gebhart/patrepeval huggingface dataset:
Epitope mapping of the carcinoembryonic antigen by monoclonal antibodies and establishment of a new improved radioimmunoassay system. (1987)

A comprehensive mapping of epitopes on the carcinoembryonic antigen (CEA) molecule has been achieved by analyses of the specificities of 146 monoclonal antibodies (MAbs) from more than 300 hybridomas established recently. The reactivities of MAbs were analyzed by radioimmunoassays (RIA) with highly purified preparations of CEA and related antigens including normal fecal antigen-1 (NFA-1), NFA-2 in normal adult feces, nonspecific cross-reacting antigen (NCA) in lung and NCA-2 in meconium. The MAbs could be divided into five groups: group I, 23 clones directed to the NCA-common part of the CEA molecule; group II, 31 clones directed to the normal fecal cross-reacting antigen (NFCA)-common part; group III, 46 clones directed to the NFA-1-common part; group IV, 33 clones reactive with the heterogeneous carbohydrate part; and group V, 13 clones directed to the CEA-distinctive part which seemed to be highly specific for CEA. Mutual inhibitions of CEA binding between MAbs of the individual groups revealed that at least 25 different subgroups can be defined i.e., 4, 7, 8, 4, and 2 subgroups in groups I to V, respectively. The epitopes recognized by the group IV MAbs were found to be sensitive to oxidation with periodate, while the epitopes defined by MAbs of the other groups were resistant to this treatment. A solid-phase sandwich-type RIA system for CEA was established by using 2 MAbs from groups II and III as the CEA catcher and an MAb of group V as the tracer. This assay was shown to exhibit improved cancer-specificity and accuracy in the estimation of serum CEA levels.
Identification of IL-10 and TGF-β Transcripts Involved in the Inhibition of T-Lymphocyte Proliferation During Cell Contact With Human Mesenchymal Stem Cells (2006)

Mesenchymal stem cells (MSC) inhibit the response of allogeneic T lymphocytes in culture. Because the mechanisms of this effect may differ according to the existence of cell contact, we investigated the differences in gene expression of inhibitory molecules during MSC-T lymphocyte coculture when cell contact does and does not occur. Human MSC and T lymphocytes were cultured together in standard and transwell cultures. MSC gene expression was analyzed by semiquantitative real-time RT-PCR. MSC elicited a high dose-dependent inhibition of T lymphocytes in cultures with cell contact, but inhibition occurred even without cell contact. In both cases, we observed significant upregulation of IDO, LIF, and HLA-G, along with downregulation of HGF and SDF1. In cultures with cell contact, IL-10 and TGF-beta transcripts were expressed in a significantly higher level than in cultures without this contact. Furthermore, in the latter, the increased inhibition of T-cell proliferation was positively correlated with IDO gene expression and negatively correlated with SDF1 gene expression. MSC appear to induce T-cell tolerance by two distinct mechanisms. The first of these, which does not require cell contact, induces expression of the tolerogenic genes IDO, LIF, and HLA-G. The second mechanism, which is contact dependent, modulates IL-10 and TGF-beta gene expression. These two mechanisms probably play separate roles in MSC-induced tolerance in allogeneic hematopoietic stem cell transplantation.
Anterior chamber lenses. Part I: Complications and pathology and a review of designs (1987)

Clinicopathologic data to assist ophthalmologists in choosing a safe and efficacious anterior chamber intraocular lens (IOL) are rapidly becoming available. Two important factors that have led to an increased success rate with some anterior chamber IOL styles are (1) attention to lens design and (2) attention to modern manufacturing and lens finishing techniques. We now know much more about how to achieve appropriate lens flexibility, which decreases the need for perfect sizing. Increased attention has been given to the anterior-posterior vaulting characteristics of IOLs. This has reduced the incidence of various complications such as the intermittent touch syndrome and the uveal chafing syndrome. We recognize several design flaws in some lens styles. For example, there is now a considerable decrease in the number of small-diameter, round-looped anterior chamber IOLs being implanted, particularly those with a closed-loop configuration. Several problems have been and continue to be caused by some poorly manufactured anterior chamber lenses with sharp optic and haptic edges. Technology to assure smooth lens finishing and polishing is available and readily accessible to all manufacturers. Defective lenses should soon be a thing of the past.
Breast Cancer Survival Is Associated with Telomere Length in Peripheral Blood Cells (2008)

