gebhart/patrepeval huggingface dataset:
Acquiring reflectance and shape from continuous spherical harmonic illumination (2013)

We present a novel technique for acquiring the geometry and spatially-varying reflectance properties of 3D objects by observing them under continuous spherical harmonic illumination conditions. The technique is general enough to characterize either entirely specular or entirely diffuse materials, or any varying combination across the surface of the object. We employ a novel computational illumination setup consisting of a rotating arc of controllable LEDs which sweep out programmable spheres of incident illumination during 1-second exposures. We illuminate the object with a succession of spherical harmonic illumination conditions, as well as photographed environmental lighting for validation. From the response of the object to the harmonics, we can separate diffuse and specular reflections, estimate world-space diffuse and specular normals, and compute anisotropic roughness parameters for each view of the object. We then use the maps of both diffuse and specular reflectance to form correspondences in a multiview stereo algorithm, which allows even highly specular surfaces to be corresponded across views. The algorithm yields a complete 3D model and a set of merged reflectance maps. We use this technique to digitize the shape and reflectance of a variety of objects difficult to acquire with other techniques and present validation renderings which match well to photographs in similar lighting.
Panel of Anti-gp120 Monoclonal Antibodies Reacts with Same Nuclear Proteins in Uninfected Cells as Those Recognized by Autoantibodies from Patients with Systemic Lupus Erythematosus (1994)

Mouse monoclonal antibodies (MAbs) directed against the HIV-1 gp120 envelope protein were screened for their reactivity with intracellular antigens expressed in normal uninfected monocytes by indirect immunofluorescence and immunoblotting. Some of these MAbs reacted with the nuclei of normal uninfected cells, producing three main staining patterns by indirect immunofluorescence. Western blot analysis showed that these monoclonal antibodies recognize peptides of various molecular weights present in nuclei preparations of normal monocytes. Reactivity with peptides of similar molecular weight was also detected in sera from both HIV-infected individuals and patients with systemic lupus erythematosus. This evidence for antigenic similarities between HIV-1 gp120 and nuclear antigens represents a novel example of molecular mimicry of self-antigens by HIV envelope proteins, which supports the involvement of mechanisms of autoimmunity in HIV disease pathogenesis through recruitment of autoimmune responses to self-structures by HIV antigens.
Brd4 links chromatin targeting to HPV transcriptional silencing (2006)

The E2 protein encoded by human papillomaviruses (HPVs) inhibits expression of the viral E6 oncoprotein, which, in turn, regulates p53 target gene transcription. To identify cellular proteins involved in E2-mediated transcriptional repression, we isolated an E2 complex from human cells conditionally expressing HPV-11 E2. Surprisingly, the double bromodomain-containing protein Brd4, which is implicated in cell cycle control and viral genome segregation, was found associated with E2 and conferred on E2 the ability to inhibit AP-1-dependent HPV chromatin transcription in an E2-binding site-specific manner as illustrated by in vitro reconstituted chromatin transcription experiments. Knockdown of Brd4 in human cells alleviates E2-mediated repression of HPV transcription. The E2-interacting domain at the extreme C terminus and the chromatin targeting activity of a bromodomain-containing region are both essential for the corepressor activity of Brd4. Interestingly, E2-Brd4 blocks the recruitment of TFIID and RNA polymerase II to the HPV E6 promoter region without inhibiting acetylation of nucleosomal histones H3 and H4, indicating an acetylation-dependent role of Brd4 in the recruitment of E2 for transcriptional silencing of HPV gene activity. Our finding that Brd4 is a component of the virus-assembled transcriptional silencing complex uncovers a novel function of Brd4 as a cellular cofactor modulating viral gene expression.
Microfluidic culture of single human embryonic stem cell colonies (2009)

