gebhart/patrepeval huggingface dataset:
Low-field paramagnetic resonance imaging of tumor oxygenation and glycolytic activity in mice (2008)

A priori knowledge of spatial and temporal changes in partial pressure of oxygen (oxygenation; pO(2)) in solid tumors, a key prognostic factor in cancer treatment outcome, could greatly improve treatment planning in radiotherapy and chemotherapy. Pulsed electron paramagnetic resonance imaging (EPRI) provides quantitative 3D maps of tissue pO(2) in living objects. In this study, we implemented an EPRI set-up that could acquire pO(2) maps in almost real time for 2D and in minutes for 3D. We also designed a combined EPRI and MRI system that enabled generation of pO(2) maps with anatomic guidance. Using EPRI and an air/carbogen (95% O(2) plus 5% CO(2)) breathing cycle, we visualized perfusion-limited hypoxia in murine tumors. The relationship between tumor blood perfusion and pO(2) status was examined, and it was found that significant hypoxia existed even in regions that exhibited blood flow. In addition, high levels of lactate were identified even in normoxic tumor regions, suggesting the predominance of aerobic glycolysis in murine tumors. This report presents a rapid, noninvasive method to obtain quantitative maps of pO(2) in tumors, reported with anatomy, with precision. In addition, this method may also be useful for studying the relationship between pO(2) status and tumor-specific phenotypes such as aerobic glycolysis.
Performance characteristics of virtual switching (2014)

Virtual switches, like Open vSwitch, have emerged as an important part of cloud networking architectures. They connect interfaces of virtual machines and establish the connection to the outer network via physical network interface cards. Today, all important cloud frameworks support Open vSwitch as the default virtual switch. However, general understanding about the performance implications of Open vSwitch in different usage scenarios is missing. In this work we provide insights into the performance properties by systematically conducting measurements in virtual switching setups. We present quantitative and qualitative performance results of Open vSwitch in scenarios involving physical and virtual network interfaces.
Microrivets for MEMS packaging: concept, fabrication, and strength testing (1997)

Microriveting is introduced as a novel and alternative joining technique to package MEMS devices. In contrast to the existing methods, mostly surface bonding, the reported technique joins two wafer pieces together by riveting, a mechanical joining means. Advantages include wafer joining at room temperature and low voltage, and relaxed requirements for surface preparation. The microrivets, which hold a cap-base wafer pair together, are formed by filling rivet holes through electroplating. The cap wafer has a recess to house the MEMS devices and also has through-holes to serve as rivet molds. The seed layer on the base wafer becomes the base of the rivet. The process requires only simple mechanical clamping of the wafer pair during riveting, compared with the more involved procedures needed for wafer bonding. Directionality of electroplating in an electric field is what makes this process simple and robust. Strength testing is carried out to evaluate the joining with microrivets. Different modes of rivet failure under different loading conditions are identified and investigated. Effective strength between 7 and 11 MPa was measured under normal loading with nickel microrivets. Joining strengths comparable to conventional wafer bonding processes, ease of fabrication with repeatability, and compatibility with batch fabrication show that microriveting is a feasible technique to join wafers for MEMS packaging, especially when hermetic sealing is not essential.
Optical heterodyne detection at a silver scanning tunneling microscope junction (1999)

The 435 MHz beat signal between two modes of a He–Ne laser (633 nm) has been detected in the current of a scanning tunneling microscope (STM), using a silver probe to enhance the sensitivity using its plasmon resonance. The difference frequency between this optical beat and a radio frequency voltage applied to the junction has also been detected in the STM current. The difference frequency and heterodyne signals, as well as the direct current (dc) probe expansion, fit a calculation of modulated and dc thermal expansion of the probe tip, once one assumes that a surprisingly large fraction of the laser beam is absorbed at a small structure at the probe end. The beat signal due to current rectification is not observed for the experimental conditions, but the potential for utilizing the plasmon resonance to obtain such a signal using a silver probe is evaluated for other, feasible conditions where it might provide exceptional sensitivity.
CD81 gene defect in humans disrupts CD19 complex formation and leads to antibody deficiency (2010)

