gebhart/patrepeval huggingface dataset:
Postherpetic Neuralgia (2004)

Postherpetic neuralgia (PHN) is a chronic neuropathic pain syndrome defined as pain persisting more than 3 months after the resolution of herpes zoster-associated rash. It is often characterized as spontaneous aching or burning with paroxysmal shooting pains in the affected dermatome and may be accompanied by allodynia or hyperalgesia. There is an increased incidence of PHN in elderly patients, patients with ophthalmic herpes zoster, and immunocompromised patients. PHN may result from dorsal horn destruction, although pathophysiologic changes in more proximal central structures and distal peripheral structures have been described. Based on randomized, controlled studies, the most effective medical therapies include gabapentin, topical lidocaine, tricyclic antidepressants, and oral opioid analgesics. Surgical interventions for refractory cases including intrathecal drug administration, central ablative procedures, and central electrical stimulation continue to meet with limited success.
Nanophotonic particle simulation and inverse design using artificial neural networks (2018)

We propose a method to use artificial neural networks to approximate light scattering by multilayer nanoparticles. We find that the network needs to be trained on only a small sampling of the data to approximate the simulation to high precision. Once the neural network is trained, it can simulate such optical processes orders of magnitude faster than conventional simulations. Furthermore, the trained neural network can be used to solve nanophotonic inverse design problems by using back propagation, where the gradient is analytical, not numerical.
Knockout Rats via Embryo Microinjection of Zinc-Finger Nucleases (2009)

The toolbox of rat genetics currently lacks the ability to introduce site-directed, heritable mutations into the genome to create knockout animals. By using engineered zinc-finger nucleases (ZFNs) designed to target an integrated reporter and two endogenous rat genes, Immunoglobulin M (IgM) and Rab38, we demonstrate that a single injection of DNA or messenger RNA encoding ZFNs into the one-cell rat embryo leads to a high frequency of animals carrying 25 to 100% disruption at the target locus. These mutations are faithfully and efficiently transmitted through the germline. Our data demonstrate the feasibility of targeted gene disruption in multiple rat strains within 4 months time, paving the way to a humanized monoclonal antibody platform and additional human disease models.
Mutation of a phenylalanine conserved in SH3-containing tyrosine kinases activates the transforming ability of c-Abl. (1993)

c-abl is the normal cellular homolog of the v-abl transforming gene of Abelson murine leukemia virus. By constructing recombinants between c- and v-abl retroviruses, we show that a point mutation in c-Abl is sufficient to change the myristoylated form of c-Abl into a protein able to transform fibroblasts, but not capable of transforming bone marrow or inducing Abelson disease. This activating mutation, which changes the phenylalanine at amino acid 420 to valine (F420V) found in the homologous position of v-Abl, is positioned outside of the SH3 domain, a region typically modified in transforming alleles of abl. Phenylalanine 420 is perfectly conserved among tyrosine kinases with N-terminal SH3 domains (the Src and Abl families). The equivalent position in other protein tyrosine kinases is a conserved hydrophobic residue that predicts the specific family to which that kinase belongs. Mutation of phenylalanine 420 to other hydrophobic residues activates c-Abl. Unlike other transforming variants of Abl, the F420V mutant protein is not highly phosphorylated on tyrosine. Mutation of the nearby proposed autophosphorylation site, tyrosine 412, shows that this tyrosine is not strictly required for fibroblast transformation in either F420V or SH3-deleted variants of c-Abl (IV).
Sequential circuit design using synthesis and optimization (2003)

A description is given of SIS, an interactive tool for synthesis and optimization of sequential circuits. Given a state transition table or a logic-level description of a sequential circuit, SIS produces an optimized net-list in the target technology while preserving the sequential input-output behavior. Many different programs and algorithms have been integrated into SIS, allowing the user to choose among a variety of techniques at each stage of the process. It is built on top of MISII and includes all (combinational) optimization techniques therein as well as many enhancements. SIS serves as both a framework within which various algorithms can be tested and compared and as a tool for automatic synthesis and optimization of sequential circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Application of a novel immunization protocol to the production of monoclonal antibodies specific for macrophages in human placenta. (1989)

