gebhart/patrepeval huggingface dataset:
Shape-from-Template (2015)

We study a problem that we call Shape-from-Template, which is the problem of reconstructing the shape of a deformable surface from a single image and a 3D template. Current methods in the literature address the case of isometric deformations, and relax the isometry constraint to the convex inextensibility constraint, solved using the so-called maximum depth heuristic. We call these methods zeroth-order since they use image point locations (the zeroth-order differential structure) to solve the shape inference problem from a perspective image. We propose a novel class of methods that we call first-order. The key idea is to use both image point locations and their first-order differential structure. The latter can be easily extracted from a warp between the template and the input image. We give a unified problem formulation as a system of PDEs for isometric and conformal surfaces that we solve analytically. This has important consequences. First, it gives the first analytical algorithms to solve this type of reconstruction problems. Second, it gives the first algorithms to solve for the exact constraints. Third, it allows us to study the well-posedness of this type of reconstruction: we establish that isometric surfaces can be reconstructed unambiguously and that conformal surfaces can be reconstructed up to a few discrete ambiguities and a global scale. In the latter case, the candidate solution surfaces are obtained analytically. Experimental results on simulated and real data show that our isometric methods generally perform as well as or outperform state of the art approaches in terms of reconstruction accuracy, while our conformal methods largely outperform all isometric methods for extensible deformations.
A Unified Framework for Shot Type Classification Based on Subject Centric Lens (2020)

Shots are key narrative elements of various videos, e.g. movies, TV series, and user-generated videos that are thriving over the Internet. The types of shots greatly influence how the underlying ideas, emotions, and messages are expressed. The technique to analyze shot types is important to the understanding of videos, which has seen increasing demand in real-world applications in this era. Classifying shot type is challenging due to the additional information required beyond the video content, such as the spatial composition of a frame and camera movement. To address these issues, we propose a learning framework Subject Guidance Network (SGNet) for shot type recognition. SGNet separates the subject and background of a shot into two streams, serving as separate guidance maps for scale and movement type classification respectively. To facilitate shot type analysis and model evaluations, we build a large-scale dataset MovieShots, which contains 46K shots from 7K movie trailers with annotations of their scale and movement types. Experiments show that our framework is able to recognize these two attributes of shot accurately, outperforming all the previous methods.
High density interconnects and flexible hybrid assemblies for active biomedical implants (2001)

Advanced microtechnologies offer new opportunities for the development of active implants that go beyond the design of pacemakers and cochlea implants. Examples of future implants include neural and muscular stimulators, implantable drug delivery systems, intracorporal monitoring devices and body fluid control systems. The active microimplants demand a high degree of device miniaturization without compromising on design flexibility and biocompatibility requirements. With the need for integrating various microcomponents for a complex retina stimulator device, we have developed a novel technique for microassembly and high-density interconnects employing flexible, ultra-thin polymer based substrates. Pads for interconnections, conductive lines, and microelectrodes were embedded into the polyimide substrate as thin films. Photolithography and sputtering has been employed to pattern the microstructures. The novel "MicroFlex interconnection (MFI)" technology was developed to achieve chip size package (CSP) dimensions without the requirement of using bumped flip chips (FC). The MFI is based on a rivet like approach that yields an electrical and mechanical contact between the pads on the flexible polyimide substrate and the bare chips or electronic components. Center to center bond pad distances smaller than 100 /spl mu/m were accomplished. The ultra thin substrates and the MFI technology was proven to be biocompatible. Electrical and mechanical tests confirmed that interconnects and assembly of bare chips are reliable and durable. Based on our experience with the retina stimulator implant, we defined design rules regarding the flexible substrate, the bond pads, and the embedded conductive tracks. It is concluded that the MFI opens new venues for a novel generation of active implants with advanced sensing, actuation, and signal processing properties.
Structural Studies and Organic Ligand-binding Properties of Bovine Plasma Albumin (1970)

