gebhart/patrepeval huggingface dataset:
In vivo administration of anti-CD3 monoclonal antibodies or immunotoxins in murine recipients of allogeneic T cell-depleted marrow for the promotion of engraftment (1991)

The role of host anti-donor cells in rejection of fully allogeneic donor T cell-depleted marrow was investigated by using mAb or immunotoxins directed against T cell or NK cell determinants. Immunotoxins consisting of mAb conjugated to a low oligosaccharide-containing fraction of purified ricin toxin A chain (RTA) facilitated in vivo-depletion of target cell populations. BALB/c and DBA/1 donors were selected based upon their expression (BALB/c) or lack of (DBA/1) hemopoietic histocompatibility (Hh1) Ag, which may serve as targets for donor rejection in C57BL/6 hosts. When studies directed toward eliminating CD3+ cells were performed in both systems, injections of intact anti-CD3 mAb or anti-CD3-RTA reproducibly produced the highest engraftment values. The fact that engraftment values obtained with anti-CD3 or anti-CD3-RTA therapy in allogeneic systems were substantially higher than in syngeneic controls suggested that engraftment stimulatory proteins were released upon TCR engagement. Elevated levels of cytokines and a high mortality rate in allogeneic recipients confirmed that this was the case. Nonstimulatory preparations of anti-CD3F(ab')2 fragments and anti-CD3F(ab')2-RTA promoted engraftment of both types of allogeneic marrow, as measured by short term 125I-IUdR assays, suggesting that stimulation was not a prerequisite for engraftment. Recipients of anti-CD3F(ab')2 or anti-CD3F(ab')2-RTA showed a marked reduction of host CD3+ cells as measured by immunofluorescence and flow cytometry. In long term chimerism studies, recipients of Hh1-disparate marrow and anti-CD3F(ab')2 had a dramatic increase in donor cell engraftment as compared to controls, indicating that positive effects on engraftment were long lived. Studies further showed that BALB/c donor cells exhibiting an Hh1 disparity were rejected by host cells expressing NK1.1 or Ly-1 (NK cells and T cells). In contrast, DBA/1 donor cells that were not Hh1-disparate were rejected by cells expressing Ly-1, but not NK1.1 (T cells only). These studies provide definitive data that CD3+ cells participate in the rejection of either Hh1+ or Hh1null T cell-depleted allografts and offer new strategies for alloengraftment using regimens containing nonmitogenic anti-CD3.
A spatially resolved optical emission sensor for plasma etch monitoring (1997)

A spatially resolved optical emission spectroscopy sensor has been developed, and the resulting reconstructed radial emission profiles from an ArI and ArII line compare well with Ar sputter etch uniformity profiles. The new sensor collects light from a wedge shaped field of view, and is rotated around a single collection point in order to observe the entire plasma through a relatively small viewpoint.
Functional status of cells from lymphoid and myeloid tissues in mice with severe combined immunodeficiency disease. (1984)

Cells from mice with severe combined immunodeficiency disease (SCID) were tested in assays that measure myeloid and lymphoid function. Results showed that C.B-17 scid and their normal counterparts (C.B-17) have similar levels of spleen colony-forming units. The frequency of in vitro myeloid colony-forming units in C.B-17 scid spleen is elevated, but the absolute number of colony-forming units in C.B-17 scid and C.B-17 spleen is similar. The absolute number of bone marrow colony-forming units in C.B-17 scid and C.B-17 mice is comparable. Cells from C.B-17 scid spleen are consistently negative in all tests of B and T cell function. C.B-17 scid splenocytes fail to proliferate in response to T and B cell mitogens or to allogeneic lymphocytes in a one-way MLR; C.B-17 scid cells do serve as stimulators in MLR. B lymphocyte colony-forming units are absent, as are cytotoxic lymphocyte precursors and cells that can generate T cell colonies with cytotoxic progenitors. The microenvironment of the C.B-17 scid mouse is conducive to lymphocyte differentiation, because functional B and T cells are easily detectable in mice reconstituted with normal bone marrow cells. The results of this study indicate that scid specifically impairs the differentiation of stem cells into mature lymphocytes; myeloid cell differentiation is not affected.
A Novel Dexamethasone-releasing, Anti-inflammatory Coating for Neural Implants (2005)