A monolayer depletion/adoptive immunization protocol that biased the immune response towards recognition of placental macrophage (pMO) antigens was established. BALB/c spleen cells immune to human pMO were adsorbed onto monolayers of the B-cell line QIMR-WIL. Monolayer-depleted or unfractionated cells were transferred to irradiated recipients, which subsequently were restimulated with pMO then killed for hybridoma production. Screening of hybridomas revealed an increased proportion of pMO-specific hybridomas following transfer and fusion of monolayer-depleted cells. Two monoclonal antibodies (mAb), L9 and L21, which were generated through application of this protocol, are described. L9 recognized an antigen on cells within the villi in sections of term placenta and freshly isolated pMO. With time in culture, expression of this antigen decreased markedly. Macrophages, but no other cell type, in placental cell suspensions expressed this antigen. L9 failed to react with any peripheral blood cells. Immunoprecipitation and SDS-PAGE analyses indicated that two proteins of molecular weight (MW) 40,000 and 43,000 were recognized by L9. Sections of term placenta and freshly isolated pMO failed to react with L21. After 2-3 days in culture, however, most macrophages expressed this antigen. L21 reacted weakly with peripheral monocytes and granulocytes but not other normal peripheral blood cells. Myeloid cell lines reacted strongly with this mAb only after activation with PMA. SDS-PAGE analyses of the L21 immunoprecipitate under non-reducing conditions revealed a single band of 61,000 MW, while two bands of 46,000 and 49,000 MW were detected under reducing conditions. Cellular distribution and molecular weight analyses indicated that the antigens recognized by these two mAb were apparently distinct from previously defined myeloid antigens.
Fyn inhibition rescues established memory and synapse loss in Alzheimer mice (2015)

Targeting Fyn can reverse memory deficits found in AD mouse models, and rescue synapse density loss characteristic of the disease. Thus, AZD0530 is a promising candidate to test as a potential therapy for AD.
Sugared biomaterial binding lectins: achievements and perspectives (2016)

Lectins, a distinct group of glycan-binding proteins, play a prominent role in the immune system ranging from pathogen recognition and tuning of inflammation to cell adhesion or cellular signalling. The possibilities of their detailed study expanded along with the rapid development of biomaterials in the last decade. The immense knowledge of all aspects of glycan-lectin interactions both in vitro and in vivo may be efficiently used in bioimaging, targeted drug delivery, diagnostic and analytic biological methods. Practically applicable examples comprise photoluminescence and optical biosensors, ingenious three-dimensional carbohydrate microarrays for high-throughput screening, matrices for magnetic resonance imaging, targeted hyperthermal treatment of cancer tissues, selective inhibitors of bacterial toxins and pathogen-recognising lectin receptors, and many others. This review aims to present an up-to-date systematic overview of glycan-decorated biomaterials promising for interactions with lectins, especially those applicable in biology, biotechnology or medicine. The lectins of interest include galectin-1, -3 and -7 participating in tumour progression, bacterial lectins from Pseudomonas aeruginosa (PA-IL), E. coli (Fim-H) and Clostridium botulinum (HA33) or DC-SIGN, receptors of macrophages and dendritic cells. The spectrum of lectin-binding biomaterials covered herein ranges from glycosylated organic structures, calixarene and fullerene cores over glycopeptides and glycoproteins, functionalised carbohydrate scaffolds of cyclodextrin or chitin to self-assembling glycopolymer clusters, gels, micelles and liposomes. Glyconanoparticles, glycan arrays, and other biomaterials with a solid core are described in detail, including inorganic matrices like hydroxyapatite or stainless steel for bioimplants.
Simultaneous band-gap narrowing and carrier-lifetime prolongation of organic–inorganic trihalide perovskites (2016)

