bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted matrisome analysis identifies thrombospondin-2 and tenascin-C in aligned collagen stroma from invasive breast carcinoma
Authors: Tomko Lucas A. , Hill Ryan C. , Barrett Alexander , Szulczewski Joseph M. , Conklin Matthew W. , Eliceiri Kevin W. , Keely Patricia J. , Hansen Kirk C. , Ponik Suzanne M. 
Published: August 2018

AbstractIncreasing evidence demonstrates an important role for the extracellular matrix (ECM) in breast cancer progression. Collagen type I, a core constituent of the fibrous ECM, undergoes a significant set of changes that accompany tumor progression, termed Tumor Associated Collagen Signatures (TACS). Late stages of this progression are characterized by the presence of bundled, straight collagen (TACS-2) that become oriented perpendicular to the tumor-stromal boundary (TACS-3). Importantly, the presence of TACS-3 collagen is an independent predictor of poor patient outcome. At present, it remains unclear whether reorganization of the collagen matrix is the consequence of mechanical or compositional tissue remodeling. Here, we identify compositional changes in ECM correlating to collagen fiber reorganization from nineteen normal and invasive ductal carcinoma (IDC) patient biopsies using matrisome-targeted proteomics. Twenty-seven ECM proteins were significantly altered in IDC samples compared to normal tissue. Further, a set of nineteen matrisome proteins positively correlate and five proteins inversely correlate with IDC tissues containing straightened collagen fibers. Tenascin-C and thrombospondin-2 significantly co-localized with aligned collagen fibers in IDC tissues. This study highlights the compositional change in matrisome proteins accompanying collagen re-organization during breast cancer progression and provides candidate proteins for investigation into cellular and structural influences on collagen alignment.
On the exact continuous mapping of fermions
Authors: Montoya-Castillo Andrés , Markland Thomas E. 
Published: August 2018

AbstractWe derive a rigorous, quantum mechanical map of fermionic creation and annihilation operators to continuous Cartesian variables that exactly reproduces the matrix structure of the many-fermion problem. We show how our scheme can be used to map a general many-fermion Hamiltonian and then consider two specific models that encode the fundamental physics of many fermionic systems, the Anderson impurity and Hubbard models. We use these models to demonstrate how efficient mappings of these Hamiltonians can be constructed using a judicious choice of index ordering of the fermions. This development provides an alternative exact route to calculate the static and dynamical properties of fermionic systems and sets the stage to exploit the quantum-classical and semiclassical hierarchies to systematically derive methods offering a range of accuracies, thus enabling the study of problems where the fermionic degrees of freedom are coupled to complex anharmonic nuclear motion and spins which lie beyond the reach of most currently available methods.
A novel molecular rotor facilitates detection of p53-DNA interactions using the Fluorescent Intercalator Displacement Assay
Authors: Goh Walter L. , Lee Min Yen , Lim Ting Xiang , Chua Joy S. , Brenner Sydney , Ghadessy Farid J. , Teo Yin Nah 
Published: August 2018

AbstractWe have investigated the use of fluorescent molecular rotors as probes for detection of p53 binding to DNA. These are a class of fluorophores that undergo twisted intramolecular charge transfer (TICT). They are non-fluorescent in a freely rotating conformation and experience a fluorescence increase when restricted in the planar conformation. We hypothesized that intercalation of a molecular rotor between DNA base pairs would result in a fluorescence turn-on signal. Upon displacement by a DNA binding protein, measurable loss of signal would facilitate use of the molecular rotor in the fluorescent intercalator displacement (FID) assay. A panel of probes was interrogated using the well-established p53 model system across various DNA response elements. A novel, readily synthesizable molecular rotor incorporating an acridine orange DNA intercalating group (AO-R) outperformed other conventional dyes in the FID assay. It enabled relative measurement of p53 sequence-specific DNA interactions and study of the dominant-negative effects of cancer-associated p53 mutants. In a further application, AO-R also proved useful for staining apoptotic cells in live zebrafish embryos.
Roles of Joule heating and spin-orbit torques in the direct current induced magnetization reversal
Authors: Li Dong , Chen Shiwei , Zuo Yalu , Yun Jijun , Cui Baoshan , Wu Kai , Guo Xiaobin , Yang Dezheng , Wang Jianbo , Xi Li 
Published: August 2018