Abstract Cyanogen bromide cleavage of bovine plasma albumin in 75% formic acid gave two fragments, N and C, in yields of 80%. After reduction of the cross-linking disulfide bonds of Fragment N, two peptides containing 88 and 98 amino acid residues were isolated. The single sulfhydryl group of albumin was found to be located in the 88 amino acid residue peptide which occupies the amino-terminal position of the molecule. After reduction of Fragment C, three peptides containing 211, 148, and 34 amino acid residues were isolated. These five peptides together account for the albumin molecule. Limited tryptic hydrolysis of defatted bovine plasma albumin at pH 8.8 and 0° gave a fragment of molecular weight of about 40,000 in a yield of 21%. The fragment is derived from the carboxyl-terminal two-thirds of the albumin molecule as shown by a comparison of its three cyanogen bromide peptides with those from albumin. These data were used for the alignment of the five cyanogen bromide peptides of albumin. Binding studies showed that the tryptic fragment and defatted albumin both had one primary site for octanoate and l-tryptophan. d-Tryptophan competitively displaced either of these two ligands from the fragment and from albumin, thus suggesting that all three ligands bind at the same site. The binding constants of the fragment for the three ligands were all about one-third of those for albumin. The ratio of the binding constants of l-and d-tryptophan for the fragment was nearly the same as that for albumin, and this was also the case for octanoate and l-tryptophan. These similarities strongly suggest that the binding site in the fragment is the one present in albumin.
The triggering signal dictates the effect of docosahexaenoic acid on lymphocyte function in vitro (1998)

Docosahexaenoic acid (DHA) is an n-3 fatty acid beneficial to several human conditions including inflammation and autoimmune disease. To better understand the effect of DHA on immunity, we monitored the rise in cytosolic free calcium, interleukin 2 receptor (IL2R) expression, and proliferation of splenic lymphocytes triggered with three different stimuli in the presence or absence of DHA. We found that 10 microg DHA/mL suppressed concanavalin A-induced mitogenesis and the mixed lymphocyte reaction while concurrently enhancing proliferation stimulated with anti-Thy-1 antibodies. Proliferation, as measured by [3H]thymidine incorporation after 2 to 5 d of culture, was affected by DHA, but earlier activation effects such as elevation of cytosolic free calcium and IL2R expression were not altered. These results imply that DHA incorporated into membrane phospholipids differentially affects the activity of distinct membrane-bound receptors and signaling molecules. This result suggests that DHA may be used to modulate immune responses selectively, e.g., to suppress undesired autoimmunity while maintaining protective immunity.
Interleukin-18 Regulation of Interferon γ Production and Cell Proliferation as Shown in Interleukin-1β–Converting Enzyme (Caspase-1)-Deficient Mice (1998)

Interleukin-18 (IL-18) is a costimulatory factor for interferongamma (IFNgamma) production. Processing of pro-IL-18 by IL-1beta-converting enzyme (ICE) leads to the release of bioactive IL-18. Compared with wild-type (WT) mice, splenocytes from ICE-deficient mice produced low IFNgamma after lipopolysaccharide (LPS) or zymosan (50% and 80% reduction). In contrast, IFNgamma production was unimpaired in ICE-deficient mice using Concanavalin A (Con A). Comparable results were obtained when endogenous IL-18 was blocked with a neutralizing antibody. LPS-induced IFNgamma was also reduced by an ICE inhibitor. Exogenous IL-18 augmented zymosan-induced IFNgamma production in WT mice. In ICE-deficient cells, IFNgamma production was only partially restored by IL-18. The reduced levels of IFNgamma in ICE-deficient mice were not due to a lack of IL-12, because zymosan induced IL-12 equally in WT and in ICE-deficient mice. IFNgamma is an important regulator of cell proliferation. In accordance, splenocytes from ICE-deficient mice proliferated more when stimulated with LPS, but not with Con A. Furthermore, in ovalbumin-sensitized ICE-deficient mice, proliferation of lymph node cells in response to the specific antigen was not altered. Exogenous IFNgamma inhibited, whereas blockade of endogenous IFNgamma or IL-18 increased, LPS induced splenocyte proliferation both in WT and in ICE-deficient mice. Our results show that IL-18 is an IL-12-independent regulator of IFNgamma production and of cell proliferation induced by microbial stimuli. However, ICE-dependent processing of IL-18 is not needed for response to mitogens or antigens.
Controlled Delivery of Antigens and Adjuvants in Vaccine Development (1996)

