deepak , Kumar Ashwani 
Published: April 2016

AbstractMycobacterium tuberculosis (Mtb) forms biofilms harbouring antibiotic-tolerant bacilli in vitro, but the factors that induce biofilm formation and the nature of the extracellular material that holds the cells together are poorly understood. Here we show that intracellular thiol reductive stress (TRS) induces formation of Mtb biofilms in vitro, which harbour drug-tolerant but metabolically active bacteria with unchanged levels of ATP/ADP, NAD+/NADH and NADP+/NADPH. The development of these biofilms requires DNA, RNA and protein synthesis. Transcriptional analysis suggests that Mtb modulates only ∼7% of its genes for survival in biofilms. In addition to proteins, lipids and DNA, the extracellular material in these biofilms is primarily composed of polysaccharides, with cellulose being a key component. Our results contribute to a better understanding of the mechanisms underlying Mtb biofilm formation, although the clinical relevance of Mtb biofilms in human tuberculosis remains unclear.
A genetic basis for the variation in the vulnerability of cancer to DNA damage
Authors: Yard Brian D. , Adams Drew J. , Chie Eui Kyu , Tamayo Pablo , Battaglia Jessica S. , Gopal Priyanka , Rogacki Kevin , Pearson Bradley E. , Phillips James , Raymond Daniel P. , Pennell Nathan A. , Almeida Francisco , Cheah Jaime H. , Clemons Paul A. , Shamji Alykhan , Peacock Craig D. , Schreiber Stuart L. , Hammerman Peter S. , Abazeed Mohamed E. 
Published: April 2016

AbstractRadiotherapy is not currently informed by the genetic composition of an individual patient’s tumour. To identify genetic features regulating survival after DNA damage, here we conduct large-scale profiling of cellular survival after exposure to radiation in a diverse collection of 533 genetically annotated human tumour cell lines. We show that sensitivity to radiation is characterized by significant variation across and within lineages. We combine results from our platform with genomic features to identify parameters that predict radiation sensitivity. We identify somatic copy number alterations, gene mutations and the basal expression of individual genes and gene sets that correlate with the radiation survival, revealing new insights into the genetic basis of tumour cellular response to DNA damage. These results demonstrate the diversity of tumour cellular response to ionizing radiation and establish multiple lines of evidence that new genetic features regulating cellular response after DNA damage can be identified.
Liver-specific overexpression of LPCAT3 reduces postprandial hyperglycemia and improves lipoprotein metabolic profile in mice
Authors: Cash J G , Hui D Y 
Published: April 2016

AbstractPrevious studies have shown that group 1B phospholipase A2-mediated absorption of lysophospholipids inhibits hepatic fatty acid β-oxidation and contributes directly to postprandial hyperglycemia and hyperlipidemia, leading to increased risk of cardiometabolic disease. The current study tested the possibility that increased expression of lysophosphatidylcholine acyltransferase-3 (LPCAT3), an enzyme that converts lysophosphatidylcholine to phosphatidylcholine in the liver, may alleviate the adverse effects of lysophospholipids absorbed after a lipid-glucose mixed meal. The injection of an adenovirus vector harboring the human LPCAT3 gene into C57BL/6 mice increased hepatic LPCAT3 expression fivefold compared with mice injected with a control LacZ adenovirus. Postprandial glucose tolerance tests after feeding these animals with a bolus lipid-glucose mixed meal revealed that LPCAT3 overexpression improved postprandial hyperglycemia and glucose tolerance compared with control mice with LacZ adenovirus injection. Mice with LPCAT3 overexpression also showed reduced very low density lipoprotein production and displayed elevated levels of the metabolic- and cardiovascular-protective large apoE-rich high density lipoproteins in plasma. The mechanism underlying the metabolic benefits of LPCAT3 overexpression was shown to be due to the alleviation of lysophospholipid inhibition of fatty acid β-oxidation in hepatocytes. Taken together, these results suggest that specific LPCAT3 induction in the liver may be a viable strategy for cardiometabolic disease intervention.
Sleep Deprivation and Advice Taking
Authors: Häusser Jan Alexander , Leder Johannes , Ketturat Charlene , Dresler Martin , Faber Nadira Sophie 
Published: April 2016

