gebhart/patrepeval huggingface dataset:
Analysis of Neutralization Specificities in Polyclonal Sera Derived from Human Immunodeficiency Virus Type 1-Infected Individuals (2008)

During human immunodeficiency virus type 1 (HIV-1) infection, patients develop various levels of neutralizing antibody (NAb) responses. In some cases, patient sera can potently neutralize diverse strains of HIV-1, but the antibody specificities that mediate this broad neutralization are not known, and their elucidation remains a formidable challenge. Due to variable and nonneutralizing determinants on the exterior envelope glycoprotein (Env), nonnative Env protein released from cells, and the glycan shielding that assembles in the context of the quaternary structure of the functional spike, HIV-1 Env elicits a myriad of binding antibodies. However, few of these antibodies can neutralize circulating viruses. We present a systematic analysis of the NAb specificities of a panel of HIV-1-positive sera, using methodologies that identify both conformational and continuous neutralization determinants on the HIV-1 Env protein. Characterization of sera included selective adsorption with native gp120 and specific point mutant variants, chimeric virus analysis, and peptide inhibition of viral neutralization. The gp120 protein was the major neutralizing determinant for most sera, although not all neutralization activity against all viruses could be identified. In some broadly neutralizing sera, the gp120-directed neutralization mapped to the CD4 binding region of gp120. In addition, we found evidence that regions of the gp120 coreceptor binding site may also be a target of neutralizing activity. Sera displaying limited neutralization breadth were mapped to the immunogenic V3 region of gp120. In a subset of sera, we also identified NAbs directed against the conserved, membrane-proximal external region of gp41. These data allow a more detailed understanding of the humoral responses to the HIV-1 Env protein and provide insights regarding the most relevant targets for HIV-1 vaccine design.
Ovarian Cancer Cells Polarize Macrophages Toward A Tumor-Associated Phenotype (2006)

Tumor-associated macrophages (TAM) may have tumor-promoting activity, but it is not clear how their phenotype is achieved. In this study, we demonstrate that ovarian cancer cells switch cocultured macrophages to a phenotype similar to that found in ovarian tumors. Tumor cells caused dynamic changes in macrophage cytokine, chemokine, and matrix metalloprotease mRNA, and protein-inducing mediators that are found in human cancer. Macrophage mannose, mannose receptor, and scavenger receptors (SR-As) were also up-regulated by coculture, but not by conditioned medium. To further validate the model, we studied SR-A regulation on TAM in vitro and in vivo. Coculture of murine macrophages from mice deficient in TNF-alpha or its receptors revealed that TNF-alpha was key to SR-A induction via its p75 receptor. SR-A expression was also reduced in TAM from ovarian cancers treated with anti-TNF-alpha Abs or grown in TNF-alpha(-/-) mice. Chemical communication between tumor cells and macrophages may be important in regulating the cancer cytokine microenvironment.
Activity of the De Novo Engineered Antimicrobial Peptide WLBU2 against Pseudomonas aeruginosa in Human Serum and Whole Blood: Implications for Systemic Applications (2005)

Cationic amphipathic peptides have been extensively investigated as a potential source of new antimicrobials that can complement current antibiotic regimens in the face of emerging drug-resistant bacteria. However, the suppression of antimicrobial activity under certain biologically relevant conditions (e.g., serum and physiological salt concentrations) has hampered efforts to develop safe and effective antimicrobial peptides for clinical use. We have analyzed the activity and selectivity of the human peptide LL37 and the de novo engineered antimicrobial peptide WLBU2 in several biologically relevant conditions. The host-derived synthetic peptide LL37 displayed high activity against Pseudomonas aeruginosa but demonstrated staphylococcus-specific sensitivity to NaCl concentrations varying from 50 to 300 mM. Moreover, LL37 potency was variably suppressed in the presence of 1 to 6 mM Mg(2+) and Ca(2+) ions. In contrast, WLBU2 maintained its activity in NaCl and physiologic serum concentrations of Mg(2+) and Ca(2+). WLBU2 is able to kill P. aeruginosa (10(6) CFU/ml) in human serum, with a minimum bactericidal concentration of <9 microM. Conversely, LL37 is inactive in the presence of human serum. Bacterial killing kinetic assays in serum revealed that WLBU2 achieved complete bacterial killing in 20 min. Consistent with these results was the ability of WLBU2 (15 to 20 microM) to eradicate bacteria from ex vivo samples of whole blood. The selectivity of WLBU2 was further demonstrated by its ability to specifically eliminate P. aeruginosa in coculture with human monocytes or skin fibroblasts without detectable adverse effects to the host cells. Finally, WLBU2 displayed potent efficacy against P. aeruginosa in an intraperitoneal infection model using female Swiss Webster mice. These results establish a potential application of WLBU2 in the treatment of bacterial sepsis.
Non-local Neural Networks (2017)

