gebhart/patrepeval huggingface dataset:
In Vitro and In Vivo Induction of a Th Cell Response Toward Peptides of the Melanoma-Associated Glycoprotein 100 Protein Selected by the TEPITOPE Program (2000)

The melanoma-associated Ag glycoprotein 100 was analyzed by the T cell epitope prediction software TEPITOPE. Seven HLA-DR promiscuous peptides predicted with a stringent threshold were used to load dendritic cells (DC), and induction of a proliferative response was monitored. PBMC of all nine donors including two patients with malignant melanoma responded to at least one of the peptides. The proliferative response was defined as a Th response by the selective expansion of CD4(+) cells, up-regulation of CD25 and CD40L, and IL-2 and IFN-gamma expression. Peptide-loaded DC also initiated a T helper response in vivo (i.e., tumor growth in the SCID mouse was significantly retarded by the transfer of PBMC together with peptide-loaded DC). Because the use of the TEPITOPE program allows for a prediction of T cell epitopes; because the predicted peptides can be rapidly confirmed by inducing a Th response in the individual patient; and because application of peptide-loaded DC suffices for the in vivo activation of helper cells, vaccination with MHC class II-binding peptides of tumor-associated Ags becomes a feasible and likely powerful tool in the immunotherapy of cancer.
Correlation of Murine Embryonic Stem Cell Gene Expression Profiles with Functional Measures of Pluripotency (2005)

Global gene expression profiling was performed on murine embryonic stem cells (ESCs) induced to differentiate by removal of leukemia inhibitory factor (LIF) to identify genes whose change in expression correlates with loss of pluripotency. To identify appropriate time points for the gene expression analysis, the dynamics of loss of pluripotency were investigated using three functional assays: chimeric mouse formation, embryoid body generation, and colony-forming ability. A rapid loss of pluripotency was detected within 24 hours, with very low residual activity in all assays by 72 hours. Gene expression profiles of undifferentiated ESCs and ESCs cultured for 18 and 72 hours in the absence of LIF were determined using the Affymetrix GeneChip U74v2. In total, 473 genes were identified as significantly differentially expressed, with approximately one third having unknown biological function. Among the 275 genes whose expression decreased with ESC differentiation were several factors previously identified as important for, or markers of, ESC pluripotency, including Stat3, Rex1, Sox2, Gbx2, and Bmp4. A significant number of the decreased genes also overlap with previously published mouse and human ESC data. Furthermore, several membrane proteins were among the 48 decreased genes correlating most closely with the functional assays, including the stem cell factor receptor c-Kit. Through identification of genes whose expression closely follows functional properties of ESCs during early differentiation, this study lays the foundation for further elucidating the molecular mechanisms regulating the maintenance of ESC pluripotency and facilitates the identification of more reliable molecular markers of the undifferentiated state.
delta Agent: association of delta antigen with hepatitis B surface antigen and RNA in serum of delta-infected chimpanzees. (1980)

The hepatitis B virus-associated beta antigen was found in the serum of experimentally infected chimpanzee as an internal component of a discrete subpopulation of hepatitis B surface antigen (HBsAg) particles. The 35- to 37-nm particles banded in CsCl at 1.24-1.25 g/cm3 and sedimented with a mobility intermediate between that of the hepatitis B virion and that of the 22-nm form of HBsAg. The particles contained only indistinct internal structure by electron microscopy and were not unique to delta agent infection, similar particles without delta-antigen activity being observed in the preinfection serum of HBsAg carrier chimpanzees. A small RNA (Mr, 5 X 10(5)) was temporally associated with delta antigen in the serum of infected chimpanzees and copurified with the delta-antigen-associated particles. This RNA is smaller than the genomes of known RNA viruses but larger than the viroids of higher plants.
Endoscopic argon plasma coagulation (APC) first clinical experiences in flexible endoscopy. (1994)