AbstractJudgements and decisions in many political, economic or medical contexts are often made while sleep deprived. Furthermore, in such contexts individuals are required to integrate information provided by – more or less qualified – advisors. We asked if sleep deprivation affects advice taking. We conducted a 2 (sleep deprivation: yes vs. no) ×2 (competency of advisor: medium vs. high) experimental study to examine the effects of sleep deprivation on advice taking in an estimation task. We compared participants with one night of total sleep deprivation to participants with a night of regular sleep. Competency of advisor was manipulated within subjects. We found that sleep deprived participants show increased advice taking. An interaction of condition and competency of advisor and further post-hoc analyses revealed that this effect was more pronounced for the medium competency advisor compared to the high competency advisor. Furthermore, sleep deprived participants benefited more from an advisor of high competency in terms of stronger improvement in judgmental accuracy than well-rested participants.
NOTCH1 inhibition enhances the efficacy of conventional chemotherapeutic agents by targeting head neck cancer stem cell
Authors: Zhao Zhi-Li , Zhang Lu , Huang Cong-Fa , Ma Si-Rui , Bu Lin-Lin , Liu Jian-Feng , Yu Guang-Tao , Liu Bing , Gutkind J. Silvio , Kulkarni Ashok B. , Zhang Wen-Feng , Sun Zhi-Jun 
Published: April 2016

AbstractCancer stem cells (CSCs) are considered responsible for tumor initiation and chemoresistance. This study was aimed to investigate the possibility of targeting head neck squamous cell carcinoma (HNSCC) by NOTCH1 pathway inhibition and explore the synergistic effect of combining NOTCH inhibition with conventional chemotherapy. NOTCH1/HES1 elevation was found in human HNSCC, especially in tissue post chemotherapy and lymph node metastasis, which is correlated with CSCs markers. NOTCH1 inhibitor DAPT (GSI-IX) significantly reduces CSCs population and tumor self-renewal ability in vitro and in vivo. Flow cytometry analysis showed that NOTCH1 inhibition reduces CSCs frequency either alone or in combination with chemotherapeutic agents, namely, cisplatin, docetaxel, and 5-fluorouracil. The combined strategy of NOTCH1 blockade and chemotherapy synergistically attenuated chemotherapy-enriched CSC population, promising a potential therapeutic exploitation in future clinical trial.
3D Printed Reversible Shape Changing Components with Stimuli Responsive Materials
Authors: Mao Yiqi , Ding Zhen , Yuan Chao , Ai Shigang , Isakov Michael , Wu Jiangtao , Wang Tiejun , Dunn Martin L. , Qi H. Jerry 
Published: April 2016

AbstractThe creation of reversibly-actuating components that alter their shapes in a controllable manner in response to environmental stimuli is a grand challenge in active materials, structures, and robotics. Here we demonstrate a new reversible shape-changing component design concept enabled by 3D printing two stimuli responsive polymers—shape memory polymers and hydrogels—in prescribed 3D architectures. This approach uses the swelling of a hydrogel as the driving force for the shape change, and the temperature-dependent modulus of a shape memory polymer to regulate the time of such shape change. Controlling the temperature and aqueous environment allows switching between two stable configurations – the structures are relatively stiff and can carry load in each – without any mechanical loading and unloading. Specific shape changing scenarios, e.g., based on bending, or twisting in prescribed directions, are enabled via the controlled interplay between the active materials and the 3D printed architectures. The physical phenomena are complex and nonintuitive, and so to help understand the interplay of geometric, material, and environmental stimuli parameters we develop 3D nonlinear finite element models. Finally, we create several 2D and 3D shape changing components that demonstrate the role of key parameters and illustrate the broad application potential of the proposed approach.
The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater
Authors: Cui You-Wei , Zhang Hong-Yu , Ding Jie-Ran , Peng Yong-Zhen 
Published: April 2016

AbstractWith annual increases in the generation and use of saline wastewater, the need to avoid environmental problems such as eutrophication is critical. A previous study identified ways to start up a halophilic sludge domesticated from estuarine sediments to remove nitrogen from wastewater with a salinity of 30 g/L. This investigation expands that work to explore the impact of salinity on nitrogen removal. This study demonstrated that the mixed halophilic consortia removed nitrogen from wastewater with a salinity of 30–85 g/L. A kinetic analysis showed that halophilic nitrifiers selected based on hypersalinity were characterized by low Ks, μmax and specific ammonium oxidization rates. This explains the decrease in ammonium removal efficiency in the high salinity operational phases. Salinity inhibited ammonia oxidizing bacteria (AOB) activity, as well as the number of dominant AOB, but did not significantly affect the AOB dominant species. Three most dominant AOB lineages in the halophilic sludge were Nitrosomonas marina, Nitrosomonas europaea, and Nitrosococcus mobilis. Nitrosomonas europaea and Nitrosococcus mobilis were mainly affected by salinity, while nitrite accumulation and ammonia loading played the key role in determining the abundance of Nitrosococcus mobilis and Nitrosococcus europaea. The study contributes insights about shifts in halophilic nitrifying bacterial populations.
Identifying Reproducible Molecular Biomarkers for Gastric Cancer Metastasis with the Aid of Recurrence Information
Authors: Li Mengyao , Hong Guini , Cheng Jun , Li Jing , Cai Hao , Li Xiangyu , Guan Qingzhou , Tong Mengsha , Li Hongdong , Guo Zheng 
Published: April 2016

