bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ndfip-mediated degradation of Jak1 tunes cytokine signalling to limit expansion of CD4+ effector T cells
Authors: O’Leary Claire E. , Riling Christopher R. , Spruce Lynn A. , Ding Hua , Kumar Suresh , Deng Guoping , Liu Yuhong , Seeholzer Steven H. , Oliver Paula M. 
Published: April 2016

AbstractNedd4 family E3 ubiquitin ligases have been shown to restrict T-cell function and impact T-cell differentiation. We show here that Ndfip1 and Ndfip2, activators of Nedd4 family ligases, together limit accumulation and function of effector CD4+ T cells. Using a three-part proteomics approach in primary T cells, we identify stabilization of Jak1 in Ndfip1/2-deficient T cells stimulated through the TCR. Jak1 degradation is aborted in activated T cells that lack Ndfips. In wild-type cells, Jak1 degradation lessens CD4+ cell sensitivity to cytokines during TCR stimulation, while in Ndfip-deficient cells cytokine responsiveness persists, promoting increased expansion and survival of pathogenic effector T cells. Thus, Ndfip1/Ndfip2 regulate the cross talk between the T-cell receptor and cytokine signalling pathways to limit inappropriate T-cell responses.
Experimental perfect state transfer of an entangled photonic qubit
Authors: Chapman Robert J. , Santandrea Matteo , Huang Zixin , Corrielli Giacomo , Crespi Andrea , Yung Man-Hong , Osellame Roberto , Peruzzo Alberto 
Published: April 2016

AbstractThe transfer of data is a fundamental task in information systems. Microprocessors contain dedicated data buses that transmit bits across different locations and implement sophisticated routing protocols. Transferring quantum information with high fidelity is a challenging task, due to the intrinsic fragility of quantum states. Here we report on the implementation of the perfect state transfer protocol applied to a photonic qubit entangled with another qubit at a different location. On a single device we perform three routing procedures on entangled states, preserving the encoded quantum state with an average fidelity of 97.1%, measuring in the coincidence basis. Our protocol extends the regular perfect state transfer by maintaining quantum information encoded in the polarization state of the photonic qubit. Our results demonstrate the key principle of perfect state transfer, opening a route towards data transfer for quantum computing systems.
Giant exchange interaction in mixed lanthanides
Authors: Vieru Veacheslav , Iwahara Naoya , Ungur Liviu , Chibotaru Liviu F. 
Published: April 2016

AbstractCombining strong magnetic anisotropy with strong exchange interaction is a long standing goal in the design of quantum magnets. The lanthanide complexes, while exhibiting a very strong ionic anisotropy, usually display a weak exchange coupling, amounting to only a few wavenumbers. Recently, an isostructural series of mixed "Equation missing" (Ln = Gd, Tb, Dy, Ho, Er) have been reported, in which the exchange splitting is estimated to reach hundreds wavenumbers. The microscopic mechanism governing the unusual exchange interaction in these compounds is revealed here by combining detailed modeling with density-functional theory and ab initio calculations. We find it to be basically kinetic and highly complex, involving non-negligible contributions up to seventh power of total angular momentum of each lanthanide site. The performed analysis also elucidates the origin of magnetization blocking in these compounds. Contrary to general expectations the latter is not always favored by strong exchange interaction.
Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging
Authors: Rose P. B. , Erickson A. S. , Mayer M. , Nattress J. , Jovanovic I. 
Published: April 2016

AbstractWeapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as “searching for a needle in a haystack” because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of active interrogation using an external radiation source. However, the similarity of these materials to shielding and the required radiation doses that may exceed regulatory limits prevent this method from being widely used in practice. We introduce a low-dose active detection technique, referred to as low-energy nuclear reaction imaging, which exploits the physics of interactions of multi-MeV monoenergetic photons and neutrons to simultaneously measure the material’s areal density and effective atomic number, while confirming the presence of fissionable materials by observing the beta-delayed neutron emission. For the first time, we demonstrate identification and imaging of uranium with this novel technique using a simple yet robust source, setting the stage for its wide adoption in security applications.
Fine-tuning of macrophage activation using synthetic rocaglate derivatives
Authors: Bhattacharya Bidisha , Chatterjee Sujoy , Devine William G. , Kobzik Lester , Beeler Aaron B. , Porco John A. , Kramnik Igor 
Published: April 2016