The organic-inorganic hybrid lead trihalide perovskites have been emerging as the most attractive photovoltaic materials. As regulated by Shockley-Queisser theory, a formidable materials science challenge for improvement to the next level requires further band-gap narrowing for broader absorption in solar spectrum, while retaining or even synergistically prolonging the carrier lifetime, a critical factor responsible for attaining the near-band-gap photovoltage. Herein, by applying controllable hydrostatic pressure, we have achieved unprecedented simultaneous enhancement in both band-gap narrowing and carrier-lifetime prolongation (up to 70% to ∼100% increase) under mild pressures at ∼0.3 GPa. The pressure-induced modulation on pure hybrid perovskites without introducing any adverse chemical or thermal effect clearly demonstrates the importance of band edges on the photon-electron interaction and maps a pioneering route toward a further increase in their photovoltaic performance.
Study of the temperature-dependent nitrogen retention in tungsten surfaces using X-ray photoelectron spectroscopy (2018)

Nitrogen is foreseen as seeding species in future magnetic confinement fusion reactors in order to reduce the power load from the plasma onto the divertor target tiles by radiative cooling. As a side effect it also gets implanted into the tungsten wall and forms tungsten nitrides (WxN). The temperature-dependent WxN formation was investigated in dedicated laboratory experiments. N ions of 300 eV kinetic energy were implanted into W samples under ultra-high vacuum conditions in the temperature range 300 K to 800 K. The N retention in W was monitored and quantitatively analysed by X-ray photoelectron spectroscopy (XPS). A method to calculate the statistical error of the measured data based on Bayesian statistics was developed. Argon sputter depth profiling was combined with XPS to measure N in W depth profiles which were compared with simulated N implantation profiles. Annealing of samples implanted with N at 300 K does not cause a loss of N up to 800 K. However, the retained N amount decreases linearly with increasing implantation temperature. It was found that this reduction is due to ion-irradiation-induced N release at elevated temperatures. Over the whole temperature range N diffusion into depth was not observed. N accumulation measurements showed no evidence for a phase transition in the WxN layer. However, high resolution XPS measurements revealed that below 600 K a second photoelectron peak occurs in the N 1s signal which can be attributed to different local atomic arrangements of WxN.
Visual summaries of popular landmarks from community photo collections (2009)

We present a novel data-driven algorithm that leverages online image repositories such as Flickr for automatically generating tourist maps. Our hypothesis is that, given a large enough dataset of images with geo-based metadata, clusters of matching images from that dataset tend to provide reliable cues as to what the popular tourist spots may be. Our algorithm takes the geographical area of interest as input and retrieves geotagged photos from online photo collections. By clustering the photos based on their locations and identifying the popular tags for each cluster, our algorithm generates a set of points of interest (POIs) for the area. After retrieving additional photos based on these discovered POI tags, we use image matching to find the most representative landmark view for each POI. Finally, we remove clutter from the representative image and apply tooning to generate a map icon for each landmark.
Incremental Fusion of Structure-from-Motion and GPS Using Constrained Bundle Adjustments (2012)

Two problems occur when bundle adjustment (BA) is applied on long image sequences: large calculation time and drift (or error accumulation). In recent work, the calculation time is reduced by local BAs applied in an incremental scheme. The drift may be reduced by fusion of GPS and Structure-from-Motion. An existing fusion method is BA minimizing a weighted sum of image and GPS errors. This paper introduces two constrained BAs for fusion which enforce an upper bound for the reprojection error. These BAs are alternatives to the existing fusion BA which does not guarantee a small reprojection error and requires a weight as input. Then, the three fusion BAs are integrated in an incremental Structure-from-Motion method based on local BA. Last, we will compare the fusion results on long monocular image sequences and low cost GPS.
The dominant role of bone marrow-derived cells in CTL induction following plasmid DNA immunization at different sites (1997)