AbstractTo precisely diagnose metastasis state is important for tailoring treatments for gastric cancer patients. However, the routinely employed radiological and pathologic tests for tumour metastasis have considerable high false negative rates, which may retard the identification of reproducible metastasis-related molecular biomarkers for gastric cancer. In this research, using three datasets, we firstly shwed that differentially expressed genes (DEGs) between metastatic tissue samples and non-metastatic tissue samples could hardly be reproducibly detected with a proper statistical control when the metastatic and non-metastatic samples were defined by TNM stage alone. Then, assuming that undetectable micrometastases are the prime cause for recurrence of early stage patients with curative resection, we reclassified all the “non-metastatic” samples as metastatic samples whenever the patients experienced tumour recurrence during follow-up after tumour resection. In this way, we were able to find distinct and reproducible DEGs between the reclassified metastatic and non-metastatic tissue samples and concordantly significant DNA methylation alterations distinguishing metastatic tissues and non-metastatic tissues of gastric cancer. Our analyses suggested that the follow-up recurrence information for patients should be employed in the research of tumour metastasis in order to decrease the confounding effects of false non-metastatic samples with undetected micrometastases.
1,25(OH)2D3 dependent overt hyperactivity phenotype in klotho-hypomorphic mice
Authors: Leibrock Christina B. , Voelkl Jakob , Kuro-o Makoto , Lang Florian , Lang Undine E 
Published: April 2016

AbstractKlotho, a protein mainly expressed in kidney and cerebral choroid plexus, is a powerful regulator of 1,25(OH)2D3 formation. Klotho-deficient mice (kl/kl) suffer from excessive plasma 1,25(OH)2D3-, Ca2+- and phosphate-concentrations, leading to severe soft tissue calcification and accelerated aging. NH4Cl treatment prevents tissue calcification and premature ageing without affecting 1,25(OH)2D3-formation. The present study explored the impact of excessive 1,25(OH)2D3 formation in NH4Cl-treated kl/kl-mice on behavior. To this end kl/kl-mice and wild-type mice were treated with NH4Cl and either control diet or vitamin D deficient diet (LVD). As a result, plasma 1,25(OH)2D3-, Ca2+- and phosphate-concentrations were significantly higher in untreated and in NH4Cl-treated kl/kl-mice than in wild-type mice, a difference abrogated by LVD. In each, open field, dark-light box, and O-maze NH4Cl-treated kl/kl-mice showed significantly higher exploratory behavior than untreated wild-type mice, a difference abrogated by LVD. The time of floating in the forced swimming test was significantly shorter in NH4Cl treated kl/kl-mice compared to untreated wild-type mice and to kl/kl-mice on LVD. In wild-type animals, NH4Cl treatment did not significantly alter 1,25(OH)2D3, calcium and phosphate concentrations or exploratory behavior. In conclusion, the excessive 1,25(OH)2D3 formation in klotho-hypomorphic mice has a profound effect on murine behavior.
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors
Authors: Meng Hengkai , Liu Pi , Sun Hongbing , Cai Zhen , Zhou Jie , Lin Jianping , Li Yin 
Published: April 2016

AbstractEngineering the cofactor specificity of a natural enzyme often results in a significant decrease in its activity on original cofactor. Here we report that a NADH-dependent dehydrogenase (d-LDH) from Lactobacillus delbrueckii 11842 can be rationally engineered to efficiently use both NADH and NADPH as cofactors. Point mutations on three amino acids (D176S, I177R, F178T) predicted by computational analysis resulted in a modified enzyme designated as d-LDH*. The Kcat/Km of the purified d-LDH* on NADPH increased approximately 184-fold while the Kcat/Km on NADH also significantly increased, showing for the first time that a rationally engineered d-LDH could exhibit comparable activity on both NADPH and NADH. Further kinetic analysis revealed that the enhanced affinity with NADH or NADPH and the significant increased Kcat of d-LDH* resulted in the significant increase of d-LDH* activity on both NADPH and NADH. This study thus demonstrated that the cofactor specificity of dehydrogenase can be broadened by using targeted engineering approach, and the engineered enzyme can efficiently function in NADH-rich, or NADPH-rich, or NADH and NADPH-rich environment.
Amplitude dynamics favors synchronization in complex networks
Authors: Gambuzza Lucia Valentina , Gómez-Gardeñes Jesus , Frasca Mattia 
Published: April 2016