AbstractCurrent-induced magnetization reversal via spin-orbit torques (SOTs) has been intensively studied in heavy-metal/ferromagnetic-metal/oxide heterostructures due to its promising application in low-energy consumption logic and memory devices. Here, we systematically study the function of Joule heating and SOTs in the current-induced magnetization reversal using Pt/Co/SmOx and Pt/Co/AlOx structures with different perpendicular magnetic anisotropies (PMAs). The SOT-induced effective fields, anisotropy field, switching field and switching current density (Jc) are characterized using electric transport measurements based on the anomalous Hall effect and polar magneto-optical Kerr effect (MOKE). The results show that the current-generated Joule heating plays an assisted role in the reversal process by reducing switching field and enhancing SOT efficiency. The out-of-plane component of the damping-like-SOT effective field is responsible for the magnetization reversal. The obtained Jc for Pt/Co/SmOx and Pt/Co/AlOx structures with similar spin Hall angles and different PMAs remains roughly constant, revealing that the coherent switching model cannot fully explain the current-induced magnetization reversal. In contrast, by observing the domain wall nucleation and expansion using MOKE and comparing the damping-like-SOT effective field and switching field, we conclude that the current-induced magnetization reversal is dominated by the depinning model and Jc also immensely relies on the depinning field.
Dynamic expression of HOPX in alveolar epithelial cells reflects injury and repair during the progression of pulmonary fibrosis
Authors: Ota Chiharu , Ng-Blichfeldt John-Poul , Korfei Martina , Alsafadi Hani N. , Lehmann Mareike , Skronska-Wasek Wioletta , M. De Santis Martina , Guenther Andreas , Wagner Darcy E. , Königshoff Melanie 
Published: August 2018

AbstractMechanisms of injury and repair in alveolar epithelial cells (AECs) are critically involved in the progression of various lung diseases including idiopathic pulmonary fibrosis (IPF). Homeobox only protein x (HOPX) contributes to the formation of distal lung during development. In adult lung, alveolar epithelial type (AT) I cells express HOPX and lineage-labeled Hopx+ cells give rise to both ATI and ATII cells after pneumonectomy. However, the cell function of HOPX-expressing cells in adult fibrotic lung diseases has not been investigated. In this study, we have established a flow cytometry-based method to evaluate HOPX-expressing cells in the lung. HOPX expression in cultured ATII cells increased over culture time, which was accompanied by a decrease of proSP-C, an ATII marker. Moreover, HOPX expression was increased in AECs from bleomycin-instilled mouse lungs in vivo. Small interfering RNA-based knockdown of Hopx resulted in suppressing ATII-ATI trans-differentiation and activating cellular proliferation in vitro. In IPF lungs, HOPX expression was decreased in whole lungs and significantly correlated to a decline in lung function and progression of IPF. In conclusion, HOPX is upregulated during early alveolar injury and repair process in the lung. Decreased HOPX expression might contribute to failed regenerative processes in end-stage IPF lungs.
Colorimetric Aptasensor of Vitamin D3: A Novel Approach to Eliminate Residual Adhesion between Aptamers and Gold Nanoparticles
Authors: Alsager Omar A. , Alotaibi Khalid M. , Alswieleh Abdullah M. , Alyamani Baraa J. 
Published: August 2018

