gebhart/patrepeval huggingface dataset:
Synergistic neutralization of human immunodeficiency virus type 1 by combinations of human monoclonal antibodies (1994)

The ability of antibodies to the V3 region and the CD4-binding domain (CD4bd) of human immunodeficiency virus type 1 (HIV-1) to act in synergy to neutralize HIV has been demonstrated previously. However, synergy between antibodies to other HIV-1 epitopes has not been studied. We have used 21 combinations of human monoclonal antibodies (MAbs) directed against different epitopes of the gp120 and gp41 proteins of HIV-1 to evaluate their ability to act in synergy to neutralize HIV-1. Combinations of anti-V3 and anti-CD4bd antibodies, anti-V3 and anti-gp120 C-terminus antibodies, anti-CD4bd and anti-C-terminus antibodies, anti-V3 and anti-gp41 antibodies, and anti-CD4bd and anti-gp41 antibodies were tested. Our results show that some, but not all anti-V3 antibodies can act in synergy with anti-CD4bd antibodies. In addition, for the first time, antibodies to the C-terminus region have been found to act in synergy with the anti-CD4bd antibodies. Various anti-CD4bd MAbs also act in synergy when used together. The use of such cocktails of human MAbs for passive immunization against HIV-1 may prove to be important for therapy in postexposure settings and for prevention of maternal-fetal transmission of the virus. The results also provide information on the types of antibodies that should be elicited by an effective vaccine.
Squeeze-and-Excitation Networks (2018)

Convolutional neural networks are built upon the convolution operation, which extracts informative features by fusing spatial and channel-wise information together within local receptive fields. In order to boost the representational power of a network, several recent approaches have shown the benefit of enhancing spatial encoding. In this work, we focus on the channel relationship and propose a novel architectural unit, which we term the "Squeeze-and-Excitation" (SE) block, that adaptively recalibrates channel-wise feature responses by explicitly modelling interdependencies between channels. We demonstrate that by stacking these blocks together, we can construct SENet architectures that generalise extremely well across challenging datasets. Crucially, we find that SE blocks produce significant performance improvements for existing state-of-the-art deep architectures at minimal additional computational cost. SENets formed the foundation of our ILSVRC 2017 classification submission which won first place and significantly reduced the top-5 error to 2.251%, achieving a ~25% relative improvement over the winning entry of 2016. Code and models are available at https://github.com/hujie-frank/SENet.
The RAGE Axis in Early Diabetic Retinopathy (2005)

In early diabetic retinopathy, the RAGE axis, comprising the cellular receptor and its AGE ligands, is amplified within the retina and is accentuated along the vitreoretinal interface. Antagonism of the RAGE axis in NPDR reduces neurovascular perturbations, providing an important therapeutic target for intervention.
Plasmonics: the next chip-scale technology (2006)

The development of chip-scale electronics and photonics has led to remarkable data processing and transport capabilities that permeate almost every facet of our lives. Plasmonics is an exciting new device technology that has recently emerged. It exploits the unique optical properties of metallic nanostructures to enable routing and manipulation of light at the nanoscale. A tremendous synergy can be attained by integrating plasmonic, electronic, and conventional dielectric photonic devices on the same chip and taking advantage of the strengths of each technology.
On the theory of filamentary double injection and electroluminescence in molecular crystals (1974)

A theoretical model based on the filamentary double injection in solids is presented, and expressions for the intensity of electroluminescence in molecular crystals as a function of applied electric field, current density, and temperature are derived. The computed results are in good agreement with presently available experimental results for undoped and doped anthracene crystals.
Optical sensor for the visual detection of mercury using mesoporous silica anchoring porphyrin moiety (2005)

A low cost, solid optical sensor for the rapid detection of low concentrations of Hg2+ in aqueous media was prepared by the monolayer functionalization of mesoporous silica with 5,10,15,20-tetraphenylporphinetetrasulfonic acid (TPPS), anchored by N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride (TMAC). The detection is based on the color change of TPPS from orange to green as a result of the formation of a charge-transfer complex with Hg2+. The intensity of the charge-transfer band varies linearly with Hg2+ in the concentration range from zero to 2.5 x 10(-7) mol dm(-3). The lower detection limit observed for Hg2+ concentration is 1.75 x 10(-8) mol dm(-3). The material exhibits good chemical and mechanical stability, and did not show any degradation of TPPS for a period of eight months. The sensor was applied for the analysis of various environmental samples. The effects of pH, sample volume, reaction time, amount of material, and the presence of foreign ions on the detection method are discussed.
The Year in Cardiology 2012: focus on cardiovascular disease prevention (2013)

