gebhart/patrepeval huggingface dataset:
C Terminus of Infectious Bursal Disease Virus Major Capsid Protein VP2 Is Involved in Definition of the T Number for Capsid Assembly (2001)

Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is a double-stranded RNA virus. The IBDV capsid is formed by two major structural proteins, VP2 and VP3, which assemble to form a T=13 markedly nonspherical capsid. During viral infection, VP2 is initially synthesized as a precursor, called VPX, whose C end is proteolytically processed to the mature form during capsid assembly. We have computed three-dimensional maps of IBDV capsid and virus-like particles built up by VP2 alone by using electron cryomicroscopy and image-processing techniques. The IBDV single-shelled capsid is characterized by the presence of 260 protruding trimers on the outer surface. Five classes of trimers can be distinguished according to their different local environments. When VP2 is expressed alone in insect cells, dodecahedral particles form spontaneously; these may be assembled into larger, fragile icosahedral capsids built up by 12 dodecahedral capsids. Each dodecahedral capsid is an empty T=1 shell composed of 20 trimeric clusters of VP2. Structural comparison between IBDV capsids and capsids consisting of VP2 alone allowed the determination of the major capsid protein locations and the interactions between them. Whereas VP2 forms the outer protruding trimers, VP3 is found as trimers on the inner surface and may be responsible for stabilizing functions. Since elimination of the C-terminal region of VPX is correlated with the assembly of T=1 capsids, this domain might be involved (either alone or in cooperation with VP3) in the induction of different conformations of VP2 during capsid morphogenesis.
Fabrication and characterization of a PAM modified PHBV/BG scaffold (2009)

为了改进简历活动和在骨头使用的支架的机械力量，同时修理，一篇小说多孔(β-hydroxybutyrate-co-β-hydroxyvalerate )(PHBV ) PAM-poly， /bioactive 玻璃(BG ) 支架被开始相片的聚合准备。当 BG 粒子被增加同时地增加简历活动和矩阵的力量时， PAM 被用来改进 PHBV 矩阵的 hydrophilicity。从压克力酰胺和增加的 BG 的 grafted 酰胺组和 Si-O 一半被 Fourier 证实转变红外线的 Spectrometry (FTIR ) 。在 grafting 前后的脚手架的微形态学被扫描电子显微镜学(SEM ) 观察。产生图象证明 PAM-PHBV/BG 支架有很好连接的毛孔结构和可能方便让房间种并且排出代谢物的适当毛孔尺寸。比重方法被用来评估支架的毛孔性质，结果证明支架有一个平均的孔直到 82.0% 。水银侵入 porosimetry (MIP ) 显示 PAM-PHBV/BG 支架的毛孔主要在 75 和 150 μm 之间被散布。压缩力量测试被采用评估支架的机械性质。当时，结果证明 PAM-PHBV/BG 支架有相对高的压缩力量(0.91 MPa ) 与纯 PHBV 支架相比。而且，纯 PHBV 支架的性质， PHBV/BG 支架也被评估。最新准备的 PAM-PHBV/BG 支架可以值得作为骨头修理材料的进一步的学习。
Coupling element based mobile terminal antenna structures (2006)

In this paper, internal low-volume antenna structures for mobile terminals are studied. The work concentrates on the possibilities to reduce the volume of mobile terminal antenna elements by efficiently utilizing the radiation of the currents on the mobile terminal chassis. Essentially nonresonant coupling elements are used to optimally couple to the dominating characteristic wavemodes of the chassis. The antenna structures are tuned to resonance with matching circuits. During the last few years, the approach has achieved growing interest—also among industrial manufacturers of mobile terminals. There exist, however, no systematical feasibility and performance studies of the idea. During the work, two antenna models with very low-volume coupling elements are designed and in total four prototypes are constructed. The simulation and measurement results show that the studied antenna concept is a very promising alternative for traditional antenna technologies. The presented analysis provides useful and novel information for the designs of the future low-profile and low-volume mobile terminal antennas.
Nuclear RNA Foci in the Heart in Myotonic Dystrophy (2005)

The disease mechanism underlying myotonic dystrophy type 1 (DM1) pathogenesis in skeletal muscle may involve sequestration of RNA binding proteins in nuclear foci of expanded poly(CUG) RNA. Here we report evidence for a parallel mechanism in the heart. Accumulation of expanded poly(CUG) RNA in nuclear foci is associated with sequestration of muscleblind proteins and abnormal regulation of alternative splicing in DM1 cardiac muscle. A toxic effect of RNA with an expanded repeat may contribute to cardiac disease in DM1.
Removal of Fluoride Ion from Wastewater by a Hydrous Cerium Oxide Adsorbent (1990)