AbstractColorimetric aptasensors based on gold nanoparticles (AuNPs) commonly feature ssDNA probes nonspecifically adsorbed to surface gold particles. A major limitation of this versatile method is the incomplete dissociation of the adsorbed nontarget binding segments of the aptamer sequence upon target binding. This results in weak or nonexistent sensor performance by preventing the particles from aggregating when the optimized salt concentration is added. Rather than removing the nonbinding nucleotides flanking the binding region of the aptamer, proposed herein is an alternative strategy, simply introducing a centrifugation and resuspension step after target recognition that eliminates residual binding between the aptamer and the surface of the particles. The performance of two different vitamin D3 (VTD3) aptamers were tested. The method enhanced the performance of the sensor that used the higher detection limit (1 µM) aptamer by fourfold. The superiority of the proposed method became apparent in a nonworking colorimetric sensor became a highly sensitive sensor with a one nanomolar detection level and excellent discrimination against potential interfering molecules including VTD2 when the centrifugation and resuspension process was implemented. The level of VTD3 in human blood was determined colorimetrically after extraction with n-hexane. The results were in agreement with those obtained by HPLC. The proposed method could be applied to aptamers targeting small molecules with no need to reprocess the SELEX-isolated sequence by knowing the binding region and removing the flanking primers.
Neural Representations Behind ‘Social Norm’ Inferences In Humans
Authors: Pegado Felipe , Hendriks Michelle H. A. , Amelynck Steffie , Daniels Nicky , Bulthé Jessica , Masson Haemy Lee , Boets Bart , de Beeck Hans Op 
Published: August 2018

AbstractHumans are highly skilled in social reasoning, e.g., inferring thoughts of others. This mentalizing ability systematically recruits brain regions such as Temporo-Parietal Junction (TPJ), Precuneus (PC) and medial Prefrontal Cortex (mPFC). Further, posterior mPFC is associated with allocentric mentalizing and conflict monitoring while anterior mPFC is associated with self-reference (egocentric) processing. Here we extend this work to how we reason not just about what one person thinks but about the abstract shared social norm. We apply functional magnetic resonance imaging to investigate neural representations while participants judge the social congruency between emotional auditory utterances in relation to visual scenes according to how ‘most people’ would perceive it. Behaviorally, judging according to a social norm increased the similarity of response patterns among participants. Multivoxel pattern analysis revealed that social congruency information was not represented in visual and auditory areas, but was clear in most parts of the mentalizing network: TPJ, PC and posterior (but not anterior) mPFC. Furthermore, interindividual variability in anterior mPFC representations was inversely related to the behavioral ability to adjust to the social norm. Our results suggest that social norm inferencing is associated with a distributed and partially individually specific representation of social congruency in the mentalizing network.
Multifunctional Nanotherapeutics for the Treatment of neuroAIDS in Drug Abusers
Authors: Jayant Rahul Dev , Tiwari Sneham , Atluri Venkata , Kaushik Ajeet , Tomitaka Asahi , Yndart Adriana , Colon-Perez Luis , Febo Marcelo , Nair Madhavan 
Published: August 2018

AbstractHIV and substance abuse plays an important role in infection and disease progression. Further, the presence of persistent viral CNS reservoirs makes the complete eradication difficult. Thus, neutralizing the drug of abuse effect on HIV-1 infectivity and elimination of latently infected cells is a priority. The development of a multi-component [antiretroviral drugs (ARV), latency reactivating agents (LRA) and drug abuse antagonist (AT)] sustained release nanoformulation targeting the CNS can overcome the issues of HIV-1 cure and will help in improving the drug adherence. The novel magneto-liposomal nanoformulation (NF) was developed to load different types of drugs (LRAs, ARVs, and Meth AT) and evaluated forin-vitro and in-vivoBBB transmigration and antiviral efficacy in primary CNS cells. We established the HIV-1 latency model using human astrocyte cells (HA) and optimized the dose of LRA for latency reversal, Meth AT inin-vitrocell culture system. Further, PEGylated magneto-liposomal NF was developed, characterized for size, shape, drug loading and BBB transportin-vitro. Results showed that drug released in a sustained manner up to 10 days and able to reduce the HIV-1 infectivity up to ~40–50% (>200 pg/mL to <100 pg/mL) continuously using single NF treatment ± Meth treatmentin-vitro. The magnetic treatment (0.8 T) was able to transport (15.8% ± 5.5%) NF effectively without inducing any toxic effects due to NF presence in the brain. Thus, our approach and result showed a way to eradicate HIV-1 reservoirs from the CNS and possibility to improve the therapeutic adherence to drugs in drug abusing (Meth) population. In conclusion, the developed NF can provide a better approach for the HIV-1 cure and a foundation for future HIV-1 purging strategies from the CNS using nanotechnology platform.
Identification and expression analysis of putative chemoreception genes from Cyrtorhinus lividipennis (Hemiptera: Miridae) antennal transcriptome
Authors: Wang Gui-Yao , Zhu Jing-Lei , Zhou Wen-Wu , Liu Su , Khairul Quais Md , Ansari Naved Ahmad , Zhu Zeng-Rong 
Published: August 2018