Current data suggest that advances in cardiovascular (CV) treatment have resulted in significant reduction in CV mortality but also in prolongation of life with disability. Focus on CV prevention is likely to reverse this unfavourable trend. In this review we provide information on the new European guidelines on CV prevention and discuss biomarkers and vascular imaging techniques which can assist in refining CV risk prediction. Finally, we provide new information on lifestyle and pharmacological advances which are likely to result in significant CV risk reduction.
Coupling matrix-assisted laser desorption/ionization to liquid separations (1997)

This review discusses the off-line and on-line coupling of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to liquid chromatography (LC) and capillary electrophoresis (CE). Off-line methods involve collecting fractions or depositing a sample on a prepared target prior to MALDI analysis. Because LC fraction collection is straightforward, off-line MALDI LC-MS is relatively easy to implement and widely used. Collecting CE fractions poses a greater challenge due to the small sample volume and the high voltage electrical connection that must be maintained during separation. Methods for off-line MALDI CE-MS employing a porous glass joint, liquid sheath flow, low-volume buffer, or direct deposition are discussed. On-line coupling of MALDI to liquid separations involves introducing the sample directly into the mass spectrometer, using either a continuous-flow (CF) probe or an aerosol spray. With CF MALDI, liquid samples are delivered to the probe through a silica capillary. Aerosol MALDI relies on a pneumatic nebulizer to deliver samples to the mass spectrometer, where ions are formed through irradiation of the particles. CF MALDI and aerosol MALDI have both been coupled to LC separations, although further refinements in both techniques are needed. Future prospects for liquid separations and both off-line and on-line MALDI are discussed. © 1998 John Wiley & Sons, Inc., Mass Spectrom Rev 16, 283–299, 1997
Epidermal Growth Factor Induction of Phenotype-dependent Cell Cycle Arrest in Vascular Smooth Muscle Cells Is through the Mitogen-activated Protein Kinase Pathway (2003)

The heterogeneity of vascular smooth muscle cells is well established in tissue culture, but their differential responses to growth factors are not completely defined. We wished to identify effects of epidermal growth factor (EGF) on vascular smooth muscle cells in distinct phenotypes, such as spindle and epithelioid. We found that the EGF receptors were abundant in epithelioid cells but not spindle cells. EGF treatment inhibited serum-independent DNA synthesis, which was absent in spindle cells, of epithelioid cells. Additionally, using a pulse-chase assay, we found that bromodeoxyuridine-labeled cells failed to re-enter the S phase in the presence of EGF. These EGF effects were abolished by either inhibiting the EGF receptor tyrosine kinase with AG1478 or inhibiting the mitogen-activated protein kinase pathway with PD98059. In response to treatment with EGF, the EGF receptor was phosphorylated, which was correlated with phosphorylation and activation of p42/44 mitogen-activated protein kinases. Inhibition of EGF receptor phosphorylation and mitogen-activated protein kinase activation resulted in a reversal of the EGF-induced inhibition of bromodeoxyuridine incorporation and cell cycle arrest. Subsequent studies revealed that the activation of the EGF receptor and the mitogen-activated protein kinase pathway in epithelioid cells induced expression of the cell cycle inhibitory protein p27Kip1 but not p21Cip1. Taken together, our data demonstrate that the EGF receptor is abundantly expressed in epithelioid vascular smooth muscle cells and that the activation of this receptor results in cell cycle arrest through activation of the mitogen-activated protein kinase pathway.
Allergen exposure induces the activation of allergen‐specific Th2 cells in the airway mucosa of patients with allergic respiratory disorders (1993)

Biopsy specimens were obtained from the bronchial or the nasal mucosa of three patients with grass pollen-induced bronchial asthma or rhinitis 48 h after positive bronchial or nasal provocation test with grass pollen extract. T cell clones (TCC), derived from these and control specimens, were then assessed for their phenotype, allergen-specificity, profile of cytokine secretion and ability to provide B cell help for IgE synthesis. Out of 50 and 61 CD4+ TCC derived from the bronchial mucosa of the two patient with atopic asthma 11 (22%) and 19 (31%), respectively, showed both proliferation and cytokine production in response to grass pollen allergens under major histocompatibility complex-restricted conditions. Of these 21 (70%) exhibited a clear-cut type 2 T helper (Th2) profile and induced IgE synthesis in autologous peripheral blood B cells in the presence of grass allergens. All the other 9 grass-specific clones showed a Th0 pattern of cytokine secretion, but only 1 provided moderate help for IgE synthesis. In contrast, the majority of TCC, derived under the same experimental conditions from the bronchial mucosa of two nonatopic patients with toluene diisocyanate-induced asthma, were CD8+ and most of them produced interferon-gamma or interferon-gamma and interleukin-5, but not interleukin-4, in response to nonspecific stimulation. Of 22 CD4+ TCC3 (14%) derived from the grass-stimulated mucosa of the patient with allergic rhinitis, but none of those derived from the unstimulated nostril of the same patient, exhibited proliferation and cytokine production in response to grass allergens. All had a clear-cut Th2 profile and provided help for IgE synthesis by autologous B cells. These data indicate that inhalation of the relevant allergen results in the activation of allergen-specific Th2 lymphocytes in the airway mucosa of patients with allergic respiratory disorders. These cells may play a central role in determining the nature of the inflammatory response in the airways of atopic patients.
Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool (2013)