AbstractDrug-resistant bacteria represent a significant global threat. Given the dearth of new antibiotics, host-directed therapies (HDTs) are especially desirable. As IFN-gamma (IFNγ) plays a central role in host resistance to intracellular bacteria, including Mycobacterium tuberculosis, we searched for small molecules to augment the IFNγ response in macrophages. Using an interferon-inducible nuclear protein Ipr1 as a biomarker of macrophage activation, we performed a high-throughput screen and identified molecules that synergized with low concentration of IFNγ. Several active compounds belonged to the flavagline (rocaglate) family. In primary macrophages a subset of rocaglates 1) synergized with low concentrations of IFNγ in stimulating expression of a subset of IFN-inducible genes, including a key regulator of the IFNγ network, Irf1; 2) suppressed the expression of inducible nitric oxide synthase and type I IFN and 3) induced autophagy. These compounds may represent a basis for macrophage-directed therapies that fine-tune macrophage effector functions to combat intracellular pathogens and reduce inflammatory tissue damage. These therapies would be especially relevant to fighting drug-resistant pathogens, where improving host immunity may prove to be the ultimate resource.
Expression of Active Fluorophore Proteins in the Milk of Transgenic Pigs Bypassing the Secretory Pathway
Authors: Mukherjee Ayan , Garrels Wiebke , Talluri Thirumala R. , Tiedemann Daniela , Bősze Zsuzsanna , Ivics Zoltán , Kues Wilfried A. 
Published: April 2016

AbstractWe describe the expression of recombinant fluorescent proteins in the milk of two lines of transgenic pigs generated by Sleeping Beauty transposon-mediated genetic engineering. The Sleeping Beauty transposon consisted of an ubiquitously active CAGGS promoter driving a fluorophore cDNA, encoding either Venus or mCherry. Importantly, the fluorophore cDNAs did not encode for a signal peptide for the secretory pathway, and in previous studies of the transgenic animals a cytoplasmic localization of the fluorophore proteins was found. Unexpectedly, milk samples from lactating sows contained high levels of bioactive Venus or mCherry fluorophores. A detailed analysis suggested that exfoliated cells of the mammary epithelium carried the recombinant proteins passively into the milk. This is the first description of reporter fluorophore expression in the milk of livestock, and the findings may contribute to the development of an alternative concept for the production of bioactive recombinant proteins in the udder.
Pressure Induced Enhancement of Superconductivity in LaRu2P2
Authors: Li Baoxuan , Lu Pengchao , Liu Jianzhong , Sun Jian , Li Sheng , Zhu Xiyu , Wen Hai-Hu 
Published: April 2016

AbstractTo explore new superconductors beyond the copper-based and iron-based systems is very important. The Ru element locates just below the Fe in the periodic table and behaves like the Fe in many ways. One of the common thread to induce high temperature superconductivity is to introduce moderate correlation into the system. In this paper, we report the significant enhancement of superconducting transition temperature from 3.8 K to 5.8 K by using a pressure only of 1.74 ± 0.05 GPa in LaRu2P2 which has an iso-structure of the iron-based 122 superconductors. The ab-initio calculation shows that the superconductivity in LaRu2P2 at ambient pressure can be explained by the McMillan’s theory with strong electron-phonon coupling. However, it is difficult to interpret the enhancement of Tc versus pressure within this picture. Detailed analysis of the pressure induced evolution of resistivity and upper critical field Hc2(T) reveals that the increase of Tc with pressure may be accompanied by the involvement of extra electron-boson interaction. This suggests that the Ru-based system has some commonality as the Fe-based superconductors.
Oil-free hyaluronic acid matrix for serial femtosecond crystallography
Authors: Sugahara Michihiro , Song Changyong , Suzuki Mamoru , Masuda Tetsuya , Inoue Shigeyuki , Nakane Takanori , Yumoto Fumiaki , Nango Eriko , Tanaka Rie , Tono Kensuke , Joti Yasumasa , Kameshima Takashi , Hatsui Takaki , Yabashi Makina , Nureki Osamu , Numata Keiji , Iwata So 
Published: April 2016

