gebhart/patrepeval huggingface dataset:
Digital-pixel focal plane array development (2010)

Since 2006, MIT Lincoln Laboratory has been developing Digital-pixel Focal Plane Array (DFPA) readout integrated circuits (ROICs). To date, four 256 × 256 30 &#956;m pitch DFPA designs with in-pixel analog to digital conversion have been fabricated using IBM 90 nm CMOS processes. The DFPA ROICs are compatible with a wide range of detector materials and cutoff wavelengths; HgCdTe, QWIP, and InGaAs photo-detectors with cutoff wavelengths ranging from 1.6 to 14.5 &#956;m have been hybridized to the same digital-pixel readout. The digital-pixel readout architecture offers high dynamic range, A/C or D/C coupled integration, and on-chip image processing with low power orthogonal transfer operations. The newest ROIC designs support two-color operation with a single Indium bump connection. Development and characterization of the two-color DFPA designs is presented along with applications for this new digital readout technology.
Understanding Acid Lability of Cysteine Protecting Groups (2013)

Cys-disulfide bonds contribute to the stabilization of peptide and protein structures. The synthesis of these molecules requires a proper protection of Cys residues, which is crucial to prevent side-reactions and also to achieve the correct Cys connectivity. Here we undertook a mechanistic study of a set of well-known acid-labile Cys protecting groups, as well other new promising groups, in order to better understand the nature of their acid-lability. The stability of the carbocation generated during the acid treatment was found to have a direct impact on the removal of the protective groups from the corresponding protected Cys-containing peptides. Hence a combination of steric and conjugative effects determines the stability of the carbocations generated. Here we propose diphenylmethyl (Dpm) as a promising protecting group on the basis of its intermediate relative carbocation stability. All the optimized geometries and energies presented in this study were determined using a B3LYP/6-31G(d,p) calculation. The results discussed herein may be of broader applicability for the development of new protecting groups.
Nuclear Import of Exogenous FGF1 Requires the ER‐Protein LRRC59 and the Importins Kpnα1 and Kpnβ1 (2012)

Fibroblast growth factor 1 (FGF1) taken up by cells into endocytic vesicles can be translocated across vesicular membranes into the cytosol and the nucleus where it has a growth regulatory activity. Previously, leucine-rich repeat containing 59 (LRRC59) was identified as an intracellular binding partner of FGF1, but its biological role remained unknown. Here, we show that LRRC59 is strictly required for nuclear import of exogenous FGF1. siRNA-mediated depletion of LRRC59 did not inhibit the translocation of FGF1 into cytosol, but blocked the nuclear import of FGF1. We also found that an nuclear localization sequence (NLS) in FGF1, Ran GTPase, karyopherin-α1 (Kpnα1), and Kpnβ1 were required for nuclear import of FGF1. Nuclear import of exogenous FGF2, which depends on CEP57/Translokin, was independent of LRRC59, but was dependent on Kpnα1 and Kpnβ1, while the nuclear import of FGF1 was independent of CEP57. LRRC59 is a membrane-anchored protein that localizes to the endoplasmic reticulum (ER) and the nuclear envelope (NE). We found that LRRC59 possesses NLS-like sequences in its cytosolic part that can mediate nuclear import of soluble LRRC59 variants, and that the localization of LRRC59 to the NE depends on Kpnβ1. We propose that LRRC59 facilitates transport of cytosolic FGF1 through nuclear pores by interaction with Kpns and movement of LRRC59 along the ER and NE membranes.
Synthesis and evaluation of the 2,4-diaminoquinazoline series as anti-tubercular agents (2014)

The 2,4-diaminoquinazoline class of compounds has previously been identified as an effective inhibitor of Mycobacterium tuberculosis growth. We conducted an extensive evaluation of the series for its potential as a lead candidate for tuberculosis drug discovery. Three segments of the representative molecule N-(4-fluorobenzyl)-2-(piperidin-1-yl)quinazolin-4-amine were examined systematically to explore structure-activity relationships influencing potency. We determined that the benzylic amine at the 4-position, the piperidine at 2-position and the N-1 (but not N-3) are key activity determinants. The 3-deaza analog retained similar activity to the parent molecule. Biological activity was not dependent on iron or carbon source availability. We demonstrated through pharmacokinetic studies in rats that good in vivo compound exposure is achievable. A representative compound demonstrated bactericidal activity against both replicating and non-replicating M. tuberculosis. We isolated and sequenced M. tuberculosis mutants resistant to this compound and observed mutations in Rv3161c, a gene predicted to encode a dioxygenase, suggesting that the compound may act as a pro-drug.
Synthesis and characterization of PVP-coated large core iron oxide nanoparticles as an MRI contrast agent (2008)