A new adsorption process has been developed and shown practical for removal of fluoride ion from waste water to effect concentrations of 1 mg/L or less. The adsorbent developed for this process consists of polyolefinic resin beads carrying hydrous cerium oxide podwer with a large specific area. It is high in selectivity for fluoride ion and exhibits an adsorption capacity of 8 to 25 mg-F/mL-adsorbent at fluorine concentrations of 0.2 to 20 mg/L, with adsorption conforming to the Freundlich isotherm, and is readily regenerated by alkalis for repeated, long-term use. This process consists essentially of adjustment to PH 2 to 5, fluorine adsorption, adsorbent regeneration by NaOH and precipitiation of CaF2 from used regenerant by addition of CaCl2.
Regulatory elements and transcription factors controlling basal and cytokine-induced expression of the gene encoding intercellular adhesion molecule 1. (1994)

The gene encoding intercellular adhesion molecule 1 (ICAM-1) is transcriptionally induced in response to inflammatory and immunomodulatory cytokines. To investigate the mechanisms controlling ICAM-1 gene expression, we have identified regulatory DNA sequences responsible for maintaining basal and mediating induced transcription in response to tumor necrosis factor alpha (TNF-alpha) and interferon gamma (IFN-gamma). Regulatory elements centered 115, 60, and 40 bp upstream from the ICAM-1 transcription start site were implicated in cytokine-independent gene expression. Regulatory elements dedicated to TNF-alpha and IFN-gamma were identified 190 and 90 bp, respectively, upstream from the ICAM-1 transcription start site. A combination of mutagenesis and DNA-binding assays revealed that the TNF-alpha response element is composite, consisting of binding sites for both C/EBP and NF-kappa B. The IFN-gamma response element behaved as a simple regulatory element that selectively binds to an IFN-gamma-inducible activity composed, at least in part, of p91. These observations provide a framework for understanding how extracellular signals dynamically regulate the adhesive properties of mammalian cells.
VEGF and flt (1996)

In the ischemic brain the macrophages, neurons, and glial cells appear to contain VEGF. The VEGF receptor flt was induced in endothelial cells along with the progression of angiogenesis in infarct. The VEGF/flt system is thus considered to be involved in the healing process of brain infarct.
The Relationship of Dietary ω-3 Long-Chain Polyunsaturated Fatty Acid Intake With Incident Age-Related Macular Degeneration (2008)

Dietary lipid intake is a modifiable factor that may influence the likelihood of developing sight-threatening forms of AMD. Our findings suggest that dietary omega-3 long-chain polyunsaturated fatty acid intake is associated with a decreased risk of progression from bilateral drusen to CGA.
An experimental system for the evaluation of retroviral vector design to diminish the risk for proto-oncogene activation (2007)

Pathogenic activation of the LMO2 proto-oncogene by an oncoretroviral vector insertion in a clinical trial for X-linked severe combined immunodeficiency (X-SCID) has prompted safety concerns. We used an adeno-associated virus vector to achieve targeted insertion of a gamma-retroviral long terminal repeat (LTR) driving a GFP expression cassette with flanking loxP sites in a human T-cell line at the precise location of vector integration in one of the patients with X-SCID. The LTR-GFP cassette was inserted into the first intron of the LMO2 gene, resulting in strong activation of LMO2. Cre-mediated cassette exchange was used to replace the original LTR-GFP cassette with one flanked by insulator elements leading to a several fold reduction in LMO2 expression. The LTR-GFP cassette was also replaced with a globin gene regulatory cassette that failed to activate the LMO2 gene in lymphoid cells. A gamma-retroviral vector with 2 intact LTRs resulted in activation of the LMO2 gene when inserted into the first intron, but a self-inactivating lentiviral vector with an internal cellular promoter and flanking insulator elements did not activate the LMO2 gene. Thus, this system is useful for comparing the safety profiles of vector cassettes with various regulatory elements for their potential for proto-oncogene activation.
A Scalable Hierarchical Distributed Language Model (2008)