Argon plasma coagulation (APC) is a new mode of non-contact electrocoagulation in which current is applied to tissues by means of ionised argon gas (argon plasma). In open surgery, APC is used for the haemostasis of superficial, diffuse haemorrhages from parenchymatous organs and for the devitalization of various tissues. Experimental studies have shown the superiority of APC to standard electrocoagulation modes and surgical techniques due to its efficiency and limited tissue traumatisation. After developing and designing special probes which can be applied through flexible endoscopes and after testing these in in vitro studies, we have been able to utilise APC in both the gastrointestinal tract and the tracheobronchial system. From June, 1991 to September, 1992, 102 patients were treated endoscopically in 189 sessions with APC in the upper and lower gastrointestinal tract as well as in the respiratory system. The indications were malignant and benign tumours, diffuse haemorrhages of various origins and sites, tissue overgrowth after stent implantation, tissue remnants after endoscopic adenomectomy, and the conditioning of fistulas prior to fibrin sealing. In all cases, APC in flexible endoscopy was highly effective and easy to perform, with advantages over standard electrocoagulation. No problems or complications were observed. The limited depth of tissue coagulation (2-3 mm) with concomitant, efficient tissue coagulation allows application even in critical areas where there is risk of perforation, such as the duodenum or colon. For many indications, APC has replaced the Nd:YAG-laser, which was formerly used widely in our unit, Except for vaporisation of extended tumours, the APC shows remarkable advantages in nearly all applications.(ABSTRACT TRUNCATED AT 250 WORDS)
Translational models of ocular disease (2013)

Abstract Animals provide indispensable models to translate basic mechanistic discoveries and realize their therapeutic potential in humans. Conversely, advances in human medicine often inform management of similar conditions in clinical veterinary medicine. In this paper, key experimental model species are introduced, with emphasis on genetic contributions of the mouse. Its role and those of larger animal models are described in common ocular research areas including intraocular neoplasia, corneal epithelial and stromal disease, cataract, uveitis, glaucoma, and retinal dystrophies. Emphasis is placed on those conditions shared by humans and domestic animals, with the intent of exploring how the study of comparable conditions in humans, domestic animals, and laboratory animals informs one another.
Experimental characterization of components for active soft orthotics (2012)

In this paper, we present the characterization of soft pneumatic actuators currently under development for active soft orthotics. The actuators are tested statically and dynamically to characterize force and displacement properties needed for use in system design. They are shown to demonstrate remarkably repeatable performance, and very predictable behavior as actuator size (initial length) is varied to adjust total actuation. The results of the characterization are then used to inform design rules for selecting the size and number of actuators for a soft leg orthotic that can produce the force/moment/velocity properties required for a target wearer. The device was tested on a silicone model with inner frame and articulated ankle. Additionally, a portable pneumatic system was developed and characterized, that can actuate the pneumatic actuator over 800 times before refilling the gas supply.
Fifteenth Spiers Memorial Lecture. Thermodynamics of polymer solutions (1970)

The first page of this article is displayed as the abstract.
Anti-Inflammatory Activity of N-Butanol Extract from Ipomoea stolonifera In Vivo and In Vitro (2014)

Ipomoea stolonifera (I. stolonifera) has been used for the treatment of inflammatory diseases including rheumatism and rheumatoid arthritis in Chinese traditional medicine. However, the anti-inflammatory activity of I. stolonifera has not been elucidated. For this reason, the anti-inflammatory activity of n-butanol extract of I. stolonifera (BE-IS) was evaluated in vivo by using acute models (croton oil-induced mouse ear edema, carrageenan-induced rat paw edema, and carrageenan-induced rat pleurisy) and chronic models (cotton pellet-induced rat granuloma, and complete Freund's adjuvant (CFA)-induced rat arthritis). Results indicated that oral administration of BE-IS significantly attenuated croton oil-induced ear edema, decreased carrageenan-induced paw edema, reduced carrageenan-induced exudates and cellular migration, inhibited cotton pellet-induced granuloma formation and improved CFA-induced arthritis. Preliminary mechanism studies demonstrated that BE-IS decreased the levels of myeloperoxidase (MPO) and malondialdehyde (MDA), increased the activity of anti-oxidant enzyme superoxide dismutase (SOD) in vivo, and reduced the production of nitric oxide (NO), prostaglandin E2 (PGE2), tumor necrosis factor-α (TNF-α), interleukin (IL)-1β and IL-6 in lipopolysaccharide-activated RAW264.7 macrophages in vitro. Results obtained in vivo and in vitro demonstrate that BE-IS has considerable anti-inflammatory potential, which provided experimental evidences for the traditional application of Ipomoea stolonifera in inflammatory diseases.
A Knowledge-Based System for Capturing Human-Computer Interaction Events: CHIME (1991)