We have developed a miniaturized microfluidic culture system that allows experimentation on individual human embryonic stem cell (hESC) colonies in dynamic (flow applied) or static (without flow) conditions. The system consists of three inlet channels that converge into a cell-culture channel and provides the capability to spatially and temporally deliver specific treatments by using patterned laminar fluid flow to different parts of a single hESC colony. We show that microfluidic culture for 96 h with or without flow results in similar maintenance of hESC self-renewal, the capability to differentiate into three germ cell lineages, and to maintain a normal karyotype, as in standard culture dishes. Localized delivery of a fluorescent nucleic acid dye was achieved with laminar flow, producing staining only in nuclei of exposed cells. Likewise, cells in desired regions of colonies could be removed with enzymatic treatment and collected for analysis. Re-coating the enzyme treated area of the channel with extracellular matrix led to re-growth of hESC colonies into this region. Our study demonstrates the culture of hESCs in a microfluidic device that can deliver specific treatments to desired regions of a single colony. This miniaturized culture system allows in situ treatment and analysis with the ability to obtain cell samples from part of a colony without micromanipulation and to perform sensitive molecular analysis while permitting further growth of the hESC colony.
Identification of Amino Acid Residues in the Capsid Proteins of Adeno-Associated Virus Type 2 That Contribute to Heparan Sulfate Proteoglycan Binding (2003)

The adeno-associated virus type 2 (AAV2) uses heparan sulfate proteoglycan (HSPG) as its primary cellular receptor. In order to identify amino acids within the capsid of AAV2 that contribute to HSPG association, we used biochemical information about heparin and heparin sulfate, AAV serotype protein sequence alignments, and data from previous capsid studies to select residues for mutagenesis. Charged-to-alanine substitution mutagenesis was performed on individual residues and combinations of basic residues for the production and purification of recombinant viruses that contained a green fluorescent protein (GFP) reporter gene cassette. Intact capsids were assayed for their ability to bind to heparin-agarose in vitro, and virions that packaged DNA were assayed for their ability to transduce normally permissive cell lines. We found that mutation of arginine residues at position 585 or 588 eliminated binding to heparin-agarose. Mutation of residues R484, R487, and K532 showed partial binding to heparin-agarose. We observed a general correlation between heparin-agarose binding and infectivity as measured by GFP transduction; however, a subset of mutants that partially bound heparin-agarose (R484A and K532A) were completely noninfectious, suggesting that they had additional blocks to infectivity that were unrelated to heparin binding. Conservative mutation of positions R585 and R588 to lysine slightly reduced heparin-agarose binding and had comparable effects on infectivity. Substitution of AAV2 residues 585 through 590 into a location predicted to be structurally equivalent in AAV5 generated a hybrid virus that bound to heparin-agarose efficiently and was able to package DNA but was noninfectious. Taken together, our results suggest that residues R585 and R588 are primarily responsible for heparin sulfate binding and that mutation of these residues has little effect on other aspects of the viral life cycle. Interactive computer graphics examination of the AAV2 VP3 atomic coordinates revealed that residues which contribute to heparin binding formed a cluster of five basic amino acids that presented toward the icosahedral threefold axis from the surrounding spike protrusion. Three other kinds of mutants were identified. Mutants R459A, H509A, and H526A/K527A bound heparin at levels comparable to that of wild-type virus but were defective for transduction. Another mutant, H358A, was defective for capsid assembly. Finally, an R459A mutant produced significantly lower levels of full capsids, suggesting a packaging defect.
Supportive development of functional tissues for biomedical research using the MINUSHEET® perfusion system (2012)

Functional tissues generated under in vitro conditions are urgently needed in biomedical research. However, the engineering of tissues is rather difficult, since their development is influenced by numerous parameters. In consequence, a versatile culture system was developed to respond the unmet needs.Optimal adhesion for cells in this system is reached by the selection of individual biomaterials. To protect cells during handling and culture, the biomaterial is mounted onto a MINUSHEET® tissue carrier. While adherence of cells takes place in the static environment of a 24 well culture plate, generation of tissues is accomplished in one of several available perfusion culture containers. In the basic version a continuous flow of always fresh culture medium is provided to the developing tissue. In a gradient perfusion culture container epithelia are exposed to different fluids at the luminal and basal sides. Another special container with a transparent lid and base enables microscopic visualization of ongoing tissue development. A further container exhibits a flexible silicone lid to apply force onto the developing tissue thereby mimicking mechanical load that is required for developing connective and muscular tissue. Finally, stem/progenitor cells are kept at the interface of an artificial polyester interstitium within a perfusion culture container offering for example an optimal environment for the spatial development of renal tubules.The system presented here was evaluated by various research groups. As a result a variety of publications including most interesting applications were published. In the present paper these data were reviewed and analyzed. All of the results point out that the cell biological profile of engineered tissues can be strongly improved, when the introduced perfusion culture technique is applied in combination with specific biomaterials supporting primary adhesion of cells.
A Novel Small-molecule Tumor Necrosis Factor α Inhibitor Attenuates Inflammation in a Hepatitis Mouse Model (2014)

