bluuebunny/crossref_metadata_2025_split huggingface dataset:
A higher order visual neuron tuned to the spatial amplitude spectra of natural scenes
Authors: Dyakova Olga , Lee Yu-Jen , Longden Kit D. , Kiselev Valerij G. , Nordström Karin 
Published: October 2015

AbstractAnimal sensory systems are optimally adapted to those features typically encountered in natural surrounds, thus allowing neurons with limited bandwidth to encode challengingly large input ranges. Natural scenes are not random, and peripheral visual systems in vertebrates and insects have evolved to respond efficiently to their typical spatial statistics. The mammalian visual cortex is also tuned to natural spatial statistics, but less is known about coding in higher order neurons in insects. To redress this we here record intracellularly from a higher order visual neuron in the hoverfly. We show that the cSIFE neuron, which is inhibited by stationary images, is maximally inhibited when the slope constant of the amplitude spectrum is close to the mean in natural scenes. The behavioural optomotor response is also strongest to images with naturalistic image statistics. Our results thus reveal a close coupling between the inherent statistics of natural scenes and higher order visual processing in insects.
Quantifying the stabilizing effects of protein–ligand interactions in the gas phase
Authors: Allison Timothy M. , Reading Eamonn , Liko Idlir , Baldwin Andrew J. , Laganowsky Arthur , Robinson Carol V. 
Published: October 2015

AbstractThe effects of protein–ligand interactions on protein stability are typically monitored by a number of established solution-phase assays. Few translate readily to membrane proteins. We have developed an ion-mobility mass spectrometry approach, which discerns ligand binding to both soluble and membrane proteins directly via both changes in mass and ion mobility, and assesses the effects of these interactions on protein stability through measuring resistance to unfolding. Protein unfolding is induced through collisional activation, which causes changes in protein structure and consequently gas-phase mobility. This enables detailed characterization of the ligand-binding effects on the protein with unprecedented sensitivity. Here we describe the method and software required to extract from ion mobility data the parameters that enable a quantitative analysis of individual binding events. This methodology holds great promise for investigating biologically significant interactions between membrane proteins and both drugs and lipids that are recalcitrant to characterization by other means.
Acidic phospholipids govern the enhanced activation of IgG-B cell receptor
Authors: Chen Xiangjun , Pan Weiling , Sui Yinqiang , Li Hua , Shi Xiaoshan , Guo Xingdong , Qi Hai , Xu Chenqi , Liu Wanli 
Published: October 2015

AbstractB cells that express the isotype-switched IgG-B cell receptor (IgG-BCR) are one of the driving forces for antibody memory. To allow for a rapid memory IgG antibody response, IgG-BCR evolved into a highly effective signalling machine. Here, we report that the positively charged cytoplasmic domain of mIgG (mIgG-tail) specifically interacts with negatively charged acidic phospholipids. The key immunoglobulin tail tyrosine (ITT) in mIgG-tail is thus sequestered in the membrane hydrophobic core in quiescent B cells. Pre-disruption of such interaction leads to excessive recruitment of BCRs and inflated BCR signalling upon antigen stimulation, resulting in hyperproliferation of primary B cells. Physiologically, membrane-sequestered mIgG-tail can be released by antigen engagement or Ca2+ mobilization in the initiation of B cell activation. Our studies suggest a novel regulatory mechanism for how dynamic association of mIgG-tail with acidic phospholipids governs the enhanced activation of IgG-BCR.
Charge-transfer crystallites as molecular electrical dopants
Authors: Méndez Henry , Heimel Georg , Winkler Stefanie , Frisch Johannes , Opitz Andreas , Sauer Katrein , Wegner Berthold , Oehzelt Martin , Röthel Christian , Duhm Steffen , Többens Daniel , Koch Norbert , Salzmann Ingo 
Published: October 2015