The ability to capture and analyze human-computer interaction (HCI) data is an important part of the iterative interface development process. In this paper, we claim that in order to perform accurate and extensive analysis of HCI events, an automated technique has to be used. We describe steps towards identifying desirable features of such a technique and present a list of those features. We present the key characteristics and architecture of a knowledge-based monitoring system, CHIME. We claim that the more knowledge a monitor has about the semantics of an application the more useful the data it collects. Finally, we report on the results of an exploratory study to assess the adequacy of key CHIME assumptions and architecture.
Changes in cartilage composition and physical properties due to stromelysin degradation (1995)

Exposure of intact cartilage to SLN caused specific, molecular-level degradation of matrix molecules, which resulted in changes in the swelling behavior and marked deterioration of functional physical properties of the tissue.
Low actuation voltage RF MEMS switches with signal frequencies from 0.25 GHz to 40 GHz (2003)

A novel low-voltage radio-frequency microelectromechanical system (RF MEMS) switch is reported. The device switching voltages are 14-17 volts. When the device is operated in an 'on' state, an insertion loss of less than 0.5 dB with a return loss of -15 dB at 40 GHz was measured. When operated in its 'off' state, an isolation of better than 27 dB over the frequency band from 0.25 GHz to 40 GHz was achieved. The RF MEMS switch equivalent circuit model shows that the 'on' resistance is 0.3 /spl Omega/ and the 'off' capacitance is 90 fF, which results in a figure of merit of 6000 GHz.
Explaining collaborative filtering recommendations (2000)

Automated collaborative filtering (ACF) systems predict a person's affinity for items or information by connecting that person's recorded interests with the recorded interests of a community of people and sharing ratings between like-minded persons. However, current recommender systems are black boxes, providing no transparency into the working of the recommendation. Explanations provide that transparency, exposing the reasoning and data behind a recommendation. In this paper, we address explanation interfaces for ACF systems - how they should be implemented and why they should be implemented. To explore how, we present a model for explanations based on the user's conceptual model of the recommendation process. We then present experimental results demonstrating what components of an explanation are the most compelling. To address why, we present experimental evidence that shows that providing explanations can improve the acceptance of ACF systems. We also describe some initial explorations into measuring how explanations can improve the filtering performance of users.
Virtual bellows: constructing high quality stills from video (2002)

Cameras with bellows give photographers flexibility for controlling perspective, but once the picture is taken, its perspective is set. We introduce 'virtual bellows' to provide control over perspective after a picture has been taken. Virtual bellows can be used to align images taken from different viewpoints, an important initial step in applications such as creating a high-resolution still image from video. We show how the virtual bellows, which implements the projective group, is an exact model fit to both pan and tilt. Specifically, we identify two important classes of image sequences accommodated by the virtual bellows. Examples of constructing high-quality stills are shown for the two cases: multiple frames taken of a flat object, and multiple frames taken from a fixed point.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rituximab therapy in rheumatoid arthritis in daily practice. (2008)

A single cycle of rituximab, in combination with continued methotrexate, provided significant improvement in disease activity at Week 24, with good tolerance, in patients with severe and active RA despite anti-TNF-alpha agents and/or with contraindication to these drugs, in this daily practice study.
A study of regular architectures for digital implementation of neural networks (2003)

Investigations making use of a regular processor architecture for multilayer neural networks (NNs) are described. By comparing bus-coupling, ring, and mesh topologies, the authors theoretically analyzed the required data transmission count and calculation count for one iteration of training for a NN with one hidden layer. For a minimum data transmission count, an optimal number of processor elements (PEs) exists in the case of mesh, whereas no global optimum occurs for the bus-coupling and ring topologies. The minimum total computation count obtained by the mesh is less than 1/6 (1/30) of the ring (bus-coupling). The investigation also includes the relation of PE performance and computation time, in which the bit-serial design is compared to the bit-parallel. An example of a block description of a PE for the mesh topology is described. >
Differences in the Expression of Human Class I MHC Alleles and Their Associated Peptides in the Presence of Proteasome Inhibitors (2001)

