gebhart/patrepeval huggingface dataset:
Varicella-zoster virus (1991)

Over the past 15 years or so, we have witnessed a dramatic increase in the generation of nucleic acid sequence data. The impact of this process has been felt particularly in animal virology, so that we now have complete genome sequences for representatives of most of the virus families. It is apparent that complete sequence determination of any virus genome is now a practical short or medium term goal. This is illustrated most clearly by the herpesviruses, whose large genomes have provided a challenge suited to serious genome sequencers. Thus, four complete herpesvirus sequences have been published to date. Those for Epstein-Barr virus (EBV) and human cytomegalovirus (HCMV) were derived at the MRC Laboratory of Molecular Biology in Cambridge, U.K. (Baer et al., 1984; Chee et al., 1990) and those for varicella-zoster virus (VZV) and herpes simplex virus type 1 (HSV-1) were obtained at the MRC Virology Unit in Glasgow, U.K. (Davison & Scott, 1986; McGeoch et al., 1988).
Gram-Scale Synthesis and Biofunctionalization of Silica-Coated Silver Nanoparticles for Fast Colorimetric DNA Detection (2005)

A direct silica-coating method has been developed for the gram-scale synthesis of well-dispersed Ag@SiO(2) nanoparticles. Subsequent surface functionalization via the well-established silica surface chemistry provided arching points for straightforward bioconjugation with amino-terminated oligonucleotides. Fast hybridization kinetics of the resulting robust oligo-modified Ag@SiO(2) nanoprobes with complementary target oligonucleotides render themselves very useful for the fast colorimetric DNA detection based on the sequence-specific hybridization properties of DNA. Additionally, the reliable protocols developed in this study for preparing and functionalizing Ag@SiO(2) nanoparticles can be readily extended to other silica-coated nanoparticles, which can also provide a specific platform for the covalent attachment of biomolecules such as amino-rich proteins, enzymes, or amino-terminated oligonucleotides for diverse bioapplications.
Bending sensor combining multicore fiber with a mode-selective photonic lantern (2015)

A bending sensor is demonstrated using the combination of a mode-selective photonic lantern (PL) and a multicore fiber. A short section of three-core fiber with strongly coupled cores is used as the bend sensitive element. The supermodes of this fiber are highly sensitive to the refractive index profiles of the cores. Small bend-induced changes result in drastic changes of the supermodes, their excitation, and interference. The multicore fiber is spliced to a few-mode fiber and excites bend dependent amounts of each of the six linearly polarized (LP) modes guided in the few-mode fiber. A mode selective PL is then used to demultiplex the modes of the few-mode fiber. Relative power measurements at the single-mode PL output ports reveal a high sensitivity to bending curvature and differential power distributions according to bending direction, without the need for spectral measurements. High direction sensitivity is demonstrated experimentally as well as in numerical simulations. Relative power shifts of up to 80% have been measured at radii of approximately 20 cm, and good sensitivity was observed with radii as large as 10 m, making this sensing system useful for applications requiring both large and small curvature measurements.
Controlled Super-Lateral Growth of Si Films for Microstructural Manipulation and Optimization (1998)

This paper reviews a particular form of pulsed-laser-based thin-film crystallization method referred to as controlled super-lateral growth (C-SLG). By systematically manipulating and controlling the locations, shapes, and extent of melting induced by the incident laser pulses, the C-SLG approach — notably in a version referred to as sequential lateral solidification (SLS) — can lead to realization of a variety of microstructurally designed crystalline Si films with low structural defect densities, including 1. large-grained and grain-boundary-location controlled polycrystalline films, 2. directionally solidified microstructures, or 3. location-controlled single-crystal regions.
A Model for Predicting the Risk of Cancer Consequent to Retroviral Gene Therapy (1992)