The purpose of this study was to synthesize biocompatible polyvinylpyrrolidone (PVP)-coated iron oxide (PVP-IO) nanoparticles and to evaluate their efficacy as a magnetic resonance imaging (MRI) contrast agent. The PVP-IO nanoparticles were synthesized by a thermal decomposition method and characterized by x-ray diffraction (XRD), transmission electron microscopy (TEM), dynamic light scattering (DLS), and a superconducting quantum interface device (SQUID). The core size of the particles is about 8-10 nm and the overall size is around 20-30 nm. The measured r(2) (reciprocal of T(2) relaxation time) and r2∗ (reciprocal of T2∗ relaxation time) are 141.2 and 338.1 (s mM)(-1), respectively. The particles are highly soluble and stable in various buffers and in serum. The macrophage uptake of PVP-IO is comparable to that of Feridex as measured by a Prussian blue iron stain and phantom study. The signal intensity of a rabbit liver was effectively reduced after intravenous administration of PVP-IO. Therefore PVP-IO nanoparticles are potentially useful for T(2)-weighted MR imaging.
Hepatitis C Virus NS5A Protein Modulates c-Jun N-terminal Kinase through Interaction with Tumor Necrosis Factor Receptor-associated Factor 2 (2003)

The nonstructural 5A (NS5A) protein of hepatitis C virus (HCV) is a phosphoprotein possessing various functions. We have previously reported that the HCV NS5A protein interacts with tumor necrosis factor (TNF) receptor-associated factor (TRAF) domain of TRAF2 (Park, K.-J., Choi, S.-H., Lee, S. Y., Hwang, S. B., and Lai, M. M. C. (2002) J. Biol. Chem. 277, 13122-13128). Both TNF-alpha- and TRAF2-mediated nuclear factor-kappaB (NF-kappaB) activations were inhibited by NS5A-TRAF2 interaction. Because TRAF2 is required for the activation of both NF-kappaB and c-Jun N-terminal kinase (JNK), we investigated HCV NS5A protein for its potential capacity to modulate TRAF2-mediated JNK activity. Using in vitro kinase assay, we have found that NS5A protein synergistically activated both TNF-alpha- and TRAF2-mediated JNK in human embryonic kidney 293T cells. Furthermore, synergism of NS5A-mediated JNK activation was inhibited by dominant-negative form of MEK kinase 1. Our in vivo binding data show that NS5A does not inhibit interaction between TNF receptor-associated death domain and TRAF2 protein, indicating that NS5A and TRAF2 may form a ternary complex with TNF receptor-associated death domain. These results indicate that HCV NS5A protein modulates TNF signaling of the host cells and may play a role in HCV pathogenesis.
3D point cloud segmentation: A survey (2013)

3D point cloud segmentation is the process of classifying point clouds into multiple homogeneous regions, the points in the same region will have the same properties. The segmentation is challenging because of high redundancy, uneven sampling density, and lack explicit structure of point cloud data. This problem has many applications in robotics such as intelligent vehicles, autonomous mapping and navigation. Many authors have introduced different approaches and algorithms. In this survey, we examine methods that have been proposed to segment 3D point clouds. The advantages, disadvantages, and design mechanisms of these methods are analyzed and discussed. Finally, we outline the promising future research directions.
Fully bipolar, 120-Msample/s 10-b track-and-hold circuit (1992)