We have studied the contributions of proteasome inhibitor-sensitive and -insensitive proteases to the generation of class I MHC-associated peptides. The cell surface expression of 13 different human class I MHC alleles was inhibited by as much as 90% or as little as 40% when cells were incubated with saturating concentrations of three different proteasome inhibitors. Inhibitor-resistant class I MHC expression was not due to TAP-independent expression or preexisting internal stores of peptides. Furthermore, it did not correlate with the amount or specificity of residual proteasome activity as determined in in vitro proteolysis assays and was not augmented by simultaneous incubation with multiple inhibitors. Mass spectrometry was used to directly characterize the peptides expressed in the presence and absence of proteasome inhibitors. The number of peptide species detected correlated with the levels of class I detected by flow cytometry. Thus, for many alleles, a significant proportion of associated peptide species continue to be generated in the presence of saturating levels of proteasome inhibitors. Comparison of the peptide-binding motifs of inhibitor-sensitive and -resistant class I alleles further suggested that inhibitor-resistant proteolytic activities display a wide diversity of cleavage specificities, including a trypsin-like activity. Sequence analysis demonstrated that inhibitor-resistant peptides contain diverse carboxyl termini and are derived from protein substrates dispersed throughout the cell. The possible contributions of inhibitor-resistant proteasome activities and nonproteasomal proteases residing in the cytosol to the peptide profiles associated with many class I MHC alleles are discussed.
A Prospective Study of Two Conservative Treatments for Ganglia of the Wrist (1999)

This randomized prospective study assessed whether multiple puncture of the ganglion wall improves the results of simple ganglion aspiration. We found that 32% of ganglia resolved after aspiration alone in comparison with 22% after aspiration and multiple puncture. This difference was not significant. However, only 18% of patients requested formal surgical excision, suggesting that aspiration allays fears of malignancy and allows the patient to accept a minor cosmetic embarrassment.
Use of Gradient Plates To Study Combined Effects of Temperature, pH, and NaCl Concentration on Growth of Monascus ruber van Tieghem, an Ascomycetes Fungus Isolated from Green Table Olives (2005)

The effect of temperature, pH, and sodium chloride concentration on the growth of the Ascomycetes fungus Monascus ruber van Tieghem, the main spoilage microorganism during storage of table olives, was studied by using the gradient plate technique. Gradients of NaCl (3 to 9%, wt/vol) at right angles to gradients of pH (2 to 6.8) were prepared for the plates, which were incubated at 25, 30, and 35 degrees C. Visible fungal growth, expressed in optical density units, was recorded by image analysis and graphically presented in the form of three-dimensional grids. Results obtained from the plates indicated that the fungus was salt and acid tolerant, being able to grow at NaCl concentrations of up to 9% (wt/vol) and pH values of as low as 2.2, depending on the incubation temperature. The inhibitory effect of NaCl increased as the pH decreased progressively at 25 and 30 degrees C but not at 35 degrees C. Growth was better at 30 and 25 degrees C as judged by the larger extent of the plates covered by mycelium compared with that at 35 degrees C, where no growth was observed at pHs below 3.7. Differentiation between vegetative (imperfect-stage) and reproductive (perfect-stage) growth was evident on all plates, providing useful information about the effect of environmental conditions on the form of fungal growth. When the growth/no-growth surface model was obtained by applying linear logistic regression, it was found that all factors (pH, NaCl, and temperature) and their interactions were significant. Plots of growth/no-growth interfaces for P values of 0.1, 0.5, and 0.9 described the results satisfactorily at 25 and 35 degrees C, whereas at 35 degrees C the model predicted lower minimum pH values for growth in the range of 7 to 10% NaCl than those observed on the plates. Overall, it is suggested that the fungus cannot be inhibited by any combination of pH and NaCl within the limits of the brine environment, so further processing is required to ensure product stability in the market.
Function of Polo-like Kinase 3 in NF-κB-mediated Proapoptotic Response (2005)

