gebhart/patrepeval huggingface dataset:
Multiple target detection and tracking with guaranteed framerates on mobile phones (2009)

In this paper we present a novel method for real-time pose estimation and tracking on low-end devices such as mobile phones. The presented system can track multiple known targets in real-time and simultaneously detect new targets for tracking. We present a method to automatically and dynamically balance the quality of detection and tracking to adapt to a variable time budget and ensure a constant frame rate. Results from real data of a mobile phone Augmented Reality system demonstrate the efficiency and robustness of the described approach. The system can track 6 planar targets on a mobile phone simultaneously at framerates of 23 fps.
Protection against P. aeruginosa with an adenovirus vector containing an OprF epitope in the capsid (2005)

Pseudomonas aeruginosa is an important opportunistic pathogen that can cause chronic and often life-threatening infections of the respiratory tract, particularly in individuals with cystic fibrosis (CF). Because infections with P. aeruginosa remain the major cause of the high morbidity and mortality of CF, a vaccine against P. aeruginosa would be very useful for preventing this disorder. The outer membrane protein F (OprF) of P. aeruginosa is a promising vaccine candidate and various B cell epitopes within OprF have been identified. Given that adenovirus (Ad) vectors have strong immunogenic potential and can function as adjuvants for genetic vaccines, the present study evaluates the immunogenic and protective properties of a novel replication-deficient Ad vector in which the Ad hexon protein was modified to include a 14-amino acid epitope of P. aeruginosa OprF (Epi8) in loop 1 of the hypervariable region 5 of the hexon (AdZ.Epi8). Immunization of C57BL/6 mice with AdZ.Epi8 resulted in detectable serum anti-P. aeruginosa and anti-OprF humoral responses. These responses were haplotype dependent, with higher serum anti-OprF titers in CBA mice than in BALB/c or C57BL/6 mice. AdZ.Epi8 induced Epi8-specific IFN-gamma-positive CD4 and CD8 T cell responses and resulted in protection against a lethal pulmonary challenge with agar-encapsulated P. aeruginosa. Importantly, repeated administration of AdZ.Epi8 resulted in boosting of the anti-OprF humoral and anti-Epi8 cellular response, whereas no boosting effect was present in the response against the transgene beta-galactosidase. These observations suggest that Ad vectors expressing pathogen epitopes in their capsid will protect against an extracellular pathogen and will allow boosting of the epitope-specific humoral response with repeated administration, a strategy that should prove useful in developing Ad vectors as vaccines where humoral immunity will be protective.
Solution‐Phase Synthesis of Short Oligo‐2′‐deoxyribonucleotides by Using Clustered Nucleosides as a Soluble Support (2013)

Abstract 5′‐ O ‐(4,4′‐Dimethoxytrityl)thymidine was attached to a pentaerythrityl‐derived core, and the resulting tetravalent nucleoside cluster and the next dendritic generations served as a soluble support for the synthesis of short oligo‐2′‐deoxyribonucleotides in solution. Couplings using a small excess (1.5 equiv. per 5′‐OH group) of the standard phosphoramidite building blocks proved efficient, and the products could be purified by quantitative precipitation from methanol. Ammonolysis released nearly homogeneous oligonucleotides (CCT, GCT, ACT, and AGCCT) in high yields.
Synthesis, characterization, and immunogenicity in mice of Shigella sonnei O-specific oligosaccharide-core-protein conjugates (2009)