AbstractGround-state integer charge transfer is commonly regarded as the basic mechanism of molecular electrical doping in both, conjugated polymers and oligomers. Here, we demonstrate that fundamentally different processes can occur in the two types of organic semiconductors instead. Using complementary experimental techniques supported by theory, we contrast a polythiophene, where molecular p-doping leads to integer charge transfer reportedly localized to one quaterthiophene backbone segment, to the quaterthiophene oligomer itself. Despite a comparable relative increase in conductivity, we observe only partial charge transfer for the latter. In contrast to the parent polymer, pronounced intermolecular frontier-orbital hybridization of oligomer and dopant in 1:1 mixed-stack co-crystallites leads to the emergence of empty electronic states within the energy gap of the surrounding quaterthiophene matrix. It is their Fermi–Dirac occupation that yields mobile charge carriers and, therefore, the co-crystallites—rather than individual acceptor molecules—should be regarded as the dopants in such systems.
Nanometer-size hard magnetic ferrite exhibiting high optical-transparency and nonlinear optical-magnetoelectric effect
Authors: Ohkoshi Shin-ichi , Namai Asuka , Imoto Kenta , Yoshikiyo Marie , Tarora Waka , Nakagawa Kosuke , Komine Masaya , Miyamoto Yasuto , Nasu Tomomichi , Oka Syunsuke , Tokoro Hiroko 
Published: October 2015

AbstractDevelopment of nanometer-sized magnetic particles exhibiting a large coercive field (Hc) is in high demand for densification of magnetic recording. Herein, we report a single-nanosize (i.e., less than ten nanometers across) hard magnetic ferrite. This magnetic ferrite is composed of ε-Fe2O3, with a sufficiently high Hc value for magnetic recording systems and a remarkably high magnetic anisotropy constant of 7.7 × 106 erg cm−3. For example, 8.2-nm nanoparticles have an Hc value of 5.2 kOe at room temperature. A colloidal solution of these nanoparticles possesses a light orange color due to a wide band gap of 2.9 eV (430 nm), indicating a possibility of transparent magnetic pigments. Additionally, we have observed magnetization-induced second harmonic generation (MSHG). The nonlinear optical-magnetoelectric effect of the present polar magnetic nanocrystal was quite strong. These findings have been demonstrated in a simple iron oxide, which is highly significant from the viewpoints of economic cost and mass production.
Characterization of aggregate/aggresome structures formed by polyhedrin of Bombyx mori nucleopolyhedrovirus
Authors: Guo Zhong-Jian , Tao Liu-Xing , Dong Xian-Yun , Yu Meng-Han , Tian Ting , Tang Xu-Dong 
Published: October 2015

AbstractVirus infections often lead to formation of aggregates and aggresomes in host cells. In this study, production of aggregates and aggresomes by the highly expressed protein polyhedrin of Bombyx mori nucleopolyhedrovirus (BmNPV) at 24 h postinfection (p.i.) was detected with a fluorescent molecular dye and verified by colocalization of polyhedrin with aggresomal markers, GFP-250 and γ−tubulin. Polyhedrin aggregates showed hallmark characteristics of aggresomes: formation was microtubule-dependent; they colocalized with heat shock cognates/proteins of the 70-kDa family (HSC/HSP70s), ubiquitinated proteins and recruited the mitochondria. Aggregated polyhedrin protein gradually gained its active conformation accompanying progress of BmNPV infection. At 48 h p.i. recovered polyhedrin bound directly to Bombyx mori microtubule-associated protein 1-light chain 3 (BmLC3), an autophagosome marker and was colocalized with BmLC3 to the isolation membrane of autophagosome, implying the involvement of polyhedrin in cellular autophagy. Inhibition of autophagy by 3-methyladenine (3-MA) dramatically resulted in decrease of polyhedrin expression and polyhedra particle production. These observations suggested that highly expressed polyhedrin forms aggregate to get involved in cellular autophagy then play an important role in polyhedra production.
Giant Dielectric Permittivity in Ferroelectric Thin Films: Domain Wall Ping Pong
Authors: Quan Jiang An , Jian Meng Xiang , Wei Zhang David , Hyuk Park Min , Yoo Sijung , Jin Kim Yu , Scott James F. , Seong Hwang Cheol 
Published: October 2015

AbstractThe dielectric permittivity in ferroelectric thin films is generally orders of magnitude smaller than in their bulk. Here, we discover a way of increasing dielectric constants in ferroelectric thin films by ca. 500% by synchronizing the pulsed switching fields with the intrinsic switching time (nucleation of domain plus forward growth from cathode to anode). In a 170-nm lead zirconate titanate thin film with an average grain size of 850 nm this produces a dielectric constant of 8200 with the maximum nucleus density of 3.8 μm−2, which is one to three orders of magnitude higher than in other dielectric thin films. This permits smaller capacitors in memory devices and is a step forward in making ferroelectric domain-engineered nano-electronics.
Worldwide Prevalence of Human Papillomavirus and Relative Risk of Prostate Cancer: A Meta-analysis
Authors: Yang Lin , Xie Shuanghua , Feng Xiaoshuang , Chen Yuheng , Zheng Tongzhang , Dai Min , Zhou Cindy Ke , Hu Zhibin , Li Ni , Hang Dong 
Published: October 2015