Theoretical estimates of the risk of cancer resulting from accidental insertion of retroviral gene therapy vectors into oncogenically vulnerable genomic sites may prove an important supplement to experimentally derived data in estimating risk/benefit ratios for future gene therapy trials. We have approached risk assessment by considering either a single vector insertion event or a single natural mutation to be potentially oncogenic, should either occur in a cell that would otherwise end with one less than the total number of mutations required for frank neoplasia. Estimates of the relative probabilities of these two phenomena yield a relative risk assessment, which in conjunction with epidemiologic data on natural cancer frequencies can be converted into an assessment of absolute risk. This approach yields an estimated range of relative risk over 10 years of about 1.00000026 to 25 for cells bearing single copies of inserted vectors; the upper limit is higher for multiple copies. These estimates, if accurate, imply that small experimental human or animal gene therapy cohorts will rarely, if ever, manifest vector-related cancers and that more precise future risk assessments will require additional data on natural and vector-induced mutation rates.
Ultrahigh resolution optical coherence tomography with femtosecond Ti：sapphire laser and photonic crystal fiber (2008)

光连贯断层摄影术(10 月) 与超离频轴的分辨率被完成由超级连续统由从商业 Ti 联合飞米第二脉搏产生了：蓝宝石激光进空气硅石微观结构纤维。可见光谱从在 540 nm 集中的 450 ～ 700 nm 超级连续统能被产生。0.64 亩 m 的一个空间轴的 10 月决定被完成。10 月系统的敏感是有在样品的事件光力量 3 mW 的 108 dB，仅仅在理论限制下面的 7dB。Subcellular 10 月成像也被表明，显示出为生物医学的申请的大潜力。
Chained Multi-stream Networks Exploiting Pose, Motion, and Appearance for Action Classification and Detection (2017)

General human action recognition requires understanding of various visual cues. In this paper, we propose a network architecture that computes and integrates the most important visual cues for action recognition: pose, motion, and the raw images. For the integration, we introduce a Markov chain model which adds cues successively. The resulting approach is efficient and applicable to action classification as well as to spatial and temporal action localization. The two contributions clearly improve the performance over respective baselines. The overall approach achieves state-of-the-art action classification performance on HMDB51, J-HMDB and NTU RGB+D datasets. Moreover, it yields state-of-the-art spatio-temporal action localization results on UCF101 and J-HMDB.
Cancer antineovascular therapy with liposome drug delivery systems targeted to BiP/GRP78 (2010)

Angiogenesis is crucial for tumor growth and hematogenous metastasis. Specifically expressed and functional protein molecules in angiogenic endothelial cells, especially on the plasma membrane, may be molecular targets for antiangiogenic drugs and drug delivery systems (DDS) in cancer therapy. To discover such target molecules, we performed subcellular proteome analysis of human umbilical vein endothelial cells (HUVECs) treated with or without vascular endothelial growth factor (VEGF) using 2-dimensional difference in-gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). Among the identified proteins, BiP/GRP78, a molecular chaperone, was highly expressed in the membrane/organelle fraction of HUVECs after VEGF treatment. The involvement of BiP in VEGF-induced angiogenesis was examined by RNA interference. BiP knockdown significantly suppressed VEGF-induced endothelial cell proliferation and VEGF-induced phosphorylation of extracellular-regulated kinase 1/2, phospholipase C-γ, and VEGF receptor-2 in HUVECs. Cell surface biotinylation analysis revealed that the cell surface expression of BiP was elevated in VEGF-activated HUVECs. Aiming to apply BiP to a target molecule in liposomal DDS, we developed liposomes modified with the WIFPWIQL peptide, which has been shown to bind to BiP, and investigated its potential for cancer therapy. The WIFPWIQL-modified liposomes (WIFPWIQL liposomes) were significantly taken up by VEGF-activated HUVECs as compared to peptide-unmodified liposomes. WIFPWIQL liposomes appeared to accumulate in tumor endothelial cells in vivo. WIFPWIQL liposomes containing doxorubicin significantly suppressed tumor growth and prolonged the survival of colon26 NL-17 carcinoma cell-bearing mice. In summary, BiP may regulate VEGF-induced endothelial cell proliferation through VEGFR-2-mediated signaling and be an effective target molecule for cancer antineovascular therapy.
PEO enhancement of platelet deposition, fibrinogen deposition, and complement C3 activation (1992)

Whereas it has been commonly thought that adding polyethylene oxide PEO to a surface would diminish the capacity of the surface to cause deposition of platelets and of fibrinogen, and to activate complement C3, we present data showing exactly the opposite. These unexpected results are obtained with low molecular weight (2000) PEO, and are not found with higher molecular weight (20,000) PEO.
Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus. (1991)