Shigellosis, an enteric disease, is on the World Health Organization's priority prevention list. In one study, the Shigella sonnei O-specific polysaccharide (O-SP)-protein conjugate showed 72% protection against disease in Israeli army recruits exposed to high rates (8-14%) of infection. The protection was related to vaccine-induced IgG anti-O-SP levels. Synthetic oligosaccharides of Shigella dysenteriae type 1, bound by their reducing ends to a carrier protein ("sun"-type configuration), induced significantly higher antibody levels than the native O-SP bound to protein by multiple-point attachments ("lattice"-type configuration). Attempts to synthesize the S. sonnei O-SP based oligosaccharides were not successful. Here, we describe the isolation, characterization, and conjugation of low-molecular-mass O-SP-core (O-SPC) fragments. The O-SPC fragments were bound by their reducing ends similar to the preparation of the synthetic S. dysenteriae type 1 conjugates. The O-SPC conjugates used oxime linkages between the terminal Kdo residues at the reducing ends of the S. sonnei saccharides and aminooxy linkers bound to BSA or a recombinant diphtheria toxin. The coupling reaction was carried out at a neutral pH and room temperature. IgG antibody levels induced in young outbred mice by the S. sonnei O-SPC conjugates were significantly higher then those elicited by the O-SP conjugates. Accordingly, we propose to evaluate clinically these conjugates.
Generalization of Deep Neural Networks for Chest Pathology Classification in X-Rays Using Generative Adversarial Networks (2018)

Medical datasets are often highly imbalanced with over-representation of common medical problems and a paucity of data from rare conditions. We propose simulation of pathology in images to overcome the above limitations. Using chest X-rays as a model medical image, we implement a generative adversarial network (GAN) to create artificial images based upon a modest sized labeled dataset. We employ a combination of real and artificial images to train a deep convolutional neural network (DCNN) to detect pathology across five classes of chest X-rays. Furthermore, we demonstrate that augmenting the original imbalanced dataset with GAN generated images improves performance of chest pathology classification using the proposed DCNN in comparison to the same DCNN trained with the original dataset alone. This improved performance is largely attributed to balancing of the dataset using GAN generated images, where image classes that are lacking in example images are preferentially augmented.
On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites (2006)

In this article we introduce a new method for the identification and the accurate characterization of protein surface cavities. The method is encoded in the program SCREEN (Surface Cavity REcognition and EvaluatioN). As a first test of the utility of our approach we used SCREEN to locate and analyze the surface cavities of a nonredundant set of 99 proteins cocrystallized with drugs. We find that this set of proteins has on average about 14 distinct cavities per protein. In all cases, a drug is bound at one (and sometimes more than one) of these cavities. Using cavity size alone as a criterion for predicting drug-binding sites yields a high balanced error rate of 15.7%, with only 71.7% coverage. Here we characterize each surface cavity by computing a comprehensive set of 408 physicochemical, structural, and geometric attributes. By applying modern machine learning techniques (Random Forests) we were able to develop a classifier that can identify drug-binding cavities with a balanced error rate of 7.2% and coverage of 88.9%. Only 18 of the 408 cavity attributes had a statistically significant role in the prediction. Of these 18 important attributes, almost all involved size and shape rather than physicochemical properties of the surface cavity. The implications of these results are discussed. A SCREEN Web server is available at http://interface.bioc.columbia.edu/screen.
Three dimensional OCT images from retina and skin (2000)

We demonstrate the functionality of an en-face optical coherence tomography (OCT) system with images from the retina and skin. En-face images collected at different depths are subsequently used to reconstruct a 3D volume of the tissue. The reconstruction allows software inferred OCT longitudinal images at any transversal position in the stack. The position in depth in the stack before creating longitudinal OCT images is also adjustable, offering a valuable guidance tool for exploring the 3D volume of the tissue. This is illustrated by Quick time movies showing either depth or lateral exploration along one of two possible different directions in the stack of transversal OCT images. Sufficient accuracy of the volume rendered is obtained in 20 seconds when the system operates at 2 frames a second. The system, equipped with the 3D rendering feature acts as a valuable diagnostic tool allowing "peeling off" of transversal and longitudinal biologic material to investigate different internal features.
Varieties of Calcium-Activated Potassium Channels (1989)