Although plasmid DNA immunization provides an effective means of inducing CTL responses to an expressed Ag, the mechanism by which CTL precursors are activated remains to be established. Insights could be gained by identifying the cells responsible for Ag presentation when DNA is introduced into different tissue sites. By immunizing parent into F1 bone marrow chimeric mice with an influenza nucleoprotein-expressing plasmid, we have demonstrated that the key cells in this presentation process for both gene gun-mediated epidermal injection and needle intramuscular injection of plasmid DNA are bone marrow derived. Furthermore, as assessed by intramuscular injection, coexpression of nucleoprotein with the costimulatory molecule B7-2, or the cytokines granulocyte-macrophage CSF and IL-12, did not convert nonhemopoietic cells into APCs. Thus, for two distinctly different modes of DNA immunization, in one case with or without coexpressed immunostimulatory factors, the APCs were consistently found to be of hemopoietic origin.
Development of a mouse model for HIV/AIDS. (2003)

A small animal model would be very valuable for HIV/AIDS vaccine testing, investigating HIV pathophysiology, and exploring anti-HIV therapeutics. Unfortunately, HIV does not replicate in mouse cells. Provision of mouse cells with human CD4, CCR5 and cyclin T1 (cycT1) has uncovered a block to HIV assembly or release. Since mouse-human cell fusions allow viral replication, mouse cells lack at least one critical factor that permits completion of the viral life cycle. To identify this factor(s) we are employing 2 similar genetic approaches. Each cell line of a panel of monochromosomal mouse-human somatic cell hybrids was individually transduced with an HIV vector encoding both cycT1 and blasticidin resistance (HIV-CIB). Each was then transfected with vesicular stomatitis virus (VSV) G protein and measurable virus was recovered from only the hybrid-containing chromosome 2. This was verified with an M-tropic envelope and was shown to be specific to HIV. In addition, the amount of p24 release from that hybrid was substantially greater than that from the parent. A second cell line expressing chromosome 2 had a similar phenotype. CycT1 has been introduced into one chromosome 2 line to monitor the spread of HIV. In a related but separate approach, an entire collection of approximately 500 mouse-human microcell hybrids was transduced with HIV-CIB and broken down into manageable pools. Virus was similarly recovered as above from a few of the pools. Those pools were then broken down to clones and several cell clones have been identified that allow virus release. Revertants that no longer have the human chromosome are now being tested for loss of phenotype. Clones will then be tested for ability to support both HIV replication and Gag processing. Human chromosomal content of the clones of greatest interest will be determined by STS content analysis. Results from the 2 approaches are expected to be in agreement and may provide direction for an expression cloning approach.
Characterization of sodium dodecyl sulfate-resistant proteolytic activity in the hyperthermophilic archaebacterium Pyrococcus furiosus (1990)

Cell extracts from Pyrococcus furiosus were found to contain five proteases, two of which (S66 and S102) are resistant to sodium dodecyl sulfate (SDS) denaturation. Cell extracts incubated at 98 degrees C in the presence of 1% SDS for 24 h exhibited substantial cellular proteolysis such that only four proteins could be visualized by amido black-Coomassie brilliant blue staining of SDS-polyacrylamide gels. The SDS-treated extract retained 19% of the initial proteolytic activity as represented by two proteases, S66 (66 kilodaltons [kDa]) and S102 (102 kDa). Immunoblot analysis with guinea pig sera containing antibodies against protease S66 indicated that S66 is related neither to S102 nor to the other proteases. The results of this analysis also suggest that S66 might be the hydrolysis product of a 200-kDa precursor which does not have proteolytic activity. The 24-h SDS-treated extract showed unusually thermostable proteolytic activity; the measured half-life at 98 degrees C was found to be 33 h. Proteases S66 and S102 were also resistant to denaturation by 8 M urea, 80 mM dithiothreitol, and 5% beta-mercaptoethanol. Purified protease S66 was inhibited by phenylmethylsulfonyl fluoride and diisopropyl fluorophosphate but not by EDTA, ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid, or iodoacetic acid. These results indicate that S66 is a serine protease. Amino acid ester hydrolysis studies showed that protease S66 was hydrolytically active towards N-benzoyl-L-arginine ethyl ester.
[6.7-Dihydroxycoumarin (Aesculetin) as a substrate for catechol-o-methyltransferase (author's transl)]. (1976)