Overexpression of tumor necrosis factor α (TNFα) is a hallmark of many inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and septic shock and hepatitis, making it a potential therapeutic target for clinical interventions. To explore chemical inhibitors against TNFα activity, we applied computer-aided drug design combined with in vitro and cell-based assays and identified a lead chemical compound, (E)-4-(2-(4-chloro-3-nitrophenyl) (named as C87 thereafter), which directly binds to TNFα, potently inhibits TNFα-induced cytotoxicity (IC50 = 8.73 μM) and effectively blocks TNFα-triggered signaling activities. Furthermore, by using a murine acute hepatitis model, we showed that C87 attenuates TNFα-induced inflammation, thereby markedly reducing injuries to the liver and improving animal survival. Thus, our results lead to a novel and highly specific small-molecule TNFα inhibitor, which can be potentially used to treat TNFα-mediated inflammatory diseases.
Decoherence and Efficiency of Quantum Error Correction (1996)

Certain physical aspects of quantum error correction are discussed for a quantum computer (n-qubit register) in contact with a decohering environment. Under rather plausible assumptions upon the form of the computer-environment interaction, the efficiency of a general correcting procedure is evaluated as a function of the spontaneous-decay duration and the rank of errors covered by the procedure. It is proved that the probability of errors can be made arbitrarily small by enhancing the correction method, provided the decohering interaction is represented by a bounded operator.
Polymorphic Short Tandem Repeats for Diagnosis of the Charcot-Marie-Tooth 1A Duplication (2001)

Combined use of the three STRs allows robust diagnosis with almost complete informativeness. In our routine diagnosis for CMT1A, they have replaced the use of other polymorphic markers, either in a manual adaptation or combined with fluorescence labeling and allele sizing on a DNA sequencer.
TAZ interacts with zonula occludens‐1 and ‐2 proteins in a PDZ‐1 dependent manner (2010)

The transcriptional coactivator TAZ recognizes L/PPxY motifs in transcription factors like Runx1/2 through its WW domain. We show that the first PDZ domain of zona occludens-1 (ZO-1) and 2 (ZO-2) interacts with the carboxy-terminal PDZ binding motif of TAZ. Deletion of this motif abrogates binding. ZO-2 colocalizes with TAZ in the nucleus of MDCK cells and ZO-2 expression alters TAZ localization in human embryonic kidney cells. Luciferase assays demonstrate ZO-2 inhibition of TAZ-mediated transactivation. We propose that zonula occludens is a negative regulator of TAZ and suggest that selected tight junction proteins control nuclear translocation and activity of TAZ.
Lipids and the ocular lens (2010)

The unusually high levels of saturation and thus order contribute to the uniqueness of human lens membranes. In addition, and unlike in most biomembranes, most of the lens lipids are associated with proteins, thus reducing their mobility. The major phospholipid of the human lens is dihydrosphingomyelin. Found in significant quantities only in primate lenses, particularly human ones, this lipid is so extremely stable that it was reported to be the only lipid remaining in a frozen mammoth 40,000 years after its death. Unusually high levels of cholesterol add peculiarity to the composition of lens membranes. Beyond the lateral segregation of lipids into dynamic domains known as rafts, the high abundance of cholesterol in the human lens leads to the formation of patches of pure cholesterol. Changes in human lens lipid composition with age and disease as well as differences among species are greater than those observed for any other biomembrane. The relationships among lens membrane composition, structure, and lipid conformation reviewed in this article are unique to the mammalian lens and offer exciting insights into lens membrane function. This review focuses on findings reported over the last two decades that demonstrate the uniqueness of mammalian lens membranes regarding their morphology and composition. Because the membranes of human lenses do undergo the most dramatic changes with age and cataractogenesis, the final sections of this review address our current knowledge of the unusual composition and organization of adult human lens membranes with and without opacification. Finally, the questions that still remain to be answered are presented.
Experimental amebiasis. III. A rapid in vitro assay for virulence of Entamoeba histolytica. (1978)