AbstractThe grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.
Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy
Authors: Nho Hyun Woo , Kalegowda Yogesh , Shin Hyun-Joon , Yoon Tae Hyun 
Published: April 2016

AbstractFor the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties.
A simple and general strategy for generating frequency-anticorrelated photon pairs
Authors: Zhang Xin , Xu Chang , Ren Zhongzhou 
Published: April 2016

AbstractCurrently, two-photon excitation microscopy is the method of choice for imaging living cells within thick specimen. A remaining problem for this technique is the damage caused by the high photon flux in the excitation region. To reduce the required flux, a promising solution is to use highly frequency-anticorrelated photon pairs, which are known to induce two-photon transitions much more efficiently. It is still an open question what the best scheme is for generating such photon pairs. Here we propose one simple general strategy for this task. As an example, we show explicitly that this general strategy can be realized faithfully within the widely applicable coherently pumped Jaynes-Cummings model. It is shown quantitatively that this strategy can generate highly frequency-anticorrelated photon pairs which can dramatically enhance two-photon excitation efficiency. We believe the proposed strategy can guide new designs for generating frequency-anticorrelated photon pairs.
Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement
Authors: Blazier J. Chris , Ruhlman Tracey A. , Weng Mao-Lun , Rehman Sumaiyah K. , Sabir Jamal S. M. , Jansen Robert K. 
Published: April 2016

AbstractGenes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.
Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana
Authors: Gao Ruimin , Liu Peng , Yong Yuhan , Wong Sek-Man 
Published: April 2016

AbstractTurnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways.
Microscopic observation of dye molecules for solar cells on a titania surface
Authors: Koshiya Shogo , Yamashita Shunsuke , Kimoto Koji 
Published: April 2016

AbstractThe lateral distribution and coverage of Ru-based dye molecules, which are used for dye-sensitized solar cells (DSCs), were directly examined on a titania surface using high-resolution scanning transmission electron microscopy (STEM). The clean surface of a free-standing titania nanosheet was first confirmed with atomic resolution and then, the nanosheet was used as a substrate. A single dye molecule on the titania nanosheet was visualized for the first time. The quantitative STEM images revealed an inhomogeneous dye-molecule distribution at the early stage of its absorption, i.e., the aggregation of the dye molecules. The majority of the titania surface was not covered by dye molecules, suggesting that optimization of the dye molecule distribution could yield further improvement of the DSC conversion efficiencies.
A miniature solar device for overall water splitting consisting of series-connected spherical silicon solar cells
Authors: Kageshima Yosuke , Shinagawa Tatsuya , Kuwata Takaaki , Nakata Josuke , Minegishi Tsutomu , Takanabe Kazuhiro , Domen Kazunari 
Published: April 2016

AbstractA novel “photovoltaics (PV) + electrolyzer” concept is presented using a simple, small and completely stand-alone non-biased device for solar-driven overall water splitting. Three or four spherical-shaped p-n junction silicon balls were successfully connected in series, named “SPHELAR.” SPHELAR possessed small projected areas of 0.20 (3PVs) and 0.26 cm2 (4PVs) and exhibited working voltages sufficient for water electrolysis. Impacts of the configuration on the PV module performance were carefully analyzed, revealing that a drastic increase in the photocurrent (≈20%) was attained by the effective utilization of a reflective sheet. Separate investigations on the electrocatalyst performance showed that non-noble metal based materials with reasonably small sizes (<0.80 cm2) exhibited substantial currents at the PV working voltage. By combining the observations of the PV characteristics, light management and electrocatalyst performance, solar-driven overall water splitting was readily achieved, reaching solar-to-hydrogen efficiencies of 7.4% (3PVs) and 6.4% (4PVs).
Knee loading inhibits osteoclast lineage in a mouse model of osteoarthritis
Authors: Li Xinle , Yang Jing , Liu Daquan , Li Jie , Niu Kaijun , Feng Shiqing , Yokota Hiroki , Zhang Ping 
Published: April 2016