Neural probabilistic language models (NPLMs) have been shown to be competitive with and occasionally superior to the widely-used n-gram language models. The main drawback of NPLMs is their extremely long training and testing times. Morin and Bengio have proposed a hierarchical language model built around a binary tree of words, which was two orders of magnitude faster than the nonhierarchical model it was based on. However, it performed considerably worse than its non-hierarchical counterpart in spite of using a word tree created using expert knowledge. We introduce a fast hierarchical language model along with a simple feature-based algorithm for automatic construction of word trees from the data. We then show that the resulting models can outperform non-hierarchical neural models as well as the best n-gram models. 1
Nanowire Lasers of Formamidinium Lead Halide Perovskites and Their Stabilized Alloys with Improved Stability (2016)

The excellent intrinsic optoelectronic properties of methylammonium lead halide perovskites (MAPbX3, X = Br, I), such as high photoluminescence quantum efficiency, long carrier lifetime, and high gain coupled with the facile solution growth of nanowires make them promising new materials for ultralow-threshold nanowire lasers. However, their photo and thermal stabilities need to be improved for practical applications. Herein, we report a low-temperature solution growth of single crystal nanowires of formamidinium lead halide perovskites (FAPbX3) that feature red-shifted emission and better thermal stability compared to MAPbX3. We demonstrate optically pumped room-temperature near-infrared (∼820 nm) and green lasing (∼560 nm) from FAPbI3 (and MABr-stabilized FAPbI3) and FAPbBr3 nanowires with low lasing thresholds of several microjoules per square centimeter and high quality factors of about 1500-2300. More remarkably, the FAPbI3 and MABr-stabilized FAPbI3 nanowires display durable room-temperature lasing under ∼10(8) shots of sustained illumination of 402 nm pulsed laser excitation (150 fs, 250 kHz), substantially exceeding the stability of MAPbI3 (∼10(7) laser shots). We further demonstrate tunable nanowire lasers in wider wavelength region from FA-based lead halide perovskite alloys (FA,MA)PbI3 and (FA,MA)Pb(I,Br)3 through cation and anion substitutions. The results suggest that formamidinium lead halide perovskite nanostructures could be more promising and stable materials for the development of light-emitting diodes and continuous-wave lasers.
Sliding window filter with application to planetary landing (2010)

Abstract We are concerned with improving the range resolution of stereo vision for entry, descent, and landing (EDL) missions to Mars and other planetary bodies. The goal is to create accurate and precise three‐dimensional planetary surface‐structure estimates by filtering sequences of stereo images taken from an autonomous landing vehicle. We describe a sliding window filter (SWF) approach based on delayed state marginalization. The SWF can run in constant time, yet still achieve experimental results close to those of the bundle adjustment solution. This technique can scale from the offline batch least‐squares solution to fast online incremental solutions. For instance, if the window encompasses all time, the solution is equivalent to full bundle adjustment; if only one time step is maintained, the solution matches the extended Kalman filter; if poses and landmarks are slowly marginalized out over time such that the state vector ceases to grow, then the filter becomes constant time, like visual odometry. Within the constant time regime, the sliding window approach demonstrates convergence properties that are close to those of the full batch solution and strictly superior to visual odometry. Experiments with real data show that ground structure estimates follow the expected convergence pattern that is predicted by theory. These experiments indicate the effectiveness of filtering long‐range stereo for EDL. © 2010 Wiley Periodicals, Inc.
The MATK Tyrosine Kinase Interacts in a Specific and SH2-dependent Manner with c-Kit (1995)

We have cloned a protein tyrosine kinase, MATK, which is expressed abundantly in megakaryocytes and the brain. We investigated whether MATK participates in the c-Kit ligand/stem cell factor (KL/SCF) signaling pathway in the megakaryocytic cell line CMK. After KL/SCF stimulation, five major proteins of molecular masses of 145, 113, 92, 76, and 63 kDa were rapidly and transiently tyrosine-phosphorylated in a time-dependent manner, peaking within 5 min, and returning to basal levels within 60 min. To study the role of MATK in the KL/SCF signaling pathway, glutathione S-transferase (GST) fusion proteins containing SH2 and SH3 domains of MATK were cloned, expressed in Escherichia coli, and purified. MATK-SH2, but not MATK-SH3, precipitated the tyrosine-phosphorylated c-Kit (molecular mass of 145 kDa) in KL/SCF-stimulated CMK cells. Other GST fusion proteins containing the SH2 domain of p85 of phosphatidylinositol 3-kinase, phospholipase C gamma-1, and ras-GAP also precipitated c-Kit. The tyrosine-phosphorylated c-Kit was co-immunoprecipitated with anti-MATK and anti-p85 antibodies in KL/SCF-stimulated CMK cells, but not in granulocyte-macrophage colony stimulating factor or interleukin-6-stimulated cells, suggesting receptor specificity. These results indicate that MATK associates with the c-Kit receptor following specific stimulation by KL/SCF via its SH2 domain and likely participates in transduction of growth signals induced by this cytokine in megakaryocytes.
Snow probe for in situ determination of wetness and density (1994)