A rapid and simple assay for cytopathogenicity of axenically cultivated Entamoeba histolytica has been developed employing baby hamster kidney (BHK) or mouse 3T3 cells conventionally tissue cultured. Three of the twelve amebal strains tested produced total destruction of the BHK cell monolayer in 2--3 hours, and these three strains are the three most virulent strains for the newborn hamster liver. Two additional strains were of moderate cytopathogenicity in vitro and of moderate virulence in vivo. Seven strains were of low cytopathogenicity and virulence. Within these three major groupings, however, the cytopathogenicity ranking was not entirely reproducible. The general correspondence of cytopathogenicity in vitro and virulence in vivo and the possibility of obtaining data within a few hours suggest such an assay may prove a useful tool in amebiasis research.
CD6: expression during development, apoptosis and selection of human and mouse thymocytes (2002)

CD6, a 130-kDa surface glycoprotein, is expressed primarily on cells of T lineage. A co-stimulatory role for CD6 in mature T cells has been shown, but the function of CD6 during thymocyte development is unknown. Since CD6 ligands are expressed on thymic epithelium, their interactions with CD6 could be important in thymic selection. In this report we show that CD6 is developmentally regulated in human and mouse thymocytes, and further demonstrate that increase in the level of CD6 expression correlates with expression of the selection marker CD69. We also show that activation via CD2 induces CD6 expression on mature human thymocytes and on a subset of immature human thymocytes that are resistant to apoptosis. In human and mouse thymocytes that express heterogeneous TCR, CD6 increases occur as double-positive thymocytes are selected to a single-positive stage. In contrast, in thymocytes from TCR transgenic mice, CD6 is barely increased following selection, suggesting that as functional avidity increases, requirements for CD6-dependent co-stimulation decrease. Taken together, these results indicate that during thymic development CD6-dependent signals may contribute both to thymocyte survival, and to the overall functional avidity of selection in both man and mouse.
Reconfiguration of Vibro-tactile Feedback Based on Drivers' Sitting Attitude (2009)

The today mainly incorporated sensory modalities vision and hearing are most often highly charged due to an increasing number, as well as a rising complexity of diversified assistance systems in vehicles. These systems, originally developed for "supporting" the driver in its tasks, increasingly directs to operation errors caused by cognitive overload. The sense of touch - as additional interaction channel - should have the ability to release cognitive load from visual and auditory channels by adapting in a natural, intuitive and non-distracting manner. A drawback of haptics is that feedback is reliant to both driver and environmental conditions. For instance, different sizes and weights of drivers' result in a changed haptic perceptivity, and vibro-tactile feedback potentially is interpreted erroneous due to personal sitting attitudes. A vibro-tactile seat, endowed with a set of unobtrusive embedded sensors and actuators, is proposed to counter action these issues. The input channel is used for determining the occupied seating surface and, in addition, is also responsible for observing disruptive vibrations, originating in the environment. These information is employed in order to reconfigure vibro-tactile output dynamically with the aim to guarantee consistent haptic perception for any person.
Evidence for serum miR-15a and miR-16 levels as biomarkers that distinguish sepsis from systemic inflammatory response syndrome in human subjects (2012)

Serum miR-15a and miR-16 can both distinguish sepsis/SIRS from normal controls. miR-15a may be a biomarker that distinguishes between sepsis and SIRS.
Rapid isolation and serum-free expansion of human CD34+ cells. (1994)