Telomeres are essential for maintaining chromosomal stability. Previous studies have indicated that individuals with shorter blood telomeres may be at higher risk of developing various types of cancer, such as in lung, bladder, and kidney. We have analyzed relative telomere length (RTL) of peripheral blood cells in relation to breast cancer incidence and prognosis. The study included 265 newly diagnosed breast cancer patients and 446 female controls. RTL was measured by real-time PCR, and our results show that the patient group displayed significantly longer telomeres compared with controls (P < 0.001). Age-adjusted odds ratios (OR) for breast cancer risk increased with increasing telomere length, with a maximal OR of 5.17 [95% confidence interval (95% CI), 3.09-8.64] for the quartile with the longest telomeres. Furthermore, RTL carried prognostic information for patients with advanced disease. Node positive (N+) patients with short telomeres (</=median) showed an increased survival compared with N+ patients with long telomeres (P = 0.001). For patients with ages <50 years with tumors >16 mm (median tumor diameter), short telomeres were associated with a significantly better outcome than longer telomeres (P = 0.006). Cox regression analysis showed that long RTL was a significant independent negative prognostic factor (hazards ratio, 2.92; 95% CI, 1.33-6.39; P = 0.007). Our results indicate that blood RTL may serve as a prognostic indicator in breast cancer patients with advanced disease.
Zymosan enhances the immune response to DNA vaccine for human immunodeficiency virus type‐1 through the activation of complement system (2001)

In the present study, the adjuvant effect of zymosan on human immunodeficiency virus type-1 (HIV-1)-specific DNA vaccine and the mechanism of this enhancement were studied in a murine model. We coinoculated zymosan with our candidate HIV-1 specific DNA vaccine (pCMV160IIIB) into skeletal muscles of BALB/c mice. Higher levels of both humoral immune response and HIV-specific delayed-type hypersensitivity (DTH) response were observed when zymosan was coinoculated with pCMV160IIIB compared with that obtained using pCMV160IIIB alone. HIV-specific cytotoxic T lymphocyte (CTL) activity was also enhanced. This enhancing activity was suppressed when coinoculated to the fifth complement (C5)-deficient DDD and AKR mice. The enhanced activity was also suppressed when anti-C3 antibody was inoculated to mice intramuscularly. There was significant induction of immunoglobulin G2a (IgG2a) and interferon-gamma (IFN-gamma) in pCMV160IIIB vaccine with zymosan. These results suggest that zymosan-mediated DNA vaccination enhances helper T cell (Th) 1-mediated immunity. The effect is suggested to be based on the consequences of its recruitment and activation of macrophages, dendritic cells or antigen-presenting cells (APC) through complement activation, especially through the alternative pathway. Taken together, these results suggest that zymosan can be an effective immunological adjuvant in DNA vaccination against HIV-1.
Short report: Antibody responses of mice immunized with a tetravalent dengue recombinant protein subunit vaccine. (2001)

Recombinant proteins containing the B domain of dengue virus serotypes 1-4 fused to the maltose binding protein (MBP) of Escherichia coli were evaluated individually and as a tetravalent vaccine candidate in mice. Sera from mice immunized with monovalent DEN-MBP recombinant protein vaccines developed high titers of serotype homologous antibody in the enzyme-linked immunosorbent assay and the plaque-reduction neutralization test. Cross-reactive antibody titers were either several dilutions lower or not detectable. Sera from mice immunized with the tetravalent DEN subunit vaccine neutralized all 4 DEN viruses in the plaque-reduction neutralization test. The neutralizing antibody titers to each individual serotype were significantly greater than any cross-reactive neutralizing antibody titers induced by the monovalent vaccines, providing evidence that the tetravalent DEN recombinant subunit vaccine produced specific neutralizing antibody to all 4 serotypes of dengue virus.
Scaling of Beowulf-class Distributed Systems (1998)

Beowulf-class systems employ inexpensive commodity processors, open source operating systems and communication libraries and commodity networking hardware to deliver supercomputer performance at the lowest possible price. Small to medium sized Beowulf systems are installed or planned at dozens of universities, laboratories and industrial sites around the world. The design space for larger systems, however, is largely unexplored. We investigate two interconnection techniques that would allow the scaling of a Beowulf class system to unprecedented sizes (hundreds or thousands of processors). The first is a commercially available high-speed backplane with fast-ethernet and gigabit ethernet switch modules. The second is a network that combines point- to-point connections and commodity switches, employing the Beowulf nodes as IP routers as well as computational engines. The first method has the drawback of a relatively high price tag - a significant but not overwhelming fraction of the cost of the system must be devoted to the switch. The second approach is inexpensive, but introduces extra latency and may restrict bandwidth depending on the topology employed. Our tests are designed to quantify these effects. We perform three sets of tests. Low-level tests measure the hardware performance of the individual components, i.e., bandwidths and latencies through various combinations of network interface cards, node- based routers and switches. System-level tests measure the bisection bandwidth and the ability of the system to communicate and compute simultaneously, under conditions designed to generate contention and heavy loads. Finally, application benchmarks measure the performance delivered to a subset of the NAS parallel benchmark suite. Low-level measurements indicate that latencies are only weakly affected by introduction of node-based routers, and that bandwidths are completely unaffected. Switches introduce between 19 and 30 microseconds of latency and linux-based routers introduce 75 microseconds. System level measurements indicate that even under load, the routed network delivers a bisection bandwidth near what one would expect by simply summing the capacities of the individual components. A very large scatter is introduced into latencies, however. Application level measurements reveal that the routed network is acceptable for some applications, but can have significant deleterious effect on others. Successful use of routed networks for very large beowulf systems will requires a deeper understanding of this issue.
Estrogen Receptor Activation Function 1 Works by Binding p160 Coactivator Proteins (1998)