AbstractDespite the increasing number of studies conducted recently to evaluate the association between HPV infections and the risk of prostate cancer, the results remain inconclusive. Furthermore, the prevalence and distribution of overall and individual HPV types worldwide in prostate cancer has not been reported until now. Therefore, we estimated the prevalence of HPV in prostate cancer by pooling data of 46 studies with 4919 prostate cancer cases, taking into account the heterogeneity of major related parameters, including study region, specimen type, HPV DNA source, detection method, publication calendar period and Gleason score. Moreover, we tested the association of HPV infections with prostate cancer risks by a meta-analysis of 26 tissue-based case-control studies. We found that the prevalence of HPV infection was 18.93% (95% CI = 17.84–20.05%) in prostate cancer cases and most of which were high-risk HPV types (17.73%, 95% CI = 16.52–18.99%). The prevalence varied by region, PCR primers used, publication calendar period and Gleason score. Our study also showed a significantly increased risk of prostate cancer with the positivity of overall HPV detected in prostate tissues (OR = 1.79, 95% CI = 1.29–2.49) and revealed the geographic variation of association strength (P < 0.001). In conclusion, HPV infections may contribute to the risk of prostate cancer.
IL-1β promotes Th17 differentiation by inducing alternative splicing of FOXP3
Authors: Mailer Reiner K. W. , Joly Anne-Laure , Liu Sang , Elias Szabolcs , Tegner Jesper , Andersson John 
Published: October 2015

AbstractCD4+FOXP3+ regulatory T (Treg) cells are essential for maintaining immunological self-tolerance. Treg cell development and function depend on the transcription factor FOXP3, which is present in several distinct isoforms due to alternative splicing. Despite the importance of FOXP3 in the proper maintenance of Treg cells, the regulation and functional consequences of FOXP3 isoform expression remains poorly understood. Here, we show that in human Treg cells IL-1β promotes excision of FOXP3 exon 7. FOXP3 is not only expressed by Treg cells but is also transiently expressed when naïve T cells differentiate into Th17 cells. Forced splicing of FOXP3 into FOXP3Δ2Δ7 strongly favored Th17 differentiation in vitro. We also found that patients with Crohn’s disease express increased levels of FOXP3 transcripts lacking exon 7, which correlate with disease severity and IL-17 production. Our results demonstrate that alternative splicing of FOXP3 modulates T cell differentiation. These results highlight the importance of characterizing FOXP3 expression on an isoform basis and suggest that immune responses may be manipulated by modulating the expression of FOXP3 isoforms, which has broad implications for the treatment of autoimmune diseases.
Size effects in the magnetic anisotropy of embedded cobalt nanoparticles: from shape to surface
Authors: Oyarzún Simón , Tamion Alexandre , Tournus Florent , Dupuis Véronique , Hillenkamp Matthias 
Published: October 2015

AbstractStrong size-dependent variations of the magnetic anisotropy of embedded cobalt clusters are evidenced quantitatively by combining magnetic experiments and advanced data treatment. The obtained values are discussed in the frame of two theoretical models that demonstrate the decisive role of the shape in larger nanoparticles and the predominant role of the surface anisotropy in clusters below 3 nm diameter.
Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra
Authors: Xiao Kaijie , Yu Fan , Fang Houqin , Xue Bingbing , Liu Yan , Tian Zhixin 
Published: October 2015

AbstractIt has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.
Molecular Magnetic Resonance Imaging of Tumor Response to Therapy
Authors: Shuhendler Adam J. , Ye Deju , Brewer Kimberly D. , Bazalova-Carter Magdalena , Lee Kyung-Hyun , Kempen Paul , Dane Wittrup K. , Graves Edward E. , Rutt Brian , Rao Jianghong 
Published: October 2015