Advances in the understanding of the pathogenesis of infectious diseases and cancer immunology have inspired many new approaches to vaccine development. Many subunit antigens and peptides that are effective for vaccination have been discovered. These subunit antigens in tum stimulate synthesis of effective adjuvants to enhance their immunogenicity. Controlled-release technology offers the potential of further improving the efficacy of conventional vaccine formulations by optimizing the temporal and spatial presentation of the-antigens and adjuvants to the immune system. The combination of sustained release and depot effect may also reduce the amount of antigens or adjuvants needed and eliminate the booster shots that are necessary for the success of many vaccinations. This review examines the contribution controlled release technology can make in various areas of vaccination, with an emphasis on tumor vaccines.
NeuN: a useful neuronal marker for diagnostic histopathology. (1996)

The monoclonal antibody A60 specifically recognizes the DNA-binding, neuron-specific protein NeuN, which is present in most neuronal cell types of vertebrates. In this study we demonstrate the potential use of NeuN as a diagnostic neuronal marker using a wide range of formalin-fixed, paraffin-embedded human surgical and autopsy specimens from the central and peripheral nervous system. After microwave antigen retrieval, almost all neuronal populations revealed strong immunoreactivity for NeuN in nuclei, perikarya, and some proximal neuronal processes, whereas more distal axon cylinders and dendritic ramifications were not stained. The stain greatly enhanced the gray matter architecture. NeuN immunoreactivity was not detected in Purkinje cells, most neurons of the internal nuclear layer of the retina, and in sympathetic chain ganglia. We examined nine gangliogliomas and 14 dysembryoplastic neuroepithelial tumors, one ganglioneuroma, and one dysplastic cerebellar gangliocytoma. The neuronal component of all of these lesions showed marked immunoreactivity for NeuN. In addition, NeuN immunoreactivity was focally seen in one of seven medulloblastomas with prominent neuronal differentiation. There was no staining of non-neuronal structures. The results indicate that NeuN immunoreactivity is a sensitive and specific neuronal marker in formalin-fixed, paraffin-embedded tissues, and may be useful in diagnostic histopathology.
<title>New optical effects in the human hard tooth tissues</title> (1990)

The results of the investigations of light propagation in the human hard tooth t issues are represented. It is shown that apart from light scattering the novel effect of waveuide light propagat ion from the enamel surface to the tooth cavity is taken place. The trajectories of light flows are the same that the direct ions of enamel prisms and dent inal tubules orientat ions. Anomal optical properties of the tooth are shown to be explained by the waveguide-scattering media model which is developed in this paper.
Dopamine, in the presence of tyrosinase, covalently modifies and inactivates tyrosine hydroxylase (1998)