The long-term stability of implanted micromachined neural probes is compromised due to the glial scar formation at the insertion site. In this study, we developed a novel nitrocellulose-based coating for the sustained local delivery of the anti-inflammatory drug dexamethasone, a synthetic glucocorticoid that effectively reduces inflammation in the CNS. In vitro dexamethasone release was observed over 16 days, with a relatively high release in the first three days and a slow, stable release thereafter. When Michigan neural recording probes coated with and without dexamethasone-loaded nitrocellulose coatings were implanted into the adult rat brains, immunohistochemical evidence shows a marked reduction of reactive astrocytes (GFAP), reactive microglia (EDl), and chondroitin sulfate proteoglycans (CS56) expression around the insertion site compared to uncoated probes. Impedance spectroscopy showed that the dexamethasone-loaded nitrocellulose coatings slightly reduce the magnitude of electrode impedance at the biologically relevant frequency of 1 kHz through an increase of capacitance. In vivo acute recordings demonstrate that extracellular recordings with coated probes are akin to non-coated probes and it is anticipated that with time, the coated probes will exhibit superior performance. In conclusion, we developed a novel nitrocellulose-based, drug releasing coating for neural electrodes that can effectively reduce scar tissue formation without adversely affecting the electrical performance of the electrodes
Venetoclax and Obinutuzumab in Patients with CLL and Coexisting Conditions (2019)

Among patients with untreated CLL and coexisting conditions, venetoclax-obinutuzumab was associated with longer progression-free survival than chlorambucil-obinutuzumab. (Funded by F. Hoffmann-La Roche and AbbVie; ClinicalTrials.gov number, NCT02242942.).
Organic Synthesis in Soft Wall-Free Microreactors: Real-Time Monitoring of Fluorogenic Reactions (2008)

A new approach of "laboratory on a chip" (LOC) devoted to organic synthesis based on electrically operated ionic liquid microdroplets used as air-stable "soft" microreactors was recently introduced. A number of challenging issues have yet to be addressed to allow standard macroscale organic chemistry to be directly transposed in these nonclassical microreactors. In particular, since standard (i.e., magnetical or mechanical) stirring methods are prohibited in such wall-free microreactors, effective alternatives have to be developed to circumvent mass-transfer limitations. With this aim in mind, a fluorogenic version of a click chemistry reaction was developed to evaluate the efficiency of alternative mixing methods on the reaction kinetics. We demonstrate that the combination of chaotic advection created by surface acoustic waves combined with a temperature increase (Marangoni effect) leads to the same kinetics regime as in standard macroscale conditions. This opens the route for application of the new generation of LOC to efficient organic synthesis in microscale.
Polarization Properties of Deep-Ultraviolet Optical Gain in Al-Rich AlGaN Structures (2012)

The polarization properties of the amplified spontaneous emission (ASE) in the deep-UV wavelengths from AlGaN/AlN structures with 70% Al content have been investigated. Samples are prepared through a novel liquid phase epitaxy mode leading to strong compositional fluctuations. Large net modal gain is quantified to 230 nm after femtosecond UV optical pumping by the variable-stripe length technique. A strong transverse electric (TE)-polarization mode of the amplified emission has been demonstrated, together with an unpolarized emission giving rise to absorption only. These measurements provide an important observation in order to understand the origin of the optical gain in AlGaN alloys with high Al content.
Multiclass object detection system in imaging sensor network using Haar-like features and Joint-Boosting algorithm (2011)