AbstractIn this paper we study phase synchronization in random complex networks of coupled periodic oscillators. In particular, we show that, when amplitude dynamics is not negligible, phase synchronization may be enhanced. To illustrate this, we compare the behavior of heterogeneous units with both amplitude and phase dynamics and pure (Kuramoto) phase oscillators. We find that in small network motifs the behavior crucially depends on the topology and on the node frequency distribution. Surprisingly, the microscopic structures for which the amplitude dynamics improves synchronization are those that are statistically more abundant in random complex networks. Thus, amplitude dynamics leads to a general lowering of the synchronization threshold in arbitrary random topologies. Finally, we show that this synchronization enhancement is generic of oscillators close to Hopf bifurcations. To this aim we consider coupled FitzHugh-Nagumo units modeling neuron dynamics.
Kaempferol stimulates gene expression of low-density lipoprotein receptor through activation of Sp1 in cultured hepatocytes
Authors: Ochiai Ayasa , Miyata Shingo , Iwase Masamori , Shimizu Makoto , Inoue Jun , Sato Ryuichiro 
Published: April 2016

AbstractA high level of plasma low-density lipoprotein (LDL) cholesterol is considered a risk factor for atherosclerosis. Because the hepatic LDL receptor (LDLR) is essential for clearing plasma LDL cholesterol, activation of LDLR is a promising therapeutic target for patients with atherosclerotic disease. Here we demonstrated how the flavonoid kaempferol stimulated the gene expression and activity of LDLR in HepG2 cells. The kaempferol-mediated stimulation of LDLR gene expression was completely inhibited by knockdown of Sp1 gene expression. Treatment of HepG2 cells with kaempferol stimulated the recruitment of Sp1 to the promoter region of the LDLR gene, as well as the phosphorylation of Sp1 on Thr-453 and Thr-739. Moreover, these kaempferol-mediated processes were inhibited in the presence of U0126, an ERK pathway inhibitor. These results suggest that kaempferol may increase the activity of Sp1 through stimulation of Sp1 phosphorylation by ERK1/2 and subsequent induction of LDLR expression and activity.
Optimized 2D array of thin silicon pillars for efficient antireflective coatings in the visible spectrum
Authors: Proust Julien , Fehrembach Anne-Laure , Bedu Frédéric , Ozerov Igor , Bonod Nicolas 
Published: April 2016

AbstractLight reflection occuring at the surface of silicon wafers is drastically diminished by etching square pillars of height 110 nm and width 140 nm separated by a 100 nm gap distance in a square lattice. The design of the nanostructure is optimized to widen the spectral tolerance of the antireflective coatings over the visible spectrum for both fundamental polarizations. Angle and polarized resolved optical measurements report a light reflection remaining under 5% when averaged in the visible spectrum for both polarizations in a wide angular range. Light reflection remains almost insensitive to the light polarization even in oblique incidence.
Identification of residues crucial for the interaction between human neuroglobin and the α-subunit of heterotrimeric Gi protein
Authors: Takahashi Nozomu , Wakasugi Keisuke 
Published: April 2016

AbstractMammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. We previously showed that human Ngb acts as a guanine nucleotide dissociation inhibitor (GDI) for the α-subunits of heterotrimeric Gi/o proteins and inhibits the decrease in cAMP concentration, leading to protection against cell death. In the present study, we used an eukaryotic expression vector driving high-level expression of human wild-type Ngb or Ngb mutants that either exhibit or lack GDI activities in human cells. We demonstrate that the GDI activity of human Ngb is tightly correlated with its neuroprotective activity. We further demonstrate that Glu53, Glu60 and Glu118 of human Ngb are crucial for both the neuroprotective activity and interaction with Gαi1. Moreover, we show that Lys46, Lys70, Arg208, Lys209 and Lys210 residues of Gαi1 are important for binding to human Ngb. We propose a molecular docking model of the complex between human Ngb and Gαi1.
What does the nose know? Olfactory function predicts social network size in human
Authors: Zou Lai-quan , Yang Zhuo-ya , Wang Yi , Lui Simon S. Y. , Chen An-tao , Cheung Eric F. C. , Chan Raymond C. K. 
Published: April 2016

AbstractOlfaction is an important medium of social communication in humans. However, it is not known whether olfactory function is associated with social network size. This study aimed to explore the underlying neural mechanism between olfactory function and social network. Thirty-one healthy individuals participated in this study. Social network size was estimated using the Social Network Index. Olfactory function was assessed with the Sniffin’ Stick Test. The results showed that there is a significant positive correlation between the size of an individual’s social network and their olfactory sensitivity. We also found that amygdala functional connectivity with the orbitofrontal cortex appeared to be related to olfactory sensitivity and social network size.