AbstractCyrtorhinus lividipennis Reuter (Hemiptera: Miridae) is an important egg predator of planthoppers which are destructive rice pests. The chemosensory genes in the mirid antennae play important roles in mating and prey-seeking behaviors. To gain a better understanding of the olfaction of C. lividipennis, we sequenced the antennal transcriptomes of the predator to identify the key olfaction genes. We identified 18 odorant binding proteins (OBPs), 12 chemosensory proteins (CSPs), 1 Niemann-Pick C2 protein (NPC2), 15 odorant receptors (ORs), 6 ionotropic receptors (IRs), 3 gustatory receptors (GRs) and 3 sensory neuron membrane proteins (SNMPs). Quantitative real-time PCR results showed that the relative transcript levels of three ClivORs (ClivOR6, 7 and 14) in the female antennae were 3 to 6 folds higher than that in the male antennae, indicating these genes were more related to oviposition site selection. The relative transcript levels of ClivCSP8 and ClivOR11 were 2.6 and 2.7 times higher in the male antennae than that of the female, respectively, indicating that these genes might be involved in mate searching. Moreover, the responses of dsorco treated predators to volatiles emitted from infested rice were significantly reduced, indicating these volatiles might serve as crucial cues in the host searching of C. lividipennis.
Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation
Authors: Yurchenko Andrey A. , Daetwyler Hans D. , Yudin Nikolay , Schnabel Robert D. , Vander Jagt Christy J. , Soloshenko Vladimir , Lhasaranov Bulat , Popov Ruslan , Taylor Jeremy F. , Larkin Denis M. 
Published: August 2018

AbstractDomestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
Complement regulatory protein CD46 induces autophagy against oxidative stress-mediated apoptosis in normal and asthmatic airway epithelium
Authors: Tsai Yi-Giien , Wen Yung-Sung , Wang Jiu-Yao , Yang Kuender D. , Sun Hai-Lun , Liou Jia-Hung , Lin Ching-Yuang 
Published: August 2018

AbstractAutophagy plays a major role in defending against oxidative stress in respiratory epithelial cells. The complement regulatory protein CD46 can enhance autophagy and decrease local complement activation at sites of inflammation. This study investigated the mechanism by which CD46 protects against oxidative stress-mediated apoptosis in respiratory epithelium in asthmatic patients. Nasal mucosa samples were obtained from 60 adults with mild asthma who received turbinectomy and 30 controls. A decreased expression of CD46 and increased apoptosis were noted in the damaged nasal epithelium from the asthmatic patients. Primary epithelial cells cultured with Dermatophagoides pteronyssinus 2 showed decreased CD46 and increased cleaved CASPASE-3A expressions. Crosslinking CD46 mAb could induce the formation of autophagosomes and LC3-II expression in primary epithelial cells. CD46 engagement could induce autophagy against hydrogen peroxide-induced epithelial cell death, whereas the autophagy inhibitor 3-methyladenine decreased this effect. In addition, CD46 engagement decreased the expressions of PRO-IL-1β and NLRP3, enhanced the expression of scaffold protein GOPC, and diminished hydrogen peroxide-induced 8-OHdG, IL-1β and IL-6 production. Silencing ATG5 in human lung epithelial A549 cells decreased CD46-activated autophagy with LC3-II. CD46 induced autophagy and decreased the oxidative stress-mediated apoptosis of respiratory epithelium, and this may offer a new therapeutic strategy to treat asthma.
Metabotropic Acetylcholine and Glutamate Receptors Mediate PI(4,5)P2 Depletion and Oscillations in Hippocampal CA1 Pyramidal Neurons in situ
Authors: Hackelberg Sandra , Oliver Dominik 
Published: August 2018