This paper proposes an efficient scheme for detecting different object classes in an imaging sensor network. The object detection system detects all the instances of objects (for which the classifier was trained) in the given image, regardless of their scales and locations. Therefore, the image can be thus seen as a set of sub-windows that are to be evaluated by the detector. The detector selects those sub-windows that contain the instances of the objects trained. The traditional approach for multiclass object detection is to use different independent classifiers to the image, at multiple locations and scales. This can be slow and requires a lot of training data. To achieve a fast and robust implementation, shared features are used. In the existing schemes, part-based models have been used for evaluating the object features, so these features being more class-specific cannot share more information among different classes. Hence in this paper, rectangular features called Haar-like features which are more generic is used and thus more number of features can be shared. The proposed scheme uses Joint-Boosting algorithm for training the multiclass object classifier. The benefits of illumination normalisation or variance normalisation technique used to neutralise the effect of changing lighting conditions are explored. Though the proposed scheme is validated for car and pedestrian classes, the training and detection techniques used in this scheme can be generalised for any object class.
Accuracy of x-ray image-based 3D localization from two C-arm views: a comparison between an ideal system and a real device (2009)

arm X-ray imaging devices are commonly used for minimally invasive cardiovascular or other interventional procedures. Calibrated state-of-the-art systems can, however, not only be used for 2D imaging but also for three-dimensional reconstruction either using tomographic techniques or even stereotactic approaches. To evaluate the accuracy of X-ray object localization from two views, a simulation study assuming an ideal imaging geometry was carried out first. This was backed up with a phantom experiment involving a real C-arm angiography system. Both studies were based on a phantom comprising five point objects. These point objects were projected onto a flat-panel detector under different C-arm view positions. The resulting 2D positions were perturbed by adding Gaussian noise to simulate 2D point localization errors. In the next step, 3D point positions were triangulated from two views. A 3D error was computed by taking differences between the reconstructed 3D positions using the perturbed 2D positions and the initial 3D positions of the five points. This experiment was repeated for various C-arm angulations involving angular differences ranging from 15&deg; to 165&deg;. The smallest 3D reconstruction error was achieved, as expected, by views that were 90&deg; degrees apart. In this case, the simulation study yielded a 3D error of 0.82 mm &plusmn; 0.24 mm (mean &plusmn; standard deviation) for 2D noise with a standard deviation of 1.232 mm (4 detector pixels). The experimental result for this view configuration obtained on an AXIOM Artis C-arm (Siemens AG, Healthcare Sector, Forchheim, Germany) system was 0.98 mm &plusmn; 0.29 mm, respectively. These results show that state-of-the-art C-arm systems can localize instruments with millimeter accuracy, and that they can accomplish this almost as well as an idealized theoretical counterpart. High stereotactic localization accuracy, good patient access, and CT-like 3D imaging capabilities render state-of-the-art C-arm systems ideal devices for X-ray based minimally invasive procedures.
Geomechanics in Reservoir Simulation: Overview of Coupling Methods and Field Case Study (2002)

The paper addresses the modeling of geomechanical effects induced by reservoir production and their influence on fluid flow in the reservoir. Geomechanical effects induced by reservoir production can be particularly pronounced in stress sensitive reservoirs, such as poorly compacted reservoirs and fractured reservoirs. The authors review the main coupled mechanisms associated with the production of these reservoirs, and describe the different approaches that can be used to solve the coupling between fluid flow and geomechanical problems. A field case study is then presented. A stress dependent reservoir simulator-ATH2VIS-was used to quantify effects associated with the production of a highly heterogeneous and compartmentalized limestone reservoir. This simulator relies on a partial coupling approach with different time steps for reservoir and geomechanical simulations and manages data exchanges at given time intervals between the ATHOSTM reservoir simulator developed at IFP and the VISAGETM geomechanical simulator (VIPS Ltd. , 2001). The results of the coupled reservoir geomechanical simulations indicate that perturbation of the reservoir mechanical equilibrium specifically leads to progressive strain localization on a limited number of faults. Only specific parts of these faults are critically stressed, depending on pore pressure variations in their vicinity, temperature variations, and fault strikes compared with stress orientation. The normal strains resulting from geomechanical computations are interpreted in terms of permeability variations using a fracture and fault permeability model to improve the dynamic description of fluid flow and history matching.
Comparison of robust and least-squares regression in computer-generated probability plots (1997)