Both convolutional and recurrent operations are building blocks that process one local neighborhood at a time. In this paper, we present non-local operations as a generic family of building blocks for capturing long-range dependencies. Inspired by the classical non-local means method in computer vision, our non-local operation computes the response at a position as a weighted sum of the features at all positions. This building block can be plugged into many computer vision architectures. On the task of video classification, even without any bells and whistles, our non-local models can compete or outperform current competition winners on both Kinetics and Charades datasets. In static image recognition, our non-local models improve object detection/segmentation and pose estimation on the COCO suite of tasks. Code is available at https://github.com/facebookresearch/video-nonlocal-net .
Application of Pathprox Runway Incursion Alerting to General Aviation Operations (2006)

This paper describes the application of the PathProx/spl trade/ runway incursion advisory and alerting system to general aviation (GA) aircraft operations. Airport surface incursions have been identified by the National Transportation Safety Board (NTSB) as one of the most significant safety hazards in civil aviation. PathProx is a system developed by Rannoch Corporation to help address this problem. It is an aircraft-based runway incursion alerting system, providing runway incursion alerts directly to the pilot(s). The testing and analyses that have been performed demonstrate significant safety benefits of PathProx. Among the other improvements in operations provided by PathProx include improved situational awareness, self-separation, and conflict detection and alerting without reliance on a ground infrastructure and ATC. It is also an enabling technology for operations such as the NASA Small Aircraft Transportation System (SATS) high volume operations.
Automated Postural Ergonomic Assessment Using a Computer Vision-Based Posture Classification (2016)

In construction, workers are frequently exposed to manual handling tasks involving repetitive and forceful activities with awkward postures. As a result, construction workers are at about a fifty percent higher risk of work-related musculoskeletal disorders (WMSDs) than workers in other industries. Several ergonomic methods for evaluating workers’ postural stresses through observations (e.g., OWAS, PATH, or RULA) have been applied to identify the risks of WMSDs during occupational tasks including construction. While inexpensive and practical to use, these methods are constrained by time-consuming procedures, observer bias, and the need for a well-trained analyst. These issues are exacerbated in the context of construction. In contrast to other factory-based (e.g., manufacturing) industries, construction is subject to irregular work patterns, relatively longer cycle time, and a wide variety of tasks. To address these issues, we propose computer vision-based posture classification that can automate existing observation-based postural evaluation methods such as OWAS. Specifically, the proposed method can classify workers’ postures according to pre-defined ergonomic checklists using shape- and radial histogram-based features from video sequences. To test the feasibility of the proposed approach, we conducted a laboratory test with five subjects by simulating three representative postures according to upper limbs, back, and lower limbs. The results from the case study demonstrate that it can provide more reliable posture classification results with about 93% of accuracy. The proposed approach enables practitioners to identify the risk of WMSDs through automated ergonomic postural evaluation of on-going tasks only by taking videos at sites, which helps to prevent WMSDs for diverse occupational tasks including construction.
Biodegradable soft elastomers: synthesis/properties of materials and fabrication of scaffolds (2012)