Dopamine has been implicated as a potential mediating factor in a variety of neurodegenerative disorders. Dopamine can be oxidized to form a reactive dopamine quinone that can covalently modify cellular macromolecules including protein and DNA. This oxidation can be enhanced through various enzymes including tyrosinase and/or prostaglandin H synthase. One of the potential targets in brain for dopamine quinone damage is tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis. The present studies demonstrated that dopamine quinone, the formation of which was enhanced through the activity of the melanin biosynthetic enzyme, tyrosinase, covalently modified and inactivated tyrosine hydroxylase. Dihydroxyphenylalanine (DOPA; the catechol-containing precursor of dopamine) also inactivated tyrosine hydroxylase under these conditions. Catecholamine-mediated inactivation occurred with both purified tyrosine hydroxylase as well as enzyme present in crude pheochromocytoma homogenates. Inactivation was associated with covalent incorporation of radiolabelled dopamine into the enzyme as assessed by immunoprecipitation, size exclusion chromatography, and denaturing sodium dodecylsulfate (SDS)-polyacrylamide gel electrophoresis. Furthermore, the covalent modification and inactivation of tyrosine hydroxylase was blocked by antioxidant compounds (dithiothreitol, reduced glutathione, or NADH). In addition to kinetic feedback inhibition and the formation of an inhibitory dopamine/Fe+3 complex, these findings suggest that a third mechanism exists by which dopamine (or DOPA) can inhibit tyrosine hydroxylase, adding further complexity to the regulation of catecholamine biosynthesis.
Differentiation of rat marrow mesenchymal stem cells into pancreatic islet beta-cells (2004)

Islet-like functional cells can be differentiated from marrow mesenchymal stem cells, which may be a new procedure for clinical diabetes stem -cell therapy, these cells can control blood glucose level in diabetic rats. MSCs may play an important role in diabetes therapy by islet differentiation and transplantation.
Comparison of methods for the analysis of therapeutic immunoglobulin G Fc-glycosylation profiles—Part 2: Mass spectrometric methods (2015)

To monitor the Fc glycosylation of therapeutic immunoglobulin G in bioprocess development, product characterization and release analytics, reliable techniques for glycosylation analysis are needed. Several analytical methods are suitable for this application. We recently presented results comparing detection methods for glycan analysis that are separation-based, but did not include mass spectrometry (MS). In the study reported here, we comprehensively compared MS-based methods for Fc glycosylation profiling of an IgG biopharmaceutical. A therapeutic antibody reference material was analyzed 6-fold on 2 different days, and the methods investigated were compared with respect to precision, accuracy, throughput and analysis time. Emphasis was put on the detection and quantitation of sialic acid-containing glycans. Eleven MS methods were compared to hydrophilic interaction liquid chromatography of 2-aminobenzamide labeled glycans with fluorescence detection, which served as a reference method and was also used in the first part of the study. The methods compared include electrospray MS of the heavy chain and Fc part after limited digestion, liquid chromatography MS of a tryptic digest, porous graphitized carbon chromatography MS of released glycans, electrospray MS of glycopeptides, as well as matrix assisted laser desorption ionization MS of glycans and glycopeptides. Most methods showed excellent precision and accuracy. Some differences were observed with regard to the detection and quantitation of low abundant glycan species like the sialylated glycans and the amount of artefacts due to in-source decay.
Tumor antigen targets and tumor immunotherapy (2006)

Tumor immunology and immunotherapy attempt to use the exquisite specificity and lytic capability of the immune system to treat malignant disease with a minimum of damage to normal tissue. Increasing knowledge of the identity of tumor antigens should point the way to effective therapeutic vaccines or more specific immunotherapeutic strategies. Tumors, however, have evolved mechanisms to inactivate cytolytic T-cells and other immune responses targeting tumor antigens. The current goal of immunotherapy research is to use contemporary advances in cellular and molecular immunology to develop strategies to overcome the disabling effects of the tumor microenvironment on the immune system attack against tumor antigen targets. This review will summarize our current knowledge of the spectrum of tumor antigen targets available for immune recognition in cancer, the obstacles to tumor immunotherapy, the use of adoptive immunotherapy to overcome some of these obstacles, the use of monoclonal antibodies to target tumor antigens for immunotherapy, and finally the potential use of heat shock proteins as targets for cancer immunotherapy.
Nucleotide sequence of a cloned woodchuck hepatitis virus genome: comparison with the hepatitis B virus sequence (1982)