Vaccinia virus has been used as a vector to express foreign genes for the production of functional and posttranslationally modified proteins. A procedure is described here that allows the rapid native purification of vaccinia-expressed proteins fused to an amino-terminal tag of six histidines. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni2+.nitrilotriacetic acid (Ni2+.NTA)-agarose and histidine-tagged proteins are selectively eluted with imidazole-containing buffers. In the case of the human serum response factor (SRF), a transcription factor involved in the regulation of the c-fos protooncogene, the vaccinia-expressed histidine-tagged SRF (SRF-6His) could be purified solely by this step to greater than 95% purity. SRF-6His was shown to resemble authentic SRF by functional criteria: it was transported to the nucleus, bound specifically the c-fos serum response element, interacted with the p62TCF protein to form a ternary complex, and stimulated in vitro transcription from the serum response element. Thus, the combination of vaccinia virus expression and affinity purification by Ni2+.NTA chromatography promises to be useful for the production of proteins in a functional and posttranslationally modified form.
Crystal Structure of the 1 : 1 Complex of 5-Fluorouracil and 9-Ethylhypoxanthine (1967)

9-Ethylhypoxanthine and 5-fluorouracil form a 1 : 1 crystalline complex. The structure of this complex has been solved by x-ray diffraction analysis. The molecules crystallize in a monoclinic lattice and form a sheet structure in which pairs of fluorouracil molecules are held together by two hydrogen bonds. The 9-ethylhypoxanthine residues fill up the rest of the molecular sheet by forming single hydrogen bonds with each uracil pair.
Self-assembled Shells Composed of Colloidal Particles:  Fabrication and Characterization (2005)

We construct shells with tunable morphology and mechanical response with colloidal particles that self-assemble at the interface of emulsion droplets. Particles self-assemble to minimize the total interfacial energy, spontaneously forming a particle layer that encapsulates the droplets. We stabilize these layers to form solid shells at the droplet interface by aggregating the particles, connecting the particles with adsorbed polymer, or fusing the particles. These techniques reproducibly yield shells with controllable properties such as elastic moduli and breaking forces. To enable diffusive exchange through the particle shells, we transfer them into solvents that are miscible with the encapsulant. We characterize the mechanical properties of the shells by measuring the response to deformation by calibrated microcantilevers.
Demonstration of extrapulmonary activity of angiotensin converting enzyme in intact tissue preparations (1990)

1. The activity of angiotensin converting enzyme (ACE) has been studied on functional parameters of intact isolated preparations of extrapulmonary tissues. The conversion of angiotensin I (A I) to angiotensin II (A II) and the cleavage of bradykinin (BK) were used as indicators of ACE activity. Captopril was employed as a specific inhibitor of ACE. 2. Captopril augmented the BK-induced contractions of the rat isolated uterus, the BK- and substance P-induced contractions of the guinea-pig ileum, and the BK-induced venoconstriction in the isolated perfused ear of the rabbit. Degradation of BK by ACE was calculated to be 52% in the rat uterus and 75% in the rabbit perfused ear. 3. Captopril inhibited the A I-induced contractions of the rat isolated colon, the A I-induced vasoconstriction in the isolated perfused ear of the rabbit and the rise in blood pressure induced by i.a. injections of A I in pithed rats. Conversion of A I to A II was calculated to be 13% in the rat colon and 26% in the rabbit perfused ear. 4. From estimations of the A II activity (bioassay on the rat colon) in the effluent of the perfused ear of the rabbit after injections of A I into the arterial inflow cannula it was calculated that approximately one tenth of A I was converted to A II during a single passage through the ear (less than 15 s). 5. The present experiments suggest that the high activity of ACE in endothelium of blood vessels of extrapulmonary tissues may provide an additional (endothelium-dependent) local vasoconstrictor mechanism by the rapid formation of A II and inactivation of BK. The ACE activity in non-vascular smooth muscles, other than those of blood vessels, may also affect the physiological functions of these tissues.
Eukaryotic initiation factor 4D, the hypusine-containing protein, is conserved among eukaryotes. (1987)