The first demonstration that internal calcium is able to regulate potassium flux across membranes was given by Gardos (19) in red blood cells. A more direct approach to this problem was taken by Meech & Strumwasser (51), who observed that a microinjection of calcium was able to hyperpolarize the cell membrane of an Aplysia neuron. This response is accompanied by an increase in membrane conductance, and its reversal potential is a function of the external potassium concentration (49). On the basis of these results, a Ca2+­ activated K+ conductance, GK(Ca), was postulated, and Meech (50) suggested that the main role of these channels probably is to link cell metabolism to membrane conductance. Since these seminal observations were made, studies using the patch-clamp (60) and reconstitution techniques (53) have demon­ strated that intracellular calcium activates several different K+ channels (for reviews see 11, 34, 37, 65). Channel conductance, calcium sensitivity, voltage dependence, and pharmacological properties have been used to distin­ guish between the different channels of this family. Channel conductance ranges from a few to several hundred picosiemens (pS) consequently, at­ tempts have been made to group K(Ca) channels according to their con­ ductance (11, 36). They have been called small potassium (SK; 10, 11) and
Increased expression of discoidin domain receptor 2 is linked to the degree of cartilage damage in human knee joints: A potential role in osteoarthritis pathogenesis (2007)

Our data indicate that 3 factors, DDR-2 expression, MMP-13 expression, and the degree of cartilage damage, are linked, such that DDR-2 promotes tissue catabolism, and tissue degradation promotes DDR-2 up-regulation and activation. Thus, the perpetuation of DDR-2 expression and activation can be seen as a vicious circle that ultimately leads to cartilage destruction in OA.
The advent of biosimilars: challenges and risks (2014)

Biosimilars represent a new class of medicinal products that will have significant impact on clinical use. They are identical on an amino acid sequence level to existing reference biopharmaceutical products (originals). However, they may exhibit differences on a protein level. This paper provides a brief overview of biosimilar development and describes the risk and challenges that should be considered during the admission of biosimilars into the clinic.
Autoantibody Responses and Pathology Regulated by B7-1 and B7-2 Costimulation in MRL/ lpr Lupus (2000)

The activation of T lymphocytes requires both Ag-mediated signaling through the TCR as well as costimulatory signals transmitted through B7-1 and/or B7-2 with CD28. The interference of B7-mediated costimulatory signals has been proposed as one immunotherapeutic intervention for the prevention autoimmune disease. This study has examined autoantibody responses and autoimmune pathology in a murine model of human systemic lupus erythematosus (SLE), the MRL-lpr/lpr mouse, genetically deficient in B7-1 or B7-2, or in mice treated with B7-1/B7-2 blocking Abs. In contrast to other studies of murine models of SLE, MRL-lpr/lpr mice treated with B7 blocking Abs exhibit strong anti-small nuclear ribonucleoprotein (snRNP) and anti-DNA autoantibody responses with some changes in isotype switching as compared with untreated animals. All MRL-lpr/lpr mice deficient in B7-1 or B7-2 produce anti-snRNP and anti-DNA titers with isotypes virtually identical with wild-type animals. However, the absence of B7-2 costimulation did interfere with the spontaneous activation and the accumulation of memory CD4+ or CD8+ T lymphocytes characteristic of wild-type MRL-lpr/lpr mice. IgG and C3 complement deposition was less pronounced in the kidneys of B7-2 deficient MRL-lpr/lpr mice, reflecting their lessor degree of glomerulonephritis. By comparison, B7-1-deficient MRL-lpr/lpr mice had more severe IgG and C3 deposits in glomeruli.
Identification of amino acids in herpes simplex virus DNA polymerase involved in substrate and drug recognition. (1988)