Human CD34+ cells were isolated from bone marrow from normal volunteers and expanded under serum-free culture conditions. CD34+ cells were cultured with interleukin-3 (IL-3), IL-1, and stem cell factor and expanded in granulocyte-macrophage colony-forming units, erythroid blast-forming units, and CD34+ cell number during the first 7-14 days of incubation. By contrast, cultures maintained in fetal calf serum under identical conditions showed much reduced expansion, as measured by all of the above parameters. The level of expansion of the CD34+ cells was dependent on the combination of growth factors used during culture. The data establish the feasibility of serum-free expansion of progenitors and suggest the clinical use of this procedure for the generation of expanded progenitor cell products for transfusion after chemotherapy to minimize treatment-related cytopenias.
Isolation and characterization of a monoclonal antibody that recognizes the human c-kit receptor (1992)

Stem cell factor (SCF) stimulates the growth of burst-forming unit- erythroid (BFU-E) and colony-forming unit granulocyte-macrophage (CFU- GM) by binding to a specific cell surface receptor. The receptor for SCF is encoded by the protooncogene c-kit. After immunizing mice with the human erythroleukemia cell line OCIM1, we obtained a monoclonal antibody (MoAb) that recognizes the human c-kit receptor. This MoAb, designated SR-1, blocks binding of 125I-human SCF to the c-kit receptor, and neutralizes the biologic effects of SCF in hematopoietic colony assays. With few exceptions, c-kit expression was identified on all hematopoietic and lymphoid cell lines tested by indirect immunofluorescent analysis using SR-1 and by binding studies with 125I- SCF. SR-1 recognizes a small fraction of normal bone marrow mononuclear cells, and these cells have the morphologic appearance of blasts. Colony assays show that BFU-E and CFU-GM display the c-kit receptor. SR- 1 does not cross-react with murine c-kit protein, indicating that the binding epitopes of the human and murine c-kit receptors are antigenically distinct. This MoAb may be useful to characterize the spectrum of cells that display the c-kit receptor and to further define the role of SCF in hematopoiesis.
Visual Effects of Pilocarpine in Glaucoma (1976)

Eighteen glaucoma patients each received four pilocarpine regimens in random sequence: 1% and 4% eyedrops and 20mug/hr and 40mug/hr ocular therapeutic systems. Unimportant changes in refraction, near vision, and distance vision occurred during the use of either ocular therapeutic system. Miosis with ocular therapeutic systems was almost always less intense and variable than with eyedrops. Refractive changes occurred in 12 patients following 1% pilocarpine and in 16 patients following 4% pilocarpine drops; decreased distance vision occurred in nine patients after 1% drops and in 12 patients after 4% drops. Fewer patients showed decreases in near vision. In all cases, visual effects peaked one half hour after eyedrop instillations and returned gradually toward normal in the next two to three hours. Intraocular pressure levels were within comparable ranges during all four treatments, but the ocular therapeutic systems maintained pressure at a more constant level.
Mobile edge computing with network resource slicing for Internet-of-Things (2018)

Network slicing is an end-to-end concept that encompasses network functions, radio accesses, and clouds for enabling customized information-centric Internet-of-Things (IoT) services. The key idea is to virtualize all the resources from radio accesses to IoT service layers, so that IoT service providers can automate resource provisioning and management for users. This paper introduces the recent standards effort on network slicing for IoT in various standards bodies such as 3 GPP, NGMN, IETF, ET SI and oneM2M. In particular, standards activities on ET SI Multi-Access Edge Computing (MEC), NGMN and 3GPP Network Slicing and Virtualization, IETF slicing on transport networks and oneM2M IoT service layer resource slicing are introduced. Finally, this paper proposes a novel Edge Computing architecture customizing required network resources at the edge cloud, as close to users as possible, to minimize network signaling overhead in providing optimal IoT services.
A Survey on Eye-Gaze Tracking Techniques (2013)

Study of eye-movement is being employed in Human Computer Interaction (HCI) research. Eye - gaze tracking is one of the most challenging problems in the area of computer vision. The goal of this paper is to present a review of latest research in this continued growth of remote eye-gaze tracking. This overview includes the basic definitions and terminologies, recent advances in the field and finally the need of future development in the field.