AbstractPersonalized cancer medicine requires measurement of therapeutic efficacy as early as possible, which is optimally achieved by three-dimensional imaging given the heterogeneity of cancer. Magnetic resonance imaging (MRI) can obtain images of both anatomy and cellular responses, if acquired with a molecular imaging contrast agent. The poor sensitivity of MRI has limited the development of activatable molecular MR contrast agents. To overcome this limitation of molecular MRI, a novel implementation of our caspase-3-sensitive nanoaggregation MRI (C-SNAM) contrast agent is reported. C-SNAM is triggered to self-assemble into nanoparticles in apoptotic tumor cells and effectively amplifies molecular level changes through nanoaggregation, enhancing tissue retention and spin-lattice relaxivity. At one-tenth the current clinical dose of contrast agent and following a single imaging session, C-SNAM MRI accurately measured the response of tumors to either metronomic chemotherapy or radiation therapy, where the degree of signal enhancement is prognostic of long-term therapeutic efficacy. Importantly, C-SNAM is inert to immune activation, permitting radiation therapy monitoring.
A Nanoparticle-based Sensor Platform for Cell Tracking and Status/Function Assessment
Authors: Yeo David , Wiraja Christian , Chuah Yon Jin , Gao Yu , Xu Chenjie 
Published: October 2015

AbstractNanoparticles are increasingly popular choices for labeling and tracking cells in biomedical applications such as cell therapy. However, all current types of nanoparticles fail to provide real-time, noninvasive monitoring of cell status and functions while often generating false positive signals. Herein, a nanosensor platform to track the real-time expression of specific biomarkers that correlate with cell status and functions is reported. Nanosensors are synthesized by encapsulating various sensor molecules within biodegradable polymeric nanoparticles. Upon intracellular entry, nanosensors reside within the cell cytoplasm, serving as a depot to continuously release sensor molecules for up to 30 days. In the absence of the target biomarkers, the released sensor molecules remain ‘Off’. When the biomarker(s) is expressed, a detectable signal is generated (On). As a proof-of-concept, three nanosensor formulations were synthesized to monitor cell viability, secretion of nitric oxide and β-actin mRNA expression.
Hyperisampsins H–M, Cytotoxic Polycyclic Polyprenylated Acylphloroglucinols from Hypericum sampsonii
Authors: Zhu Hucheng , Chen Chunmei , Tong Qingyi , Chen Xintao , Yang Jing , Liu Junjun , Sun Bin , Wang Jianping , Yao Guangmin , Luo Zengwei , Xue Yongbo , Zhang Yonghui 
Published: October 2015

AbstractSix new polycyclic polyprenylated acylphloroglucinols (PPAPs), named hyperisampsins H–M (1–6), were isolated from the aerial parts of Hypericum sampsonii, together with five known analogs (7–11). The structures of 1–6 were established by extensive spectroscopic analyses, including HRESIMS and NMR. In addition, the absolute configurations of these new compounds were determined by electronic circular dichroism (ECD) calculations. Compounds 1 and 2 represent the first examples of PPAPs possessing a unique γ-lactone ring at C-23, while 3–6 differed from normal PPAPs with an unprecedented 1,2-dioxane ring. Compounds 1–7 were evaluated for their cytotoxic activities against a panel of human cancer cell lines in vitro, of which 3, 4 and 6 exhibited significant cytotoxic activities with IC50 values ranging from 0.56 to 3.00 μM. Moreover, compound 3 induces leukemia cell apoptotic death, evidenced by activation of caspase-3, degradation of PARP, up-regulation of Bax and down-regulation of Bcl-2 and Bcl-xl.
CNOT3 suppression promotes necroptosis by stabilizing mRNAs for cell death-inducing proteins
Authors: Suzuki Toru , Kikuguchi Chisato , Sharma Sahil , Sasaki Toshio , Tokumasu Miho , Adachi Shungo , Natsume Tohru , Kanegae Yumi , Yamamoto Tadashi 
Published: October 2015

AbstractThe CCR4-NOT complex is conserved in eukaryotes and is involved in mRNA metabolism, though its molecular physiological roles remain to be established. We show here that CNOT3-depleted mouse embryonic fibroblasts (MEFs) undergo cell death. Levels of other complex subunits are decreased in CNOT3-depleted MEFs. The death phenotype is rescued by introduction of wild-type (WT), but not mutated CNOT3 and is not suppressed by the pan-caspase inhibitor, zVAD-fluoromethylketone. Gene expression profiling reveals that mRNAs encoding cell death-related proteins, including receptor-interacting protein kinase 1 (RIPK1) and RIPK3, are stabilized in CNOT3-depleted MEFs. Some of these mRNAs bind to CNOT3 and in the absence of CNOT3 their poly(A) tails are elongated. Inhibition of RIPK1-RIPK3 signaling by a short-hairpin RNA or a necroptosis inhibitor, necrostatin-1, confers viability upon CNOT3-depleted MEFs. Therefore, we conclude that CNOT3 targets specific mRNAs to prevent cells from being disposed to necroptotic death.
Mammalian Host-Versus-Phage immune response determines phage fate in vivo
Authors: Hodyra-Stefaniak Katarzyna , Miernikiewicz Paulina , Drapała Jarosław , Drab Marek , Jończyk-Matysiak Ewa , Lecion Dorota , Kaźmierczak Zuzanna , Beta Weronika , Majewska Joanna , Harhala Marek , Bubak Barbara , Kłopot Anna , Górski Andrzej , Dąbrowska Krystyna 
Published: October 2015