Describes the design and experimental results of a fully bipolar track-and-hold (T&H) circuit for use in video applications. A fully differential, open-loop approach has been chosen in order to meet the specifications with respect to track-to-hold step, droop rate, and hold-mode feedthrough. In order to obtain maximum high-frequency performance, p-n-p transistors have been omitted from the design. The T&H circuit has been realized in a 3-GHz f/sub T/ bipolar production process with a minimum emitter size of 2*9 mu m/sup 2/. The die size is 0.25 mm/sup 2/, consuming 40 mW from a single 5-V power supply. Ten-bit performance has been measured up to 12-Msample/s full-Nyquist sampling rate. At 200 Msample/2, 8-b performance has been observed over the full-Nyquist band.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Melanoma differentiation-associated gene 7/interleukin (IL)-24 is a novel ligand that regulates angiogenesis via the IL-22 receptor. (2003)

The melanoma differentiation-associated gene 7 (mda-7), also called interleukin (IL)-24, suppresses the growth of some cancers in vitro and in vivo as a result of the ectopic expression of its protein. However, the function of the secreted form of the protein in cancer has not been previously studied. The purpose of this study was to determine the antiangiogenic function of a secreted form of the MDA-7/IL-24 protein (sMDA-7/IL-24). In vitro, sMDA-7/IL-24 inhibited both endothelial cell differentiation and migration of endothelial cells induced by vascular endothelial growth factor and basic fibroblast growth factor. The sMDA-7/IL-24-mediated inhibitory effect was 10-50 times more potent than endostatin, IFN-gamma, and IFN-inducible protein 10 in vitro. Furthermore, the inhibitory effect was not mediated by IFN or IFN-inducible protein 10. IL-22 receptor mediated the antiangiogenic activity of sMDA-7/IL-24. Administration of a blocking antibody to IL-22 receptor in conjunction with sMDA-7/IL-24 led to abrogation of inhibition of endothelial differentiation. sMDA-7/IL-24 inhibited vascular endothelial growth factor-induced angiogenesis as evidenced by reduced vascularization and hemoglobin content in in vivo Matrigel plug assays. In vivo, the growth of human lung tumor cells was significantly inhibited, and vascularization was reduced when the cells were mixed with 293 cells stably expressing sMDA-7/IL-24. Systemic administration of sMDA-7/IL-24 inhibited lung tumor growth in a mouse xenograft model. Associated with tumor growth inhibition was decreased tumor microvessel density and hemoglobin content, indicating the presence of antiangiogenic activity. These data demonstrate that sMDA-7/IL-24 is a novel and potent antiangiogenic effector and support the development of MDA-7/IL-24-based therapeutics.
Bayesian Learning Using Gaussian Process for Gas Identification (2006)

In this paper, a novel gas identification approach based on Gaussian process (GP) combined with principal components analysis is proposed. The effectiveness of this approach has been successfully demonstrated on an experimentally obtained dataset. Our aim is the identification of different gases with an array of commercial Taguchi gas sensors (TGS) as well as microelectronic gas sensors. The proposed approach is shown to outperform both K nearest neighbor (KNN) and multilayer perceptron (MLP) classifiers
A Virus-Based Nanoblock with Tunable Electrostatic Properties (2005)

Five different "HIS tag" mutants of cowpea mosaic virus were made by genetically introducing six contiguous histidine residues at various locations on the virus capsid. The mutant particles showed differential affinity for binding nickel, and their electrostatic properties could be controlled as a function of the protonation state of the exposed histidine sequence. The specific addressability of the HIS tag was corroborated by the selective modification of the histidine sequence with nanogold cross-linked to the Ni-NTA moiety.
Gaseous−33He magnetic dipolar spin relaxation (1993)

We derive the nuclear-spin relaxation rate of gaseous $^{3}\mathrm{He}$ due to the magnetic-dipole interaction between the $^{3}\mathrm{He}$ nuclear spins. This dipolar relaxation rate is numerically evaluated for temperatures from 0.1 K to 550 K. At room temperature, the relaxation time for a $^{3}\mathrm{He}$ density of 10 amagats is 74.4 h. We have made a series of high-density (4--12 amagat) $^{3}\mathrm{He}$ samples for which nulcear relaxation is limited by the magnetic-dipole interaction. Both our theoretical and experimental results are particularly important for the growing use of $^{3}\mathrm{He}$, polarized through spin exchange with optically pumped Rb vapor.
Investigation of herpes simplex virus type 1 genes encoding multiply inserted membrane proteins (1991)