Herpes simplex virus (HSV) encodes a DNA polymerase that is similar in several respects to the replicative mammalian DNA polymerase alpha. Recently, these and other DNA polymerases have been shown to share several regions of protein sequence similarity. Despite these similarities, antiviral drugs that mimic natural polymerase substrates specifically inhibit herpesvirus DNA polymerases. To study amino acids involved in substrate and drug recognition, we have characterized and mapped altered drug sensitivity markers of nine HSV pol mutants and sequenced the relevant portions of these mutants. The mutations were found to occur within four relatively small regions. One such region, which we designate region A, has sequence similarity only to DNA polymerases that are sensitive to certain antiviral drugs. The other three regions contain sequences that are similar among various DNA polymerases. The multiple mutations occurring within two of these regions make it likely that the regions interact directly with drugs and substrates. Our results lead us to favor a model in which protein folding allows interactions among the four regions to form the substrate and drug binding sites.
Osteoinductive Applications of Regional Gene Therapy (2000)

Gene therapy represents the new frontier of medical science. Currently, there are no completely satisfactory treatment options for bone repair problems such as fracture nonunion, revision total joint arthroplasty, tumor resections, and fusions of the spine. Autogenous bone grafts, allograft implants, and prosthetic implants have been used to treat these problems. However, there are significant limitations associated with these methods including limited supply and limited osteogenic potential. Gene therapy, involving the manipulation of endogenous cells to generate specific proteins, offers a potential solution for these problems. By transferring genes into cells at a specific anatomic site, the osteoinductive properties of growth factors can be used at physiologic doses for a sustained period to facilitate a more significant healing response. Successful gene therapy involves four key steps: transduction, transcription, translation, and expression. To achieve gene transduction of a target cell, gene therapy models use vectors to enhance the entry and expression of exogenous deoxyribonucleic acid into the target cell's nucleus. The transduction of a gene can be performed via either an ex vivo or an in vivo approach. Although there are many potential target cells for gene therapy, the specific anatomic site, the quality of the bone, and the soft-tissue envelope, will influence the selection of the target cells for regional gene therapy. Gene therapy vectors delivered to a treatment site in osteoconductive carriers have yielded promising results. Several investigators have shown exciting results using ex vivo and in vivo regional gene therapy in animal models. Comparative studies and human clinical trials have not yet been performed but are necessary to identify the optimal genes and dosages for each specific application of regional gene therapy. In the future, the treatment options for bone loss problems will represent a clinical continuum based on the anatomic site, the condition of the target tissue bed, and the desired duration of protein production.
Association of Multiple Cellular Stress Pathways With Accelerated Atherosclerosis in Hyperhomocysteinemic Apolipoprotein E-Deficient Mice (2004)

Multiple cellular stress pathways, including ER stress, are associated with atherosclerotic lesion development in apoE-/- mice.
Reduction of disulfides by thioredoxin. Exceptional reactivity of insulin and suggested functions of thioredoxin in mechanism of hormone action. (1979)

with insulin disulfides was estimated from fluorescence measurements and the enzymatic rates to be around 1 X 10’ M-’ s-l. This is around 10,000 times higher than the second order rate constant for the reaction between insulin and dithiothreitol, demonstrating the high affinity of insulin for thioredoxin-(SH)z. Nondisulfide oxidants such as Cu2+ ions, diamide, and vitamin KI, which are known to mimic the effects of insulin on cellular hexose transport, were rapidly reduced by the thioredoxin system. The exceptional reactivity of insulin and thioredoxin-(SH)2, in vitro, is consistent with a physiological function for mammalian thioredoxin in the degradation of insulin. Functions for thioredoxin in the “thiol oxidation-reduction model” of insulin action are discussed.
Binding of the Wilms' Tumor Locus Zinc Finger Protein to the EGR-1 Consensus Sequence (1990)