Estrogen receptor-alpha contains two transactivation functions, a weak constitutive activation function (AF-1) and a hormone-dependent activation function (AF-2). AF-2 works by recruiting a large coactivator complex, composed of one or more p160s, CREB-binding protein (CBP)/p300, and P/CAF (p300 and CBP-associated factor), via direct contacts with the p160s. We report here that independent AF-1 activity also requires p160 contacts. Unlike AF-2, which binds signature NR boxes in the center of the p160 molecule, AF-1 binds to sequences near the p160 C terminus. We propose that the ability of AF-1 and AF-2 to interact with separate surfaces of the same coactivator is important for the ability of these transactivation functions to synergize.
Experimental and Numerical Analysis of Gas Transport in Shale Including the Role of Sorption (2013)

Abstract This study adds to the knowledge base of carbon dioxide sequestration and methane recovery enhancement from gas shale. If gas shale is desired to be used as a storage medium for CO2, then knowledge of how to maintain gas permeability while enhancing storage via sorption is mandatory. In this work, physical and numerical pressure-transient, pulse-decay experiments are conducted on Eagle Ford shale cores. The experiments are conducted isothermally at various pore and confining pressures that maintain a constant net effective stress. The gases investigated are helium, methane, and carbon dioxide. Porosity and permeability measurements are conducted using various techniques including numerical simulation that incorporates detailed measurements of the in-situ, core-scale porosity distribution. The research simulator is fully implicit, finite volume, unconditionally stable, and incorporates gas sorption in ultra-small pore networks. Langmuir sorption parameters are determined after matching the upstream and downstream pressure profiles simultaneously. Experiments are also interpreted using available analytical models and compared to the high-resolution simulations matched to experimental observations. Results highlight the interplay of gas slip and sorption of pure gases at core-level. Results also quantify the role of CO2 sorption in various shale fabrics and thus promote the potential for sequestration. While the gas molecular kinematic diameter plays a role in dictating the pore accessibility, and thus governs slip flow, gas sorption is more influential in determining permeability. Gas transport in wide channels, however, undermines the influence of sorption on measured permeability. While He is a non-sorptive gas, CH4 sorption isotherms are described by a Langmuir model and CO2 isotherms are similar to an n-BET model. The experiments demonstrate that He and CH4 have a similar measured permeability while carbon dioxide has a lower permeability. These differences are attributed to the strong sorption of carbon dioxide.
Fast and accurate 3D mask model for full-chip OPC and verification (2007)

A new framework has been developed to model 3D thick mask effects for full-chip OPC and verifications. In addition to electromagnetic (EM) scattering effects, the new model also takes into account the non-Hopkins oblique incidence effects commonly found in real lithography systems but missing in prior arts. Evaluations against rigorous simulations and experimental data showed the new model provides improved accuracy, compared to both the thin-mask model and the thick-mask model based on Hopkins treatment of oblique incidence.
On the complexity of differentially private data release (2009)

We consider private data analysis in the setting in which a trusted and trustworthy curator, having obtained a large data set containing private information, releases to the public a "sanitization" of the data set that simultaneously protects the privacy of the individual contributors of data and offers utility to the data analyst. The sanitization may be in the form of an arbitrary data structure, accompanied by a computational procedure for determining approximate answers to queries on the original data set, or it may be a "synthetic data set" consisting of data items drawn from the same universe as items in the original data set; queries are carried out as if the synthetic data set were the actual input. In either case the process is non-interactive; once the sanitization has been released the original data and the curator play no further role.
Reactivity of a monoclonal antibody with tissues and tumors from the human breast. Immunohistochemical localization of a new antigen and clinicopathologic correlations. (1984)