The herpes simplex virus type 1 genome contains four open reading frames (ORFs) which are predicted to encode hydrophobic proteins with the potential to cross a membrane several times. The products of these genes (genes UL10, UL20, UL43 and UL53) have not previously been identified. To investigate the role of these proteins in the virus life cycle, we attempted to inactivate the genes individually by inserting the lacZ gene from Escherichia coli within the ORFs. Using this approach we have isolated insertion mutants for UL10 and UL43, as well as a deletion mutant lacking the majority of the UL43 ORF. The growth of the UL10-lacZ virus was slightly impaired in tissue culture compared to that of the wild-type virus parent, whereas the growth of the UL43 mutants was indistinguishable from that of wild-type virus. Furthermore, deletion of the majority of the UL43 ORF did not impair the ability of the virus to replicate in vivo at the periphery, or to spread to and replicate within the nervous system, in a mouse ear model. Repeated attempts to isolate lacZ insertion mutants for UL20 and UL53 were unsuccessful, suggesting that these genes may be essential for virus growth, at least in tissue culture. Using antipeptide sera, the products of genes UL10 and UL20 have been detected.
Cloning of a maltogenic alpha-amylase from Bacillus stearothermophilus (1988)

We have cloned and expressed a novel maltogenic alpha-amylase from B. stearothermophilus on plasmid in B. subtilis. Originally the plasmid was very unstable in the absence of selection, but was stabilized due to a spontaneous, copy number reducing mutation. The promoter region and the extension of the gene have been analysed, and a provisional DNA sequence has been determined. The N-terminal of the mature amylase has been determined and shown to be in accordance with signal peptidase processing after a typical Gram-positive signal sequence of 33 amino acids.
A melanoma-specific VH antibody cloned from a fusion phage library of a vaccinated melanoma patient. (1996)

The human antimelanoma antibody V86 was cloned from a single-chain Fv molecule (scFv) fusion phage library displaying the heavy chain variable domain (VH) and light chain variable domain (VL.) repertoire of a melanoma patient immunized with genetically-modified autologous tumor cells. Previous ELISA tests for binding of the V86 fusion phage to a panel of human metastatic melanoma and carcinoma cell lines and primary cultures of normal melanocytes, endothelial, and fibroblast cells showed that measurable binding occurred only to the melanoma cells. In this communication, the strict specificity of V86 for melanoma cells was confirmed by immunohistochemical staining tests with cultured cells and frozen tissue sections. The V86 fusion phage stained melanoma cell lines but did not stain carcinoma cell lines or cultured normal cells; V86 also stained specifically the melanoma cells in sections of metastatic tissue but did not stain any of the cells in sections from normal skin, lung, and kidney or from metastatic colon and ovarian carcinomas and a benign nevus. An unexpected finding is that V86 contains a complete VH domain but only a short segment of a VL, domain, which terminates before the CDR1 region. This VL deletion resulted from the occurrence in the VL cDNA of a restriction site, which was cleaved during construction of the scFv library. Thus V86 is essentially a VH antibody. The effect of adding a VI. domain to V86 was examined by constructing scFv fusion phage libraries in which V86 was coupled to Vlambda or Vkappa domains from the original scFv library of the melanoma patient and then panning the libraries against melanoma cells to enrich for the highest affinity antibody clones. None of the V86-Vlambda clones showed significant binding to melanoma cells in ELISA tests; although binding occurred with most of the V86-Vkappa clones, it was generally weaker than the binding of V86. These results indicate that most of the VL domains in the original scFv library reduce or eliminate the affinity of V86 for melanoma cells. Accordingly, VH libraries could provide access to anti-tumor antibodies that might not be detected in scFv or Fab libraries because of the incompatibility of most randomly paired VH and VL, domains.
Flexible information presentation with XML (1999)

The development of user interfaces is often the most work intensive phase of computer system design, accounting for the majority of cut code. To assist this development, many IDEs (Integrated Development Environments) offer GUI (Graphical User Interface) builders. However, these builders are commonly built within a single computing framework, such as Java, HTML, or Visual Basic. With the emergence of a common currency of interface elements, there is an opportunity to create new tools that encourage GUI reuse across framework boundaries.
Inhibition of Tumor Cell Growth by A Specific 6-Phosphofructo-2-kinase Inhibitor,N-Bromoacetylethanolamine Phosphate, and Its Analogues (2000)