The complete nucleotide sequence of a woodchuck hepatitis virus genome cloned in Escherichia coli was determined by the method of Maxam and Gilbert. This sequence was found to be 3,308 nucleotides long. Potential ATG initiator triplets and nonsense codons were identified and used to locate regions with a substantial coding capacity. A striking similarity was observed between the organization of human hepatitis B virus and woodchuck hepatitis virus. Nucleotide sequences of these open regions in the woodchuck virus were compared with corresponding regions present in hepatitis B virus. This allowed the location of four viral genes on the L strand and indicated the absence of protein coded by the S strand. Evolution rates of the various parts of the genome as well as of the four different proteins coded by hepatitis B virus and woodchuck hepatitis virus were compared. These results indicated that: (i) the core protein has evolved slightly less rapidly than the other proteins; and (ii) when a region of DNA codes for two different proteins, there is less freedom for the DNA to evolve and, moreover, one of the proteins can evolve more rapidly than the other. A hairpin structure, very well conserved in the two genomes, was located in the only region devoid of coding function, suggesting the location of the origin of replication of the viral DNA.
The quality of life in acne: a comparison with general medical conditions using generic questionnaires (1999)

Skin diseases such as acne are sometimes thought of as unimportant, even trivial, when compared with diseases of other organ systems. To address this point directly, validated generic questionnaires were used to assess morbidity in acne patients and compare it with morbidity in patients with other chronic diseases. For 111 acne patients referred to a dermatologist, quality of life was measured using the Dermatology Life Quality Index, Rosenberg's measure of self-esteem, a version of the General Health Questionnaire (GHQ-28) and the Short Form 36 (SF-36). Clinical severity was measured using the Leeds Acne Grade. Population quality of life data for the SF-36 instrument were available from a random sample of adult local residents (n = 9334) some of whom reported a variety of long-standing disabling diseases. All quality of life instruments showed substantial deficits for acne patients that correlated with each other but not with clinically assessed acne severity. The acne patients (a relatively severely affected group) reported levels of social, psychological and emotional problems that were as great as those reported by patients with chronic disabling asthma, epilepsy, diabetes, back pain or arthritis. Acne is not a trivial disease in comparison with other chronic conditions. This should be recognized in the allocation of health care resources.
New insights into the enigma of immunoglobulin D (2010)

Immunoglobulin D (IgD) has remained a mysterious antibody class for almost half a century. IgD was initially thought to be a recently evolved Ig isotype expressed only by some mammalian species, but recent discoveries in fishes and amphibians demonstrate that IgD was present in the ancestor of all jawed vertebrates and has important immunological functions. The structure of IgD has been very dynamic throughout evolution. Mammals can express IgD through alternative splicing and class switch recombination. Active cell-dependent and T-cell-independent IgM-to-IgD class switching takes place in a unique subset of human B cells from the upper aerodigestive mucosa, which provides a layer of mucosal protection by interacting with many pathogens and their virulence factors. Circulating IgD can bind to myeloid cells such as basophils and induce antimicrobial, inflammatory, and B-cell-stimulating factors upon cross-linking, which contributes to not only immune surveillance but also inflammation and tissue damage when this pathway is overactivated under pathological conditions. Recent research shows that IgD is an important immunomodulator that orchestrates an ancestral surveillance system at the interface between immunity and inflammation.
Individual β Cells within the Intact Islet Differentially Respond to Glucose (1997)

Insulin production by the pancreatic islet is tightly coupled to the concentration of blood glucose. The mechanism by which glucose controls proinsulin biosynthesis in beta cells is poorly understood. Analysis of insulin gene expression in individual cells within whole, living islets using adenovirus gene transfer and direct observation of insulin promoter-directed green fluorescent protein activity indicates that beta cells are functionally heterogeneous. An increase in glucose concentration not only stimulates expression within individual beta cells, but unexpectedly acts to increase the total number of positive cells. The net islet response to a given glucose stimulus reflects an integrated action of beta cells with individually differing behaviors. This additional level of functional complexity may provide new insights into the pathophysiology and treatment of diabetes mellitus.