AbstractThe sensitivity of many ion channels to phosphatidylinositol-4,5-bisphosphate (PIP2) levels in the cell membrane suggests that PIP2 fluctuations are important and general signals modulating neuronal excitability. Yet the PIP2 dynamics of central neurons in their native environment remained largely unexplored. Here, we examined the behavior of PIP2 concentrations in response to activation of Gq-coupled neurotransmitter receptors in rat CA1 hippocampal neurons in situ in acute brain slices. Confocal microscopy of the PIP2-selective molecular sensors tubbyCT-GFP and PLCδ1-PH-GFP showed that pharmacological activation of muscarinic acetylcholine (mAChR) or group I metabotropic glutamate (mGluRI) receptors induces transient depletion of PIP2 in the soma as well as in the dendritic tree. The observed PIP2 dynamics were receptor-specific, with mAChR activation inducing stronger PIP2 depletion than mGluRI, whereas agonists of other Gαq-coupled receptors expressed in CA1 neurons did not induce measureable PIP2 depletion. Furthermore, the data show for the first time neuronal receptor-induced oscillations of membrane PIP2 concentrations. Oscillatory behavior indicated that neurons can rapidly restore PIP2 levels during persistent activation of Gq and PLC. Electrophysiological responses to receptor activation resembled PIP2 dynamics in terms of time course and receptor specificity. Our findings support a physiological function of PIP2 in regulating electrical activity.
Effect of alloy element on weld pool dynamics in laser welding of aluminum alloys
Authors: Miyagi Masanori , Wang Hongze , Yoshida Ryohei , Kawahito Yousuke , Kawakami Hiroshi , Shoubu Takahisa 
Published: August 2018

AbstractIn this manuscript, weld pool dynamics in laser welding of various series of aluminum alloys were investigated by the in situ X-ray phase contrast imaging system. The experimental results showed that metal irradiated by laser was evaporated immediately, which generated the keyhole. Then metal surrounding the keyhole was melted gradually with the heat from keyhole. The growth rate of keyhole depth had a positive linear correlation with the total content of low boiling temperature elements (TCE), so did the keyhole depth and diameter at the stable stage. Longitudinal view area of the molten pool had a negative linear correlation with the thermal conductivity of aluminum alloy. The measured laser absorption rate had the same variation trend with the ratio of keyhole depth to diameter, and the highest absorption rate of 58% appeared in laser welding of aluminum alloy with TCE equal to 2.1%. Violent fluctuation in keyhole shape was avoided in aluminum alloy with TCE lower than 2.1%, where the surface tension and recoil pressure of metal vapor were balanced. To sum up, the effect of alloy element on weld pool dynamics in laser welding of aluminum alloys was firstly quantified in this manuscript.
Seaweed assemblages under a climate change scenario: Functional responses to temperature of eight intertidal seaweeds match recent abundance shifts
Authors: Piñeiro-Corbeira Cristina , Barreiro Rodolfo , Cremades Javier , Arenas Francisco 
Published: August 2018

AbstractField evidence is essential to assess the consequences of climate change but a solid causal link often requires additional information obtained under controlled laboratory conditions. Additionally, the functional response to temperature may also help to discriminate species potentially more vulnerable to warming. Using a highly resolved temperature gradient, we examined the temperature dependence of photosynthesis and respiration in eight intertidal seaweeds that recently followed opposite abundance trends in NW Iberia. The temperature dependence of photosynthesis was consistently different between the macroalgae that increased and those that decreased their abundance in the last decade and a half, with photosynthesis twice more sensitive in the upward group. Unlike photosynthesis, the temperature dependence of respiration was unrelated to the abundance trend group, implying that the net metabolic scaling with temperature varied between the two groups of seaweeds. Overall, our results provide experimental support to the role of temperate as a likely driver of the changes in abundance recorded by field-monitoring studies. They also suggest that the temperature dependence of photosynthesis and respiration assessed in short-term experiments may serve as a biomarker of the potential vulnerability of some seaweed to the consequences of water warming.