6,7-Dihydroxycoumarin (Aesculetin) was found to be a substrate of rat liver Catechol-O-methylfransferase (COMT) (EC 2.1.1.6). Incubation of this substrate with S-Adenosyl-L-[methyl-14C]methionine and/or S-Adenosylmethionin-hydrogensulfate in the presence of COMT yields the highly fluorescent compounds 7-hydroxy-6-methoxycoumarin (Scopoletin) and 6-hydroxy-7-methoxycoumarin (Isoscopoletin) in the ration of about 2:1. The O-methylated products obtained from Aesculetin were identified after separation by thin layer chromatography mainly by the reversed isotope dilution technique. The fluorescence of the isolated methylethers was proportional to concentration within the range from 10(-5)-10(-7) M. A reciprocal plot of activity versus substrate concentration gives a Km of 1 X 10(-6) M.
Silk‐elastinlike protein polymers improve the efficacy of adenovirus thymidine kinase enzyme prodrug therapy of head and neck tumors (2010)

The SELP-controlled gene delivery approach could potentially improve the anticancer activity of virus-mediated gene therapy at the same time as limiting viral spread to normal organs.
Characterisation of the cannabinoid receptor system in synovial tissue and fluid in patients with osteoarthritis and rheumatoid arthritis (2008)

Our data predict that the cannabinoid receptor system present in the synovium may be an important therapeutic target for the treatment of pain and inflammation associated with OA and RA.
Mouse Strain Differences in Plasmacytoid Dendritic Cell Frequency and Function Revealed by a Novel Monoclonal Antibody (2003)

We report in this study the generation of a novel rat mAb that recognizes mouse plasmacytoid dendritic cells (pDC). This Ab, named 120G8, stains a small subset of CD11c(low) spleen cell with high specificity. This population produces high amounts of IFN-alpha upon in vitro viral stimulation. Both ex vivo- and in vitro-derived 120G8(+) cells display a phenotype identical with that of the previously described mouse pDC (B220(high)Ly6C(high)Gr1(low)CD11b(-)CD11c(low)). Mice treated with 120G8 mAb are depleted of B220(high)Ly6C(high)CD11c(low) cells and have a much-reduced ability to produce IFN-alpha in response to in vivo CpG stimulation. The mAb 120G8 stains all and only B220(high)Ly6C(high)CD11c(low) pDC in all lymphoid organs. Immunohistochemical studies performed with this mAb indicate that pDC are located in the T cell area of spleen, lymph nodes, and Peyer's patches. Although the Ag recognized by 120G8 is not yet known, we show that its expression is up-regulated by type I IFN on B cells and DC. Using this mAb in immunofluorescence studies demonstrates strain- and organ-specific differences in the frequency of pDC and other DC subsets. 129Sv mice have a much higher frequency of pDC, together with a lower frequency of conventional CD8alpha(+)CD11c(high) DC, compared with C57BL/6 mice, both in spleen and blood. The higher ability of 129Sv mice to produce IFN-alpha in vivo is related to a higher number of pDC, but also to a higher ability of pDC from 129Sv mice to produce IFN-alpha in vitro in response to viral stimulation.
Development of Stable, Water-Dispersible, and Biofunctionalizable Superparamagnetic Iron Oxide Nanoparticles (2011)

Water-dispersible superparamagnetic iron oxide nanoparticles (SPIONs) were synthesized by thermal decomposition of iron(III) acetylacetonate in the presence of triethylene glycol (TREG). The resulting TREG-coated SPIONs were not stable, undergoing agglomeration and loss of the TREG coating under prolonged storage at 37 °C or in the presence of increased saline concentrations. To avoid these problems, stable colloidal TREG-coated SPIONs were obtained by two different procedures: (i) dimercaptosuccinic acid (DMSA) ligand-exchange reactions to obtain DMSA-coated SPIONs and (ii) chemical modification of the TREG coating. Both procedures, but especially the DMSA exchange, increased the stability of the SPION suspension. Finally, the functionality of both types of particles for biological applications was demonstrated by conjugating a model antibody to the end carboxyl groups of the SPIONs and testing the immunoreactivity of the final antibody–particle conjugates by an enzyme-linked immunosorbent assay (ELISA).