When mammalian cells are grown in medium containing [3H]spermidine, a single major tritiated protein identical to eukaryotic initiation factor 4D becomes labeled. This protein contains 1 residue/molecule of tritiated hypusine (N epsilon-(4-amino-2-hydroxybutyl)lysine), a rare amino acid which has been found in no other protein. In order to investigate the conservation of this protein, we examined two nonmammalian eukaryotes, the yeast Saccharomyces cerevisiae and the insect Drosophila melanogaster, and the eubacterial prokaryote Escherichia coli for the presence of the hypusine-containing protein. When the eukaryotic cells were grown in the presence of [3H]spermidine, electrophoretic analysis revealed a single labeled protein. In each case, the apparent molecular weight was near 18,000 and the relative pI was approximately 5.2, similar to the hypusine-containing protein of mammals. Amino acid analysis confirmed the presence of tritiated hypusine in each case, and silver staining of two-dimensional polyacrylamide gels demonstrated that, in yeast and fruit flies as in mammals, the protein is relatively abundant. In the eubacterium E. coli, one tritiated protein was predominant, but its molecular weight was 24,000 and we found no evidence that it contained tritiated hypusine. We found no evidence for the existence of the hypusine-containing protein in the archaebacterium Methanococcus voltae. These data suggest that the hypusine-containing protein is conserved among eukaryotes.
Induction of nuclear factor-kappa B and the human immunodeficiency virus long terminal repeat by okadaic acid, a specific inhibitor of phosphatases 1 and 2A. (1990)

We have used a specific phosphatase inhibitor, okadaic acid, to examine the role of two phosphatases, PP1 and PP2A, in the induction of NF-kappa B and the long terminal repeat of the human immunodeficiency virus type 1 (HIV-LTR). Treatment of Jurkat cells with okadaic acid induced NF-kappa B in nuclear extracts. The rate of induction by okadaic acid was delayed compared to the induction of NF-kappa B by phorbol myristate acetate (PMA). The induction of NF-kappa B by okadaic acid was enhanced by cycloheximide or phytohemagglutinin (PHA). In contrast to PMA, okadaic acid appeared to induce NF-kappa B independently of protein kinase C (PKC). That the NF-kappa B induced by okadaic acid was functional was demonstrated by the marked increase in CAT activity that occurred in Jurkat, BJA-B, and U251 cells that were transfected with HIV-LTR-CAT and treated with okadaic acid. The increase in CAT activity triggered by okadaic acid was dependent on the presence of the NF-kappa B sites in the long terminal repeat of HIV as assessed by deletion and mutation analysis. Similarly to its effect on the induction of NF-kappa B, PHA added together with okadaic acid resulted in a further increase in CAT activity. Somewhat surprisingly, the addition of PMA inhibited the increase in CAT activity in response to okadaic acid, which suggests that the activation of PKC may also induce inhibitory factors.(ABSTRACT TRUNCATED AT 250 WORDS)
Cytogenetic evidence of clonality in a case of pigmented villonodular synovitis (1991)

Pigmented villonodular synovitis is an uncommon benign lesion that is characterized by diffuse synovial proliferation. Based on animal models, this lesion has been conjectured previously to be reactive in nature. In this report, the authors present the histologic and cytogenetic findings for a pigmented villonodular synovitis that was excised from the right knee of a 47-year-old man. Trisomy 7 was observed in 24 of 75 (35%) metaphases obtained from short-term culture of cells from this tumor. These findings suggest that some cases of pigmented villonodular synovitis represent clonal, neoplastic proliferations.
A Review of Recent Advances in Registration Techniques Applied to Minimally Invasive Therapy (2013)