The reactions of a monoclonal antibody to the MCF7 breast cancer cell line were immunohistochemically studied on a variety of breast tumors, primary and metastatic, on mammary epithelium and on nonneoplastic breast lesions. A high proportion of positive reactions was observed in ductal, lobular, and tubular carcinomas as well as in mammary Paget's disease. Mucinous, medullary, and papillary carcinomas showed a low incidence of reactivity. Carcinomas with metaplasia, carcinoids, and nonepithelial breast tumors were unreactive with the antibody. Positive immunostaining was documented also in nodal and extranodal metastatic lesions. The staining of nodal metastases was correlated with the positive reaction of the primary tumor. Reactivity was widely distributed in normal breast epithelial cells and in benign breast lesions. Staining of nonneoplastic mammary epithelial was associated with reactivity of adjacent neoplastic tissues. Staining differences between nonneoplastic and neoplastic mammary tissues were related to the intensity and cytologic distribution of the labeling. Heterogeneous reactivity of morphologically similar cells was documented in nonneoplastic and neoplastic breast epithelial cells as well as in nodal and extranodal breast carcinoma metastases. Immunohistologically detectable antigen was not correlated with prognostic factors such as histologic grade or nodal status. A retrospective study of T1NO cases failed to substantiate any prognostic value for the reactivity of primary breast tumors with this monoclonal antibody.
NeTra: a toolbox for navigating large image databases (2002)

We present an implementation of NeTra, a prototype image retrieval system that uses color texture, shape and spatial location information in segmented image database. A distinguishing aspect of this system is its incorporation of a robust automated image segmentation algorithm that allows object or region based search. Image segmentation significantly improves the quality of image retrieval when images contain multiple complex objects. Other important components of the system include an efficient color representation, and indexing of color, texture, and shape features for fast search and retrieval. This representation allows the user to compose interesting queries such as "retrieve all images that contain regions that have the color of object A, texture of object B, shape of object C, and lie in the upper one-third of the image" where the individual objects could be regions belonging to different images.
Complement-mediated lung injury and neutrophil retention after intestinal ischemia-reperfusion (1997)

Complement-mediated neutrophil activation appears to play an important role in ischemia-reperfusion (I/R) injury in a variety of tissues, including the heart, lung, and small bowel. The objective of this study was to determine whether inhibition of the alternative and classic complement cascades by administration of soluble complement receptor 1 (sCR1) prevents the increased neutrophil stiffness, lung neutrophil retention, and pulmonary microvascular injury elicited by a systemic inflammatory insult. Isolated lungs were perfused with blood obtained from animals subjected to 2 h of intestinal ischemia and 20 min of reperfusion (I/R) or control (nonischemic) surgery. Intestinal I/R resulted in a significant increase in neutrophil stiffness, lung neutrophil retention, and increased pulmonary microvascular permeability, effects that were prevented by administration of sCR1 before intestinal reperfusion. The results of this study suggest that I/R injury in the gut is a potent systemic inflammatory stimulus that induces complement-mediated neutrophil stiffness, lung neutrophil entrapment, and pulmonary microvascular dysfunction.
A high-voltage, high-current CMOS pulse generator ASIC for deep brain stimulation (2010)

A high-voltage, high-current pulse generator ASIC based on 0.35-εm high-voltage CMOS technology is presented. The chip has eight independently-controlled biphasic output channels that can generate either current- or voltage-controlled pulses. The output driver is capable of delivering current up to 1.26 mA or 5.04 mA and voltage up to 2.36 V or 9.45 V; all with 6-bit resolution. The stimulation frequency can be adjusted between 3 Hz to 5 kHz, while pulse width can vary from 20 µs to 640 εs in 20 εs steps for 100-kHz clock frequency. The timing parameters can be adjusted further by varying the clock frequency. These parameters, including pulse phase, can be programmed independently in each channel to allow different waveform generation. The foregoing provides an on-chip solution for an arbitrary function generator that can be monolithically fabricated with the rest of the circuitry. Based on its configuration this chip is an ideal solution for deep brain stimulation (DBS) electrode for targeted stimulation through current steering.
Imaging viscoelastic properties of the vitreous (2002)

It is well known that changes in the mechanical properties of tissues are correlated with the presence of disease. In the eye, the vitreous body goes through mechanical changes with age, which may eventually lead to the formation of retinal detachment. We are developing a method to detect these mechanical changes using a non-invasive technique called KAVE (Kinetic Acoustic Vitreoretinal Examination). KAVE uses acoustic radiation force as a means to produce small, localized displacements within the tissues. Returning echoes are processed using ultrasonic motion tracking so that the response of the tissue to the induced force can be evaluated. By repeating this process at a number of locations, images depicting viscoelastic properties of tissues can be formed. We have developed and tested a new mechanical model to describe vitreous mimicking phantoms. Through,. the combination of appropriate modeling and signal processing, we are able to generate images of relative parameters such as relative mass, relative elasticity, and relative viscosity. These parameters are called relative because they depend on the force applied. In this paper, we also present force-free images, which include images of the time constant /spl tau/. the damping ratio /spl xi/, and the natural frequency /spl omega/ of the phantom. These images are significant in that they lack the artifacts common in the relative property images.