Recently there have been increasing research efforts in the development of elastomeric biomaterials with desirable biocompatibility, degradation profiles and mechanical properties for use in soft tissue engineering. This review provides an update on the progresses of developing biodegradable, soft elastomeric biomaterials and their tissue engineering scaffolding techniques. Following a brief review on traditional thermoplastic elastomers, including polyurethane (PU), polyhydroxyalkanoates (PHA) and aliphatic copolyesters, detailed review is devoted to the synthesis, properties and scaffold fabrication of recently developed soft, biodegradable elastomers, including poly(polyol sebacate) (PPS), PPS-based elastomers, and citric-acid based elastomers. Although biodegradable, soft elastomeric biomaterials have advantages (compliant and biodegradable), this review also identified a number of issues associated with these elastomers, including cytotoxicity, rapid in vivo degradation rates, and poor reproducibility. Future research directions are discussed to address these issues.
Analysis of Critical Debonding Pressures of Stressed Thin Films in the Blister Test (1988)

Abstract This paper reports a model for the relationship between critical debonding pressures and the work of adhesion of thin films in the blister test. Previous models have neglected the possible role of residual stresses in the film on the critical pressure. The model reported here shows that these stresses may have a large effect on the relation between the critical pressure and the work of adhesion. A similar model is developed for an alternative blister geometry, the annular or “island” blister. It is shown that films which cannot be peeled using the standard blister test (due to exceeding the tensile strength limit of the film before initiating a debond) can be peeled by varying the geometric parameters of the island blister.
Caltech-UCSD Birds 200 (2010)

Caltech-UCSD Birds 200 (CUB-200) is a challenging image dataset annotated with 200 bird species. It was created to enable the study of subordinate categorization, which is not possible with other popular datasets that focus on basic level categories (such as PASCAL VOC, Caltech-101, etc). The images were downloaded from the website Flickr and filtered by workers on Amazon Mechanical Turk. Each image is annotated with a bounding box, a rough bird segmentation, and a set of attribute labels. forehead_color black black black breast_pattern solid solid solid breast_color white white white head_pattern plain capped plain back_color white white black wing_color grey/white grey white leg_color orange orange orange size medium large medium bill_shape needle dagger dagger wing_shape pointed tapered long primary_color white white white forehead_color red red red breast_pattern solid solid breast_color white white/red white head_pattern capped capped capped back_color wing_color white/ black white/ black white/ black white/black white/ black white/black leg_color buff black black size small medium medium bill_shape dagger multicolored allpurpose allpurpose wing_shape pointed tapered pointed primary_color black, red white, black white, black Figure 1: Images and annotations from CUB-200. Each example image is shown with a rough outline (segmentation) in green. To the right of each image is a table of attributes (one per row, 11 out of a total of 25 attributes shown), and attribute-values provided by Amazon Mechanical Turk workers looking at the image. The attribute-values in the three right-most columns in the tables are provided by different workers (across both columns and rows). The font of the attribute-value indicates the confidence of the worker: bold font means the worker was ‘definitely ’ sure of the label, thin means ‘probably’, and grey means ‘guessing’. 1
Stereochemical Aspects of the anti-HCMV Activity of Cytidine Nucleoside Analogues (1995)

The remarkable selectivity of the β-L enantiomers of 2′,3′-dideoxycytidine analogues against the viral polymerases of HIV and HBV has stimulated our interest in targeting β-L enantiomers of anti-HCMV cytidine analogues. Indeed, Ara-C, FIAC and DMDC are cytidine analogues with β-D configuration that show significant potency as anti-HCMV agents but lack selectivity. β-L enantiomers have therefore been synthesized and evaluated together with four other nucleoside analogues, and the β-L. enantiomers were found not to be inhibitory to HCMV replication. However, the three α-L isomers, α-L-Ara-C, α-L-Xylo-C and α-L-FMAU, emerged with activity against HCMV and have provided new approaches for the treatment of viral diseases with nucleoside analogues possessing the unusual L-configuration.
The general theory of van der Waals forces (1961)