The high rate of glycolysis despite the presence of oxygen and mitochondria in tumor cells implies an important role for this process in cell division. The rate of glycolysis is assumed to be dependent on the cellular concentration of fructose 2,6-bisphosphate, the concentration of which in turn depends on a bifunctional enzyme and the ratio of this enzyme's 6-phosphofructo-2-kinase versus its fructose 2,6-bisphosphatase activities. To prove the hypothesis that inhibition of glycolysis in tumor cells by 6-phosphofructo-2-kinase inhibitors would cause inhibition of tumor cell proliferation, ten N-bromoacetylethanolamine phosphate analogues were designed, synthesized, and tested. They were screened for their activities against various human tumor cell lines to study the effects of inhibition of glycolysis on cell proliferation. The relationship between the structure of these compounds and their inhibitory activity on cell proliferation was also discussed. It was found that the activity of N-(2-methoxyethyl)-bromoacetamide, N-(2-ethoxyethyl)-bromoacetamide, and N-(3-methoxypropyl)-bromoacetamide was comparable to that of the positive control AraC. These three inhibitors showed in vivo anticancer effects in P388 transplant BDF1 mice.
A Novel One-Armed Anti-c-Met Antibody Inhibits Glioblastoma Growth In vivo (2006)

Local treatment with OA-5D5 can almost completely inhibit intracerebral glioblastoma growth when SF/HGF is driving tumor growth. The mechanisms of tumor inhibition include antiproliferative, antiangiogenic, and proapoptotic effects.
Antivirals and vaccines for Enterovirus A71 (2019)

Enterovirus A71 (EV-A71) is an important emerging virus posing a threat to children under five years old. EV-A71 infection in infants or young children can cause hand-foot-and-mouth disease, herpangina, or severe neurological complications. However, there are still no effective antivirals for treatment of these infections. In this review, we summarize the antiviral compounds developed to date based on various targets of the EV-A71 life cycle. Moreover, development of a vaccine would be the most effective approach to prevent EV-A71 infection. Therefore, we also summarize the development and clinical progress of various candidate EV-A71 vaccines, including inactivated whole virus, recombinant VP1 protein, synthetic peptides, viral-like particles, and live attenuated vaccines.
Inhibition of Dengue Virus by an Ester Prodrug of an Adenosine Analog (2010)

Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen that infects humans. Neither a vaccine nor an antiviral therapy is currently available for DENV. Here, we report an adenosine nucleoside prodrug that potently inhibits DENV replication both in cell culture and in a DENV mouse model. NITD449 (2'-C-acetylene-7-deaza-7-carbamoyladenosine) was initially identified as a parental compound that inhibits all four serotypes of DENV with low cytotoxicity. However, in vivo pharmacokinetic studies indicated that NITD449 had a low level of exposure in plasma when dosed orally. To increase the oral bioavailability, we covalently linked isobutyric acids to the 3'- and 5'-hydroxyl groups of ribose via ester linkage to NITD449, leading to the prodrug NITD203 (3',5'-O-diisobutyryl-2'-C-acetylene-7-deaza-7-carbamoyl-adenosin). Pharmacokinetic analysis showed that upon oral dosing of the prodrug, NITD203 was readily converted to NITD449, resulting in improved exposure of the parental compound in plasma in both mouse and rat. In DENV-infected AG129 mice, oral dosing of the prodrug at 25 mg/kg of body weight reduced peak viremia by 30-fold. Antiviral spectrum analysis showed that NITD203 inhibited various flaviviruses (DENV, yellow fever virus, and West Nile virus) and hepatitis C virus but not Chikungunya virus (an alphavirus). Mode-of-action analysis, using a luciferase-reporting replicon, indicated that NITD203 inhibited DENV RNA synthesis. Although NITD203 exhibited potent in vitro and in vivo efficacies, the compound could not reach a satisfactory no-observable-adverse-effect level (NOAEL) in a 2-week in vivo toxicity study. Nevertheless, our results demonstrate that a prodrug approach using a nucleoside analog could potentially be developed for flavivirus antiviral therapy.