The Wilms' tumor locus (WTL) at 11p13 contains a gene that encodes a zinc finger-containing protein that has characteristics of a DNA-binding protein. However, binding of this protein to DNA in a sequence-specific manner has not been demonstrated. A synthetic gene was constructed that contained the zinc finger region, and the protein was expressed in Escherichia coli. The recombinant protein was used to identify a specific DNA binding site from a pool of degenerate oligonucleotides. The binding sites obtained were similar to the sequence recognized by the early growth response-1 (EGR-1) gene product, a zinc finger-containing protein that is induced by mitogenic stimuli. A mutation in the zinc finger region of the protein originally identified in a Wilms' tumor patient abolished its DNA-binding activity. These results suggest that the WTL protein may act at the DNA binding site of a growth factor-inducible gene and that loss of DNA-binding activity contributes to the tumorigenic process.
Perceptual user interfaces: perceptual intelligence (2000)

article Free Access Share on Perceptual user interfaces: perceptual intelligence Author: Alex Pentland Massachusetts Institute of Technology, Cambridge Massachusetts Institute of Technology, CambridgeView Profile Authors Info & Claims Communications of the ACMVolume 43Issue 3March 2000 pp 35–44https://doi.org/10.1145/330534.330536Published:01 March 2000Publication History 71citation3,588DownloadsMetricsTotal Citations71Total Downloads3,588Last 12 Months141Last 6 weeks16 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteView all FormatsPDF
Inflammatory Markers in the Tears of Patients with Ocular Surface Disease (2008)

Pro-MMP-9 levels in tears are elevated in all of the studied pathologies especially in ocular allergy and conjunctivochalasis. However, IL-1beta and IL-6 were only found to be overexpressed in conjunctivochalasis. These findings illustrate the selective implication of different molecules in each disorder.
Effects of dimethyl sulfoxide on the oxidative function of human neutrophils. (1987)

Dimethyl sulfoxide (DMSO) has been demonstrated to suppress the in vitro microbicidal activity of neutrophils. In addition, this compound has been described as having significant anti-inflammatory activity. These properties have generally been attributed to the effectiveness of this compound as a hydroxyl radical scavenger. However, DMSO can also act as a reductant under certain conditions, yielding its fully oxidized form, dimethyl sulfone (DMSO2), as the product. Therefore, we evaluated the ability of these two compounds to interfere with the production of oxidants other than the hydroxyl radical by stimulated human neutrophils. In a cell-free assay, DMSO was found to quench the oxidant activity of hypochlorous acid. Neither DMSO nor DMSO2 reacted with superoxide, hydrogen peroxide, taurine chloramine, or monochloramine in this system. However, both DMSO and DMSO2 significantly suppressed the production of superoxide, hydrogen peroxide, and hypochlorous acid by human neutrophils stimulated with either phorbol myristate acetate or opsonized zymosan. Neutrophil viability was not reduced by either DMSO or DMSO2. Inhibition of the oxidative function of stimulated neutrophils by DMSO may provide an alternative explanation for the effects of this compound on the microbicidal activity of neutrophils and as an in vivo anti-inflammatory agent.
Initial Efforts toward the Optimization of Arylomycins for Antibiotic Activity (2011)

While most clinically used antibiotics were derived from natural products, the isolation of new broad-spectrum natural products has become increasingly rare and narrow-spectrum agents are typically deemed unsuitable for development because of intrinsic limitations of their scaffold or target. However, it is possible that the spectrum of a natural product antibiotic might be limited by specific resistance mechanisms in some bacteria, such as target mutations, and the spectra of such "latent" antibiotics might be reoptimized by derivatization, just as has been done with clinically deployed antibiotics. We recently showed that the spectrum of the arylomycin natural product antibiotics, which act via the novel mechanism of inhibiting type I signal peptidase, is broader than previously believed and that resistance in several key human pathogens is due to the presence of a specific Pro residue in the target peptidase that disrupts interactions with the lipopeptide tail of the antibiotic. To begin to test whether this natural resistance might be overcome by derivatization, we synthesized analogues with altered lipopeptide tails and identified several with an increased spectrum of activity against S. aureus. The data support the hypothesis that the arylomycins are latent antibiotics, suggest that their spectrum may be optimized by derivatization, and identify a promising scaffold upon which future optimization efforts might focus.