RelA, the p65 subunit of NF-kappaB transcription factors, plays a key role in regulation of antiapoptotic and proapoptotic responses. However, the downstream target genes regulated by RelA-NF-kappaB in the initiation of proapoptotic signaling were not identified. We previously showed that RelA-NF-kappaB functioned as a proapoptotic factor by activating the p53-signaling pathway in response to doxycycline-induced superoxide. In the present study, we demonstrate that the ability of doxycycline/superoxide to induce expression of polo-like kinase 3 (Plk3) depends on NF-kappaB activity. We identified a kappaB binding site in the promoter of Plk3, and this kappaB site is directly involved in its induction by the RelA-NF-kappaB complex. Plk3 formed a complex with p53 and was involved in the phosphorylation of p53 on Ser-20 in response to superoxide. Inhibition of Plk3 expression by Plk3 small interfering RNA suppressed the doxycycline/superoxide-mediated apoptosis. Overexpression of wild-type Plk3 in HCT116 p53+/+ cells induced rapid apoptosis, whereas overexpression of wild-type Plk3 in HCT116 p53-/- cells and the kinase-defective mutant Plk3(K91R) in p53+/+ cells induced delayed onset of apoptosis. Furthermore, mutagenesis of Plk3 showed that the N-terminal domain (amino acids 1-26) is essential for the induction of delay onset of apoptosis. These data show that Plk3 is a RelA-NF-kappaB-regulated gene that induces apoptosis in both p53-dependent and -independent signaling pathways, suggesting a possible mechanism for RelA-NF-kappaB-regulated proapoptotic responses.
The αvβ6 integrin receptor for Foot-and-mouth disease virus is expressed constitutively on the epithelial cells targeted in cattle (2005)

Field strains of Foot-and-mouth disease virus (FMDV) use a number of alpha(v)-integrins as receptors to initiate infection on cultured cells, and integrins are believed to be the receptors used to target epithelial cells in animals. In this study, immunofluorescence confocal microscopy and real-time RT-PCR were used to investigate expression of two of the integrin receptors of FMDV, alpha(v)beta6 and alpha(v)beta3, within various epithelia targeted by this virus in cattle. These studies show that alpha(v)beta6 is expressed constitutively on the surfaces of epithelial cells at sites where infectious lesions occur during a natural infection, but not at sites where lesions are not normally formed. Expression of alpha(v)beta6 protein at these sites showed a good correlation with the relative abundance of beta6 mRNA. In contrast, alpha(v)beta3 protein was only detected at low levels on the vasculature and not on the epithelial cells of any of the tissues investigated. Together, these data suggest that in cattle, alpha(v)beta6, rather than alpha(v)beta3, serves as the major receptor that determines the tropism of FMDV for the epithelia normally targeted by this virus.
Structural Characterization of the Rat Cysteine-Rich Intestinal Protein Gene and Overexpression of This LIM-Only Protein in Transgenic Mice (1998)

Cysteine-rich intestinal protein (CRIP) has a double zinc-finger motif called the LIM domain. The most elementary member of the Group 2 LIM-only protein family, CRIP was initially identified as a developmentally regulated intestinal gene. Subsequently, it was found to be highly expressed in immune cells. The structural portion of the rat CRIP gene is comprised of five exons extending over i.8 kb, with the two zinc-finger motifs of the LIM domain being divided among the first three exons. In addition to transcriptional regulatory elements previously identified in the promoter, consensus sequences for AP-1, AP2, Sp-1, and a glucocorticoid response element are located within the first intron. We have developed a line of transgenic mice that overexpress the rat CRIP gene with an expression profile that mirrors that of the endogenous gene. Driven by the homologous rat CRIP promoter, expression increased threefold to sevenfold in intestine, thymus, spleen, and lung over endogenous levels. The transgenic mice had only about 50% of the white blood cell count found in nontransgenic animals. Differential leukocyte counts showed transgenic animals had proportionately fewer lymphocytes and more monocytes, eosinophils, neutrophils. Flow cytometry data suggested that mice overexpressing CRIP have more CD4+/CD8+ thymic lymphocytes. These data suggest that CRIP plays a significant role in differentiation or maturation of cells with rapid turnover such as those found in the intestine and immune system.