The amount of water present in liquid form in a snowpack exercises a strong influence on the radar and radiometric responses of snow. Conventional techniques for measuring the liquid water content m/sub /spl upsi// suffer from various shortcomings, which include poor accuracy, long analysis time, poor spatial resolution, and/or cumbersome and inconvenient procedures. This paper describes the development of a hand-held electromagnetic sensor for quick and easy determination of snow liquid water content and density. A novel design of this probe affords several important advantages over existing similar sensors. Among these are improved spatial resolution and accuracy, and reduced sensitivity to interference by objects or media outside the sample volume of the sensor. The sensor actually measures the complex dielectric constant of the snow medium, and the water content and density must be obtained through the use of empirical or semi-empirical relations. To test the suitability of existing models and allow the development of new models, the snow probe was tested against the freezing calorimeter and gravimetric density determinations. From these comparisons, valid models were selected or developed. Based on the use of these models, the following specifications were established for the snow probe: 1) liquid water content measurement accuracy=/spl plusmn/0.66% in the wetness range from 0 to 10% by volume and 2) wet snow density measurement accuracy=/spl plusmn/0.05 g/cm/sup 3/ in the density range from 0.1 to 0.6 g/cm/sup 3/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modulation bandwidth, noise, and stability of a semiconductor laser subject to strong injection locking (1997)

Operating conditions for modulation bandwidth enhancement, noise reduction, and stable locking to be simultaneously fulfilled in a semiconductor laser subject to strong optical injection are investigated. When the strength of the injection signal is fixed, the optimum detuning of the injection frequency exists as a tradeoff between bandwidth enhancement and noise reduction. When the laser is injection-locked at a given value of frequency detuning in the stable locking region, both bandwidth enhancement and noise reduction are improved as the injection parameter is increased over a wide range.
IgA-dependent cell-mediated activity against enteropathogenic bacteria: distribution, specificity, and characterization of the effector cells. (1984)

Antibody-dependent cellular cytotoxicity (ADCC) against murine enteropathogenic bacteria such as Salmonella typhimurium and Salmonella tel aviv or Shigella X16 was assessed by using IgG, IgA, and secretory IgA (sIgA) in a 2-hr in vitro assay where peripheral and intestinal lymphocytes were used as effector cells. It was found that IgG could arm splenocytes (SpL) better than IgA. However, IgG did not arm lymphocytes from Peyer's patches (PPL) or from mesenteric lymph nodes (MnL), whereas IgA of plasmacytoma origin against S. tel aviv and purified intestinal sIgA against Shigella X16 induced specific antibacterial ADCC with both SpL and PPL. When sIgA were tested with intestinal lymphocytes from the epithelium and the lamina propria, i.e., cells from the gut mucosa which first interact with enteric bacteria, it was found that both these lymphoid populations were able to express sIgA-dependent ADCC against Shigella X16. In parallel tests, cells from thymus and popliteal lymph nodes failed to express ADCC. Blocking studies with purified IgG and IgA of goat, rabbit, and mouse origin demonstrated that the Fc-alpha and Fc-gamma receptors were specifically involved in IgA- or IgG-dependent antibacterial ADCC. At least two effector populations, a macrophage and a Thy-1.2- lymphocyte, were observed to exert IgA-ADCC at the splenic level, whereas only lymphoid cells expressed this activity at the GALT level. Together, these results describe a new activity of IgA against enteropathogenic bacteria.
Fragment-Based Identification of Amides Derived from trans-2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT) (2014)