Minimally invasive and less invasive procedure is becoming more and more common in medical therapy. Image guidance is an indispensable component in minimally invasive procedures by providing critical information about the position of the target sites and the optimal manipulation of the devices, while the field of view is limited to naked eyes due to the small incision. Registration is one of the enabling technologies for computer-aided image guidance, which brings high-resolution pre-operative data into the operating room to provide more realistic information about the patient's anatomy. In this paper, we survey the recent advances in registration techniques applied to minimally and/or less invasive therapy, including a wide variety of therapies in surgery, endoscopy, interventional cardiology, interventional radiology, and hybrid procedures. The registration approaches are categorized into several groups, including projection-to-volume, slice-to-volume, video-to-volume, and volume-to-volume registration. The focus is on recent advances in registration techniques that are specifically developed for minimally and/or less invasive procedures in the following medical specialties: neuroradiology and neurosurgery, cardiac applications, and thoracic-abdominal interventions.
Involvement of tumor necrosis factor receptor superfamily (TNFRSF) members in the pathogenesis of inflammatory diseases (2003)

Current therapies for autoimmune diseases are not cures but merely palliatives, aimed at reducing symptoms. For the most part, these treatments provide nonspecific suppression of the immune system and thus do not distinguish between a pathogenic autoimmune response and a protective immune response. Recently emerging evidence not only has indicated the involvement of members of the TNF receptor/ligand superfamilies but also has revealed exciting innovative strategies for the treatment of autoimmune diseases and other chronic inflammatory diseases without depressing the immune response in general. In this review, we will discuss the regulatory mechanisms of TNF receptor/ligand family members, such as HVEM/ LIGHT, 4-1BB/4-1BBL, and GITR/GITRL that regulate T and B cell functions and participate in the process of inflammatory diseases. We will also discuss how intervening in the costimulatory pathways mediated by these molecules might have some potential as a therapeutic approach to immune disorders.
Real Time Adaptive Color Segmentation for Mars Landing Site Identification (2003)

Real time identification of planetary landing sites is of significant importance in NASA’s precision landing program. As a lander descends towards a potential landing site, it is important to determine whether or not the potential site is free of debris to allow safe landing. This requires real time processing of images acquired by the lander during the approach, so that appropriate navigational corrections can be made to direct the lander to a safe landing zone. In this paper we discuss an adaptive color segmentation technique that can aid in identifying safe landing terrain, and terrain that may be rock covered, dusty, and unfavorable to land. A new learning architecture that allows real time adaptation in a dynamically changing environment as the lander approaches a landing site is evaluated. Results indicate that a real time adaptive color segmentation approach is sufficient to identify safe landing zones. The paper also discusses the time required for adaptation, a critical parameter during an actual descent. The simulation-based case study reported in this paper is a primary step toward developing a more realistic case for landing site identification.
A 5-GHz Wireless LAN Transmitter with Integrated Tunable High-Q RF Filter (2009)

A tunable, high-Q RF filter suitable for wireless transmitters has been implemented in a standard digital 0.18-mum CMOS technology. Active circuits are used to enhance the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> of two independent LC resonators, which are cascaded to form a wide bandwidth filter that can be tuned in both center frequency and bandwidth. A 5.145-GHz stagger-tuned filter with a 200-MHz bandwidth and 0.8 dB of ripple is demonstrated in an 802.11a sliding-IF transmitter. The transmitter provides spectral mask and EVM-compliant output power of -8.26 dBm for a 64-QAM OFDM signal. At lower output power, an EVM of -32.3 dB is achieved.
Zika Virus (2016)

n 1947, a study of yellow fever yielded the first isolation of a new virus, from the blood of a sentinel rhesus macaque that had been placed in the Zika Forest of Uganda. 1 Zika virus remained in relative obscurity for nearly 70 years; then, within the span of just 1 year, Zika virus was introduced into Brazil from the Pacific Islands and spread rapidly throughout the Americas. 2 It became the first major infectious disease linked to human birth defects to be discovered in more than half a century and created such global alarm that the World Health Organization (WHO) would declare a Public Health Emergency of International Concern.
Living with crime: spaces of risk for homeless young people (2004)

This paper reports on a study of victimization, offending and fear among homeless young people in Newcastle upon Tyne, England, which employed a participatory methodology. These young people live in marginal and often invisible spaces, yet are subject to a high degree of regulation which structures their experiences of risk. Their accounts demonstrate that an ‘either/or’ distinction which often structures understanding of offenders and victims, feared and fearful, and safe and dangerous spaces has led to their experiences being poorly represented. Homeless young people are often multiply positioned in relation to crime, an understanding which challenges the current political climate in Britain.