ML-estimators (maximum likelihood) offer a promising alternative to least squares (LS) methods and the best-guess of a researcher when fitting a line to failure-time data plotted on a computer-generated probability plot. In terms or model statistics, these robust regression algorithms performed better than LS in most data sets. The Andrews function and the Ramsay function always performed better than LS. The Huber function and the Hampel function usually performed better than LS except for those data sets where the residuals did not exceed the threshold criteria and all residuals were assigned a weight of 1.0. In those situations, these two ML-estimators provided results which were equivalent to LS. The ML-estimators were particularly effective in situations involving near-neighbors in the low region of the x-space (early contiguous failures). In terms of parameter estimation, there was no noticeable difference between LS and the ML-estimators.
Unifying the Processing of XML Streams and Relational Data Streams (2006)

Relational data streams and XML streams have previously provided two separate research foci, but their unified support by a single Data Stream Management System (DSMS) is very desirable from an application viewpoint. In this paper, we propose a simple approach to extend relational DSMSs to support both kinds of streams efficiently. In our Stream Mill system, XML streams expressed as SAX events, can be easily transformed into relational streams, and vice versa. This enables a close cooperation of their query languages, resulting in great power and flexibility. For instance, XQuery can call functions defined in our SQLbased Expressive Stream Language (ESL) using the logical/ physical windows that have proved so useful on relational data streams. Many benefits are also gained at the system level, since relational DSMS techniques for load shedding, memory management, query scheduling, approximate query answering, and synopsis maintenance can now be applied to XML streams. Moreover, the many FSA-based optimization techniques developed for XPath and XQuery can be easily and efficiently incorporated in our system. Indeed, we show that YFilter, which is capable of efficiently processing multiple complex XML queries, can be easily integrated in Stream Mill via ESL user-defined and systemdefined aggregates. This approach produces a powerful and flexible system where relational and XML streams are unified and processed efficiently.
Identification of B epitopes in human papillomavirus type 16 E7 open reading frame protein (1990)

Human papillomavirus (HPV) type 16 is implicated in the aetiology of anogenital dysplasia which may progress to malignancy. HPV-16 DNA is actively transcribed in cervical carcinomas, the most abundant transcripts being from the E6 and E7 early open reading frames. The E7 protein has been shown to have transforming activity in vitro. In this report we define four immunodominant B epitopes within the protein corresponding to the E7 gene, using a panel of murine monoclonal antibodies. Three epitopes are linear and lie within the N-terminal region of the molecule, and are unique to the HPV-16 E7 protein. One epitope is non-linear and presumed to be conformational. At least three of the four epitopes of the E7 protein are detectable by immunoprecipitation from an HPV-16-infected cervical carcinoma cell line. The demonstrated immunogenicity of the E7 protein allows us to deduce that this molecule may be a potential candidate for incorporation in a vaccine against cervical cancer.
Recombinant interleukin-2-activated intracavitary lymphocytes: phenotypic characteristics and effector function. (1989)

A preclinical study of intracavitary lymphocytes (ICL) from malignant effusions of cancer patients is described. The object of this study was to evaluate the antitumor potential of ICL as a baseline for developing adoptive immunotherapy trial for ovarian carcinoma patients. The main parameters studied were functional cytolytic activity of fresh and recombinant interleukin-2 (rIL-2)-activated ICL and their phenotypic characteristics. Spontaneous cytolytic activity of ICL was detected in all samples tested against natural killer (NK)-sensitive targets (K562), while very low activity was shown against NK-resistant targets (Daudi) and fresh tumor cells. Activation in culture with rIL-2 generated cytolytic activity against NK-resistant targets and significantly augmented NK activity. The pattern of antitumor lytic activity of ICL resembles lymphokine-activated killer cell activity and is non-major histocompatibility complex restricted against a variety of tumor targets. Phenotypic characterization of fresh ICL showed the predominance of CD3+ cells with the CD4/CD8 ratio resembling that of peripheral blood lymphocytes. During culture with rIL-2, changes in phenotypic expression of activated ICL were detected: enrichment in NKH1+ cells (up to 65%), of CD8+ (up to 70%), and very late antigen (VLA)-1+ cells (up to 54%), concomitantly with a decrease in CD4+ population. The NKH1, CD8, and VLA-1 expression peaked at 2 weeks in culture and coincided with peak cytolytic activity of cultured ICL. Depletion of CD8+ cells from activated ICL resulted in a decreased proportion of cells expressing the NKH1 and VLA-1 phenotype, whereas depletion CD4+ cells led to enrichment in CD8, NKH1, and VLA-1 antigens. Cytolytic activity was significantly increased in CD4 depleted population against NK-resistant and NK-sensitive targets. In this study we found that rIL-2 activation and culture of ICL generates killer activity against NK-resistant and fresh tumor targets and that enrichment in expression of NKH1, CD8, and VLA-1 antigens is associated with effector function.
Optical film to enhance cosmetic appearance and brightness in liquid crystal displays (2007)