We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.
Cartilage-inducing factor-B is a unique protein structurally and functionally related to transforming growth factor-beta. (1987)

Cartilage-inducing factors-A (CIF-A) and -B (CIF-B), purified from bovine bone on the basis of their ability to induce the cartilage phenotype in vitro, are proteins with molecular weights of 26,000 composed of two apparently identical disulfide-linked chains.CIF-A is apparently identical to TGF-8 from human platelets (Seyedin S.
Paul Brest's Brief for an Imperial Judiciary (1981)

he who thinks the old embankments useless and destroys them, is sure to suffer from the desolation caused by overflowing water."
Mechanism of photosensitization by microsphere-bound chlorin e6 in human bladder carcinoma cells. (1991)

Photodynamic therapy is an experimental method of cancer treatment in which a photosensitizer is administered and subsequently the tumor is irradiated with light. Due to problems of prolonged skin phototoxicity with hematoporphyrin derivative, new photosensitizers and methods of localization are being sought. The goal of this study was to compare the photosensitizer chlorin e6 (Ce6) free and bound to 1-micron-diameter microspheres (MS) for phototoxicity, uptake and efflux characteristics, phagocytosis rates in malignant and benign cells, and effects of NaN3, D2O, and buthionine sulfoximine on phototoxic efficacy. Incubation of MGH-U1 human bladder carcinoma cells with Ce6-MS (0.43 microM Ce6-equivalent; 18 h) and subsequent irradiation using an argon laser-pumped dye laser at a radiant exposure of 20 J/cm2 caused 100% cell death 24 h after irradiation. In contrast, MGH-U1 cells incubated with free Ce6 (0.43 microM; 18 h) remained 100% viable 24 h after irradiation at a radiant exposure of up to 50 J/cm2. The presence of D2O during irradiation increased the phototoxicity to MGH-U1 cells, whereas the presence of NaN3 decreased it; these data support an important role for 1O2. Irradiation of MGH-U1 cells in the presence of the glutathione depleter buthionine sulfoximine also increased the phototoxicity, demonstrating a role for intracellular glutathione and possibly free radical intermediates. The cellular uptake of Ce6 was approximately 50 times lower than that of Ce6-MS at equivalent incubation concentrations. Efflux experiments showed that the phototoxicity of Ce6-MS was reduced by 40% for a 5-h washout time as compared to no washout time. In contrast, for free Ce6, the decrease was 95.3% under identical conditions. Because the total intracellular concentration of Ce6-MS after an efflux time of 5 h was only slightly changed, the decreased phototoxicity is attributed to an altered intracellular localization. Confocal laser scanning fluorescence microscopy data appear consistent with this hypothesis although they are not conclusive. The observed patterns were different at 0 and 5 h. Comparison of the phagocytosis rates of Ce6-MS by carcinoma and benign cells showed that on average 20 MS/cell were phagocytosed by MGH-U1 compared with 2.5 and 8.3 in the benign human fibroblasts and keratinocytes, respectively. After incubation with Ce6-MS (0.1 microM; 18 h) and irradiation at 10 J/cm2 the surviving fraction of MGH-U1 cells was 76.3 +/- 0.95% (mean +/- SE) and 40 +/- 3.49% for fibroblasts. In contrast, for keratinocytes the surviving fraction was 93.5 +/- 0.83%.(ABSTRACT TRUNCATED AT 400 WORDS)
Cosmetic Breast Augmentation Utilizing Autologous Fat and Liposuction Techniques (1987)

I have presented a new technique of autologous fat transplantation which utilizes fat obtained by liposuction. I believe that this technique will have wide application in the future of cosmetic and reconstructive surgery.
Albumin-Conjugated Corrole Metal Complexes:  Extremely Simple Yet Very Efficient Biomimetic Oxidation Systems (2005)