Potent, trans-2-(pyridin-3-yl)cyclopropanecarboxamide-containing inhibitors of the human nicotinamide phosphoribosyltransferase (NAMPT) enzyme were identified using fragment-based screening and structure-based design techniques. Multiple crystal structures were obtained of initial fragment leads, and this structural information was utilized to improve the biochemical and cell-based potency of the associated molecules. Many of the optimized compounds exhibited nanomolar antiproliferative activities against human tumor lines in in vitro cell culture experiments. In a key example, a fragment lead (13, KD = 51 μM) was elaborated into a potent NAMPT inhibitor (39, NAMPT IC50 = 0.0051 μM, A2780 cell culture IC50 = 0.000 49 μM) which demonstrated encouraging in vivo efficacy in an HT-1080 mouse xenograft tumor model.
Accumulation of Amyloid β and Tau and the Formation of Neurofilament Inclusions Following Diffuse Brain Injury in the Pig (1999)

Brain trauma in humans increases the risk for developing Alzheimer disease (AD) and may induce the acute formation of AD-like plaques containing amyloid beta (A beta). To further explore the potential link between brain trauma and neurodegeneration, we conducted neuropathological studies using a pig model of diffuse brain injury. Brain injury was induced in anesthetized animals via nonimpact head rotational acceleration of 110 degrees over 20 ms in the coronal plane (n = 15 injured, n = 3 noninjured). At 1, 3, 7, and 10 days post-trauma, control and injured animals were euthanized and immunohistochemical analysis was performed on brain sections using antibodies specific for A beta, beta-amyloid precursor protein (betaPP), tau, and neurofilament (NF) proteins. In addition to diffuse axonal pathology, we detected accumulation of A beta and tau that colocalized with immunoreactive betaPP and NF in damaged axons throughout the white matter in all injured animals at 3-10 days post-trauma. In a subset of brain injured animals, diffuse A beta-containing plaque-like profiles were found in both the gray and white matter, and accumulations of tau and NF rich inclusions were observed in neuronal perikarya. These results show that this pig model of diffuse brain injury is characterized by accumulations of proteins that also form pathological aggregates in AD and related neurodegenerative diseases.
Optical networking for quantum key distribution and quantum communications (2009)

Modern optical networking techniques have the potential to greatly extend the applicability of quantum communications by moving beyond simple point-to-point optical links and by leveraging existing fibre infrastructures. We experimentally demonstrate many of the fundamental capabilities that are required. These include optical-layer multiplexing, switching and routing of quantum signals; quantum key distribution (QKD) in a dynamically reconfigured optical network; and coexistence of quantum signals with strong conventional telecom traffic on the same fibre. We successfully operate QKD at 1310 nm over a fibre shared with four optically amplified data channels near 1550 nm. We identify the dominant impairment as spontaneous anti-Stokes Raman scattering of the strong signals, quantify its impact, and measure and model its propagation through fibre. We describe a quantum networking architecture which can provide the flexibility and scalability likely to be critical for supporting widespread deployment of quantum applications.
A transcribed gene, containing a variable number of tandem repeats, codes for a human epithelial tumor antigen (1990)

A monoclonal antibody, H23, that specifically recognizes a breast-tumor-associated antigen, was used to isolate a cDNA insert that codes for the antigenic epitope. Nucleotide sequencing of this cDNA, as well as a longer 850-bp cDNA insert, shows that they are composed of 60-bp (G + C)-rich tandem repeating units. The coding strand was determined and codes for a proline-rich 20-amino-acid repeat motif. A comparison of the highly conserved repeat unit with the deduced flanking amino acid sequences demonstrates conservation of specific subregions of the repeat consensus within the flanking amino acids. Hybridization of the 60-bp cDNA probe with RNAs extracted from a variety of primary and metastatic human tumors yields relatively high levels of hybrid with the breast carcinomas, as compared to lower hybrid levels with RNAs from other epithelial tumors. RNA extracted from breast tissue adjacent to the tumor or from benign breast tumors, demonstrates low or undetectable levels of hybridization. Probing Southern blots with the 60-bp repeat shows that the tumor antigen is highly polymorphic and contains a variable number of tandem repeats (VNTRs). The VNTR nature of the gene was confirmed by probing Southern blots with unique genomic sequences that are physically linked to an isolated gene fragment that also contains the tandem repeat array. Mouse cells transfected with this gene fragment produce tumor antigen that is readily detected by H23 monoclonal antibodies. The allelic forms seen in 10 different primary human tumors demonstrate 100% concordance with the various mRNA species expressed. These studies are extended to the protein forms detected by immunoblot analyses that show both a correlation of the expressed tumor antigen species with the allelic forms as well as significantly increased expression in breast cancer tissue. The above studies unequivocally establish the over-expression of a VNTR gene coding for an epithelial tumor antigen in human breast cancer tissue.