This paper presents an optical film that enhances cosmetic appearance as well as brightness in a liquid crystal display (LCD) through microprisms that have a variable pitch. The optical film utilizes Fourier transformation to optimize the arrangement of microprisms for improving the cosmetic appearance in the display. The optical film has an improved light-collimating feature that redirects light more effectively, resulting in higher brightness. This paper shows details of the design procedure, but more importantly, presents optical measurement results of an actual optical film prototype to confirm the performance improvement.
Occurrence of Autoantibodies to Annexin I, 14-3-3 Theta and LAMR1 in Prediagnostic Lung Cancer Sera (2008)

Our findings suggest potential utility of an approach to diagnosis of lung cancer before onset of symptoms that includes screening for autoantibodies to defined antigens.
Bixels: Picture Samples with Sharp Embedded Boundaries (2004)

Pixels store a digital image as a grid of point samples that can reconstruct a limited-bandwidth continuous 2-D source image. Although convenient for anti-aliased display, these bandwidth limits irreversibly discard important visual boundary information that is difficult or impossible to accurately recover from pixels alone. We propose bixels instead: they also store a digital image as a grid of point samples, but each sample keeps 8 extra bits to set embedded geometric boundaries that are infinitely sharp, more accurately placed, and directly machine-readable. Bixels represent images as piecewise-continuous, with discontinuous intensities and gradients at boundaries that form planar graphs. They reversibly combine vector and raster image features, decouple boundary sharpness from the number of samples used to store them, and do not mix unrelated but adjacent image contents, e.g blue sky and green leaf. Bixels are meant to be compatible with pixels. A bixel is a image sample point with an 8 bit code for local boundaries. We describe a boundary-switched bilinear filter kernel for bixel reconstruction and pre-filtering to find bixel samples, a bixels-to-pixels conversion method for display, and an iterative method to combine pixels and given boundaries to make bixels. We discuss applications in texture synthesis, matting and compositing. We demonstrate sharpness-preserving enlargement, warping and bixels-to-pixels conversion with example images.
The presence of citrullinated proteins is not specific for rheumatoid synovial tissue (2004)

The presence of citrullinated proteins in the inflamed synovium is not specific for RA, but rather, it may be an inflammation-associated phenomenon. The high specificity of the anti-citrullinated protein antibodies is, therefore, most likely the result of an abnormal humoral response to these proteins.
Multivariate analysis of prognostic factors in CLL: clinical stage, IGVH gene mutational status, and loss or mutation of the p53 gene are independent prognostic factors (2002)

This study evaluates the prognostic significance of genetic abnormalities (detected at or shortly after presentation), clinical stage, lymphocyte morphology, CD38 expression, and IGVH gene status in 205 patients with chronic lymphocytic leukemia (B-CLL). Deletion of chromosome 11q23, absence of a deletion of chromosome 13q14, atypical lymphocyte morphology, and more than 30% CD38 expression are significantly associated with the presence of unmutated IGVH genes. Advanced stage, male sex, atypical morphology, more than 30% CD38 expression, trisomy 12, deletion of chromosome 11q23, loss or mutation of the p53 gene, and unmutated IGVH genes are all poor prognostic factors in a univariate analysis. However, only 98% or more homology of IGVH genes to the germline sequence, loss or mutation of the p53 gene, and clinical stage retain prognostic significance in a multivariate analysis. The median survival of patients with mutated IGVH genes, unmutated IGVH genes, and loss or mutation of the p53 gene regardless of IGVH gene status is 310, 119, and 47 months, respectively. These data should facilitate the design of new trials for the management of patients presenting with advanced disease or poor prognosis early stage disease.