AbstractEmerging bacterial antibiotic resistance draws attention to bacteriophages as a therapeutic alternative to treat bacterial infection. Examples of phage that combat bacteria abound. However, despite careful testing of antibacterial activity in vitro, failures nevertheless commonly occur. We investigated immunological response of phage antibacterial potency in vivo. Anti-phage activity of phagocytes, antibodies and serum complement were identified by direct testing and by high-resolution fluorescent microscopy. We accommodated the experimental data into a mathematical model. We propose a universal schema of innate and adaptive immunity impact on phage pharmacokinetics, based on the results of our numerical simulations. We found that the mammalian-host response to infecting bacteria causes the concomitant removal of phage from the system. We propose the notion that this effect as an indirect pathway of phage inhibition by bacteria with significant relevance for the clinical outcome of phage therapy.
Antimicrobial activity of iron oxide nanoparticle upon modulation of nanoparticle-bacteria interface
Authors: Arakha Manoranjan , Pal Sweta , Samantarrai Devyani , Panigrahi Tapan K. , Mallick Bairagi C. , Pramanik Krishna , Mallick Bibekanand , Jha Suman 
Published: October 2015

AbstractInvestigating the interaction patterns at nano-bio interface is a key challenge for safe use of nanoparticles (NPs) to any biological system. The study intends to explore the role of interaction pattern at the iron oxide nanoparticle (IONP)-bacteria interface affecting antimicrobial propensity of IONP. To this end, IONP with magnetite like atomic arrangement and negative surface potential (n-IONP) was synthesized by co-precipitation method. Positively charged chitosan molecule coating was used to reverse the surface potential of n-IONP, i.e. positive surface potential IONP (p-IONP). The comparative data from fourier transform infrared spectroscope, XRD and zeta potential analyzer indicated the successful coating of IONP surface with chitosan molecule. Additionally, the nanocrystals obtained were found to have spherical size with 10–20 nm diameter. The BacLight fluorescence assay, bacterial growth kinetic and colony forming unit studies indicated that n-IONP (<50 μM) has insignificant antimicrobial activity against Bacillus subtilis and Escherichia coli. However, coating with chitosan molecule resulted significant increase in antimicrobial propensity of IONP. Additionally, the assay to study reactive oxygen species (ROS) indicated relatively higher ROS production upon p-IONP treatment of the bacteria. The data, altogether, indicated that the chitosan coating of IONP result in interface that enhances ROS production, hence the antimicrobial activity.
Highly Effective Conductance Modulation in Planar Silicene Field Effect Devices Due to Buckling
Authors: Al-Dirini Feras , Hossain Faruque M. , Mohammed Mahmood A. , Nirmalathas Ampalavanapillai , Skafidas Efstratios 
Published: October 2015

AbstractSilicene is an exciting two-dimensional material that shares many of graphene’s electronic properties, but differs in its structural buckling. This buckling allows opening a bandgap in silicene through the application of a perpendicular electric field. Here we show that this buckling also enables highly effective modulation of silicene’s conductance by means of an in-plane electric field applied through silicene side gates, which can be realized concurrently within the same silicene monolayer. We illustrate this by using silicene to implement Self-Switching Diodes (SSDs), which are two-dimensional field effect nanorectifiers realized within a single silicene monolayer. Our quantum simulation results show that the atomically-thin silicene SSDs, with sub-10 nm dimensions, achieve a current rectification ratio that exceeds 200, without the need for doping, representing a 30 fold enhancement over graphene SSDs. We attribute this enhancement to a bandgap opening due to the in-plane electric field, as a consequence of silicene’s buckling. Our results suggest that silicene is a promising material for the realization of planar field effect devices.