An extremely simple biomimetic oxidation system, consisting of mixing metal complexes of amphiphilic corroles with serum albumins, utilizes hydrogen peroxide for asymmetric sulfoxidation in up to 74% ee. The albumin-conjugated manganese corroles also display catalase-like activity, and mechanistic evidence points toward oxidant-coordinated manganese(III) as the prime reaction intermediate.
A Membrane-bound Multienzyme, Hydrogen-oxidizing, and Sulfur-reducing Complex from the Hyperthermophilic Bacterium Aquifex aeolicus (2005)

Aquifex aeolicus is a hyperthermophilic, chemolithoautotrophic, hydrogen-oxidizing, and microaerophilic bacterium growing at 85 degrees C. We have shown that it can grow on an H2/S degrees medium and produce H2S from sulfur in the later exponential phase. The complex carrying the sulfur reducing activity (electron transport from H2 to S degrees ) has been purified and characterized. It is a membrane-bound multiprotein complex containing a [NiFe] hydrogenase and a sulfur reductase connected via quinones. The sulfur reductase is encoded by an operon annotated dms (dimethyl sulfoxide reductase) that we have renamed sre and is composed of three subunits. Sequence analysis showed that it belongs to the Me2SO reductase molybdoenzyme family and is similar to the sulfur/polysulfide/thiosulfate/tetrathionate reductases. The study of catalytic properties clearly demonstrated that it can reduce tetrathionate, sulfur, and polysulfide, but cannot reduce Me2SO and thiosulfate, and that NADPH increases the sulfur reducing activity. To date, this is the first characterization of a supercomplex from a bacterium that couples hydrogen oxidation and sulfur reduction. The distinctive feature in A. aeolicus is the cytoplasmic localization of the sulfur reduction, which is in accordance with the presence of sulfur globules in the cytoplasm. Association of this sulfur-reducing complex with a hydrogen-oxygen pathway complex (hydrogenase I, bc1 complex) in the membrane suggests that subcomplexes involved in respiratory chains in this bacterium are part of supramolecular organization.
Access and Exchange of Hierarchically Structured Resources on the Web with the NESTOR Framework (2009)

The paper addresses the problem of representing, managing and exchanging hierarchically structured data in the context of Digital Library (DL) systems in order to enhance the access and exchange DL resources on the Web. We propose the NEsted SeTs for Object hieRarchies (NESTOR) framework, which relies on two set data models — the “Nested Set Model (NS-M)” and the “Inverse Nested Set Model (INS-M)” — to enable the representation of hierarchical data structures by means of a proper organization of nested sets. In particular, we show how NESTOR can be effectively exploited to enhance Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) for better access and exchange of hierarchical resources on the Web.
[Psoriasis, an autoimmune disease?]. (1993)

Whereas psoriasis is well defined as a clinical entity for more than a century, the pathogenesis of psoriasis is still open to debate, despite demonstration of multiple abnormalities in cell-kinetics, histomorphology and biochemistry. Recent research indicates altered immune function in psoriatic skin, which may explain some of the phenomena typical for this disease. The role of immunological pathomechanisms in psoriasis is further substantiated by the well-known success of immunosuppressive treatments. However, as long as putative auto-antigens, which are presumed to perpetuate the pathological immune reactions, are not identified, psoriasis cannot be classified as an autoimmune disease.
Physical mapping of resistant and susceptible soybean genomes near the soybean cyst nematode resistance gene Rhg4 (2001)

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the foremost pest of soybean (Glycine max L. Merr.). The rhg1 allele on linkage group (LG) G and the Rhg4 allele on LG A2 are important in conditioning resistance. Markers closely linked to the Rhg4 locus were used previously to screen a library of bacterial artificial chromosome (BAC) clones from susceptible 'Williams 82' and identified a single 150-kb BAC, Gm_ISb001_056_G02 (56G2). End-sequenced subclones positioned onto a restriction map provided landmarks for identifying the corresponding region from a BAC library from accession PI 437654 with broad resistance to SCN. Seventy-three PI 437654 BACs were assigned to contigs based upon HindIII restriction fragment profiles. Four contigs represented the PI 437654 counterpart of the 'Williams 82' BAC, with PCR assays connecting these contigs. Some of the markers on the PI 437654 contigs are separated by a greater physical distance than in the 'Williams 82' BAC and some primers amplify bands from BACs in the mid-portion of the connected PI 437654 BAC contigs that are not amplified from the 'Williams 82' BAC. These observations suggest that there is an insertion in the PI 437654 genome relative to the 'Williams 82' genome in the Rhg4 region.