Publisher Summary The van der Waals forces refer to the attractive forces acting between any two neutral atoms or molecules that are separated by distance large compared to their own dimensions. These forces are of a long-range nature, which decrease with distance according to a power law. The basic idea of the theory is that the interaction between the bodies is considered to take place through a fluctuating electromagnetic field. This field is always present in the interior of a material medium and it also extends beyond its boundaries because of the thermodynamic fluctuations. Any change in the electrical proper ties of the medium in a certain region will, by Maxwell's equations, lead to a change in the fluctuation field that extends beyond that region. Therefore, the part of the free energy that is related to electromagnetic fluctuations is not determined by the properties of the substance solely at the point considered.
Screening for circulating nucleic acids and caspase activity in the peripheral blood as potential diagnostic tools in lung cancer (2011)

The focus of the current investigational study was to examine whether circulating nucleic acids (i.e., DNA and microRNAs) have the potential to become suitable blood-based markers for diagnosis and progression of lung cancer. The concentrations of cell-free DNA and four circulating microRNAs (miR10b, miR34a, miR141 and miR155) as well as the caspase activity were measured in serum of 35 lung cancer patients (19 non-small-cell lung cancer, 8 small cell lung cancer patients and 8 patients with indefinite cancer type), 7 patients with benign lung tumors and 28 healthy individuals by PicoGreen, TaqMan MicroRNA, and Caspase-Glo®3/7 assay, respectively. The data were correlated with the established risk factors for lung cancer progression. The concentrations of cell-free DNA (p = 0.0001), serum microRNAs (p = 0.0001) and caspase activities (p = 0.0001) significantly discriminated cancer patients from healthy individuals. Serum DNA, caspase activities and RNA levels could not distinguish between patients with benign lung disease and cancer patients. However, the levels of miR10b (p = 0.002), miR141 (p = 0.0001) and miR155 (p = 0.007) were significantly higher in lung cancer patients than those in patients with benign disease. As determined by the Spearman-Rho test, high levels of cell-free DNA significantly correlated with elevated circulating caspase activities (p = 0.0001). In lung cancer patients high serum miR10b values associated with lymph node metastasis (p < 0.03) and elevated levels of TPA (tissue polypeptide antigen, p = 0.01), whereas high serum miR141 values associated with elevated levels of uPA (urokinase plasminogen activator, p = 0.02). The findings of our pilot study suggest that the assays for circulating DNA, microRNAs and caspase activities in blood might become novel minimally invasive diagnostic tools for detection and risk assessment of lung cancer, provided that their clinical utility can be confirmed in larger prospective trials.
Cell surface glycoconjugates as possible target structures for human natural killer cells: evidence against the involvement of glycolipids and N-linked carbohydrate chains (1993)

Natural killer (NK) cells can spontaneously kill various malignant cells, but the susceptibility towards NK cells differs greatly among different types of tumour cells. The molecules, which are recognized by NK cells, have not yet been identified, but there is ample evidence that target cell surface glycoconjugates are involved in the interaction with NK cells. In this report, we show that the recognition of K562 target cells by human NK cells depends on the presence of protein-bound determinants, implying that glycolipids are not the primary target structures on K562 cells. The NK susceptibility of K562 cells was not altered by enzymic removal of various cell surface carbohydrates or oligosaccharides, mostly related to N-linked carbohydrate chains. Treatment of K562 cells with 1-deoxynojirimycin and 1-deoxymannojirimycin, inhibitors of N-glycan processing, resulted in drastic alterations in the carbohydrate phenotype of the cell surface, as could be shown by flow cytometric analysis of the lectin-binding properties of the cells. Despite these clear changes in N-glycosylation, the NK susceptibility of K562 cells remained unaffected. Summarizing, the results described in this report show that potential target structures for NK cells are protein bound, but the involvement of a specific (N-linked) carbohydrate determinant in the interaction between NK cells and target cells could not be established.
Transcriptional Regulation of the Human iNOS Gene by IL-1β in Endothelial Cells (2001)

Both NF-kappaB and C/EBP pathways are important for the transcriptional regulation of the human iNOS gene by IL-1beta in PVEC.
A caged Ab reveals an immediate/instructive effect of BDNF during hippocampal synaptic potentiation (2001)