AbstractOsteoarthritis (OA) is a whole joint disorder that involves cartilage degradation and periarticular bone response. Changes of cartilage and subchondral bone are associated with development and activity of osteoclasts from subchondral bone. Knee loading promotes bone formation, but its effects on OA have not been well investigated. Here, we hypothesized that knee loading regulates subchondral bone remodeling by suppressing osteoclast development and prevents degradation of cartilage through crosstalk of bone-cartilage in osteoarthritic mice. Surgery-induced mouse model of OA was used. Two weeks application of daily dynamic knee loading significantly reduced OARSI scores and CC/TAC (calcified cartilage to total articular cartilage), but increased SBP (subchondral bone plate) and B.Ar/T.Ar (trabecular bone area to total tissue area). Bone resorption of osteoclasts from subchondral bone and the differentiation of osteoclasts from bone marrow-derived cells were completely suppressed by knee loading. The osteoclast activity was positively correlated with OARSI scores and negatively correlated with SBP and B.Ar/T.Ar. Furthermore, knee loading exerted protective effects by suppressing osteoclastogenesis through Wnt signaling. Overall, osteoclast lineage is the hyper responsiveness of knee loading in osteoarthritic mice. Mechanical stimulation prevents OA-induced cartilage degeneration through crosstalk with subchondral bone. Knee loading might be a new potential therapy for osteoarthritis patients.
Establishment and characterization of HROC69 – a Crohn´s related colonic carcinoma cell line and its matched patient-derived xenograft
Authors: Kuehn Florian , Mullins Christina S. , Krohn Mathias , Harnack Christine , Ramer Robert , Krämer Oliver H. , Klar Ernst , Huehns Maja , Linnebacher Michael 
Published: April 2016

AbstractColitis-associated colorectal cancer (CAC) seems to be a rather unique entity and differs in its genetic alterations, tumour formation capacities and clinical features from sporadic colorectal carcinoma. Most descriptions about tumour biology of CAC refer to ulcerative colitis; data about Crohn´s colitis related carcinomas are scarce. The majority of patients with Crohn´s disease are under immunosuppression which generates a different environment for tumour growth. We first describe the clinical case of a fast growing CAC in a long-term immunosuppressed patient with Crohn´s disease and successful establishment and characterization of carcinoma cell lines along with their corresponding patient-derived xenograft. Subsequently, these tumor models were molecularly and functionally analysed. Beside numerous chromosomal alterations, mutations in TP53, APC, PTEN and SMAD3 were identified. The cell lines express numerous cancer testis antigens, surface molecules involved in immune evasion but low levels of HLA class I molecules. They show strong invasive but in comparison weak migratory activity. The present work is the first description of patient-derived in vitro and in vivo models for CAC from a Crohn´s disease patient. They might be valuable tools for analysis of genetic and epigenetic alterations, biomarker identification, functional testing, including response prediction and the development of specific therapeutical strategies.
Effect of Light Scattering and Higher-order Aberrations on Visual Performance in Eyes with Granular Corneal Dystrophy
Authors: Kamiya Kazutaka , Kobashi Hidenaga , Igarashi Akihito , Shoji Nobuyuki , Shimizu Kimiya 
Published: April 2016

AbstractThis study was aimed to assess the relationship of intraocular forward scattering, corneal backward scattering and corneal higher-order aberrations (HOAs) with corrected distance visual acuity (CDVA) in eyes with granular corneal dystrophy (GCD). We retrospectively examined forty two eyes of 42 consecutive patients who diagnosed GCD and age-matched 20 eyes of 20 healthy subjects. We assessed objective scattering index (OSI) using the double-pass instrument (OQAS II, Visiometrics), corneal densitometry (CD) using the Scheimpflug rotating camera (Pentacam HR, Oculus) and corneal HOAs using the Hartmann-Shack aberrometry (KR-9000, Topcon). The OSI, CD and corneal HOAs were significantly larger in the GCD group than those in the control group (Mann-Whitney U test, p < 0.001). We found significant correlations of logMAR CDVA with the OSI (Spearman correlation coefficient r = 0.577, p < 0.001) and with the CD (r = 0.340, p = 0.028), but no significant association with corneal HOAs (r = 0.061, p = 0.701). Intraocular forward scattering, corneal backward scattering and corneal HOAs in eyes with GCD were higher than that in normal eyes. The CDVA was significantly correlated with intraocular forward scattering, but not with corneal HOAs in eyes with GCD, suggesting that light scattering, especially forward scattering, plays a more vital role in visual performance than corneal aberrations in eyes with GCD.