Neurotrophins have been shown to be involved in functional strengthening of central nervous system synapses. Although their general importance in this process is undisputed, it remains unresolved whether neurotrophins are truly mediators of synaptic strengthening or merely important cofactors. To address this question, we have devised a method to inactivate endogenous brain-derived neurotrophic factor (BDNF) with high time resolution by "caging" a function-blocking mAb against BDNF with a photosensitive protecting compound. Different assays were used to show that this inactivation of the Ab is reversible by UV light. Synaptic potentiation after theta-burst [corrected] stimulation in the CA1 region of acute hippocampal slices was significantly less when applying the unmodified Ab compared with the caged Ab. Importantly, photoactivation of the caged Ab during the time of induction of synaptic enhancement led to a marked decrease in potentiation. Our experiments therefore strengthen the view that endogenous BDNF has fast effects during induction of synaptic plasticity. The results additionally show that caged Abs can provide a tool for precise spatiotemporal control over endogenous protein levels.
Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma (2005)

Medulloblastoma is the most common malignant brain tumor in children. It is thought to result from the transformation of granule cell precursors (GCPs) in the developing cerebellum, but little is known about the early stages of the disease. Here, we identify a pre-neoplastic stage of medulloblastoma in patched heterozygous mice, a model of the human disease. We show that pre-neoplastic cells are present in the majority of patched mutants, although only 16% of these mice develop tumors. Pre-neoplastic cells, like tumor cells, exhibit activation of the Sonic hedgehog pathway and constitutive proliferation. Importantly, they also lack expression of the wild-type patched allele, suggesting that loss of patched is an early event in tumorigenesis. Although pre-neoplastic cells resemble GCPs and tumor cells in many respects, they have a distinct molecular signature. Genes that mark the pre-neoplastic stage include regulators of migration, apoptosis and differentiation, processes crucial for normal development but previously unrecognized for their role in medulloblastoma. The identification and molecular characterization of pre-neoplastic cells provides insight into the early steps in medulloblastoma formation, and may yield important markers for early detection and therapy of this disease.
Equipment Selection Procedure for Subsea Trees (1987)

ABSTRACT Subsea trees have typically been field-specific with different designs required for each project. Current industry trends to improve efficiency and cost effectiveness, however, indicate that increased standardization and versatility are required. This paper presents a new procedure to categorize proven equipment and simplify selection of tree components. Using the flowchart principle, the decision process is indicated for each major equipment decision or option, considering the range of equipment available in light of product features, technical specifications, rated capacities, operational histories, and costs.
ELECTRONIC EFFECT IN THE ELASTIC CONSTANT C′ OF SILICON (1963)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Norman G. Einspruch, P. Csavinszky; ELECTRONIC EFFECT IN THE ELASTIC CONSTANT C′ OF SILICON. Appl. Phys. Lett. 1 January 1963; 2 (1): 1–3. https://doi.org/10.1063/1.1753712 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioApplied Physics Letters Search Advanced Search |Citation Search
MDM2 inhibits p300-mediated p53 acetylation and activation by forming a ternary complex with the two proteins (2000)

p300 acetylates and activates the tumor suppressor p53 after DNA damage. Here, we show that MDM2, a negative-feedback regulator of p53, inhibited p300-mediated p53 acetylation by complexing with these two proteins. First, we purified a p300-MDM2-p53 protein complex from HeLa nuclear extracts, which was inactive in p53 acetylation, but active in histone acetylation. Also, wild-type, but not N-terminally deleted, MDM2 inhibited p53 acetylation by p300 in vitro and in vivo. This inhibition was specific for p53, because MDM2 did not affect acetylation of histones or the C terminus of p73 by p300. Consequently, wild-type, but not the mutant, MDM2 repressed the p300-stimulated sequence-specific DNA-binding and transcriptional activities of p53. These results demonstrate that an additional mechanism of p53 inactivation by MDM2 is to inhibit p53 acetylation by p300.