Antibody deficiencies constitute the largest group of symptomatic primary immunodeficiency diseases. In several patients, mutations in CD19 have been found to underlie disease, demonstrating the critical role for the protein encoded by this gene in antibody responses; CD19 functions in a complex with CD21, CD81, and CD225 to signal with the B cell receptor upon antigen recognition. We report here a patient with severe nephropathy and profound hypogammaglobulinemia. The immunodeficiency was characterized by decreased memory B cell numbers, impaired specific antibody responses, and an absence of CD19 expression on B cells. The patient had normal CD19 alleles but carried a homozygous CD81 mutation resulting in a complete lack of CD81 expression on blood leukocytes. Retroviral transduction and glycosylation experiments on EBV-transformed B cells from the patient revealed that CD19 membrane expression critically depended on CD81. Similar to CD19-deficient patients, CD81-deficient patients had B cells that showed impaired activation upon stimulation via the B cell antigen receptor but no overt T cell subset or function defects. In this study, we present what we believe to be the first antibody deficiency syndrome caused by a mutation in the CD81 gene and consequent disruption of the CD19 complex on B cells. These findings may contribute to unraveling the genetic basis of antibody deficiency syndromes and the nonredundant functions of CD81 in humans.
Benefit and application of antibodies against the H1 carbohydrate recognition domain of the human hepatic asialoglycoprotein receptor (2005)

The asialoglycoprotein receptor (ASGPR), composed of the subunits H1 and H2, is predominantly expressed on the sinusoidal surface of mammalian hepatocytes and involved in the endocytosis of desialylated multiantennary glycans with terminal Gal or GalNAc residues via the clathrin-coated pit pathway. Although investigated for many years, the physiological function and ligands are still unknown. Until nowadays, only polyclonal antibodies and two monoclonal against the ASGPR are reported. However, no monoclonal antibodies, which are specifically directed against the carbohydrate recognition domain (CRD), responsible for Gal binding and internalization, are available. Such antibodies would be precious tools for ASGPR examination. In addition, since the human ASGPR is a promising liver-specific therapeutic target, an antibody-based high affine and specific drug or gene delivery system would be valuable. The H1-CRD was recombinantly expressed in E.coli and purified active H1-CRD was used for immunization to produce antibodies. Because the published expression and purification method of Meier et al.26 yielded only an H1-CRD amount of 130 g/L culture, various E.coli strains, vectors, expression conditions and renaturation procedures were tested. With the optimized expression in E.coli AD494(DE3), which was transformed with the H1-CRD cDNA-encoding pET3b vector, and with the following modified purification procedure, 55mg (20mg/L) active H1-CRD were successfully produced. For analytical purpose, polyclonal antibodies directed against the H1-CRD (anti-H1) were obtained by chicken immunization and IgY purified from egg yolk by PEG precipitation. The 12g (45mg/egg) purified total IgY contained approximately 7% anti-H1 specific IgY. Total IgY and isolated anti-H1 specific IgY antibodies showed to be suitable in various immunochemical in vitro methods but not in immunocytochemistry. Although the amino acid sequences of the mouse and human ASGPR H1-CRD are 79% identical, monoclonal antibodies were successfully produced by the hybridoma technology. Eight of twenty hybridomas were selected and cloned for further characterization of their monoclonal antibodies: in vitro in immunoblotting, immunoassays, Biacore assays and in epitope mapping, on cell in flow cytometry and fluorescence microscopy and in tissue in immunohepatohistochemical tests. Two of them, C14.6 and particularly C11.1 showed a very interesting profile, not only for application in immunochemical techniques but probably also for diagnostic and therapeutic use.
Qualitative and Quantitative Analysis of Tumor Cell Metabolism via Stable Isotope Labeling Assisted Microfluidic Chip Electrospray Ionization Mass Spectrometry (2012)

In this work, a stable isotope labeling assisted microfluidic chip electrospray ionization mass spectrometry (SIL-chip-ESI-MS) platform for qualitative and quantitative analysis of cell metabolism was developed. Microfluidic cell culture, drug-induced cell apoptosis analysis, and cell metabolism measurements were performed simultaneously on the specifically designed device. MCF-7 cells were cultivated in vitro and exposed in anticancer agent (genistein and genistein-d(2)) for cell-based drug assay. A dual-isotopic labeling was presented for effective qualitative analysis of multiplex metabolites. Interestingly, three coeluting pairs of isotopomers appeared with an m/z difference of two. Despite complex biological matrixes, they can be easily recognized and identified by chip-ESI-MS/MS, which significantly facilitates candidate biomarker discovery. The quantitative performance of this system was evaluated using genistein as a model drug by means of stable isotope dilution analysis. The linear equation obtained is y = 0.06x - 3.38 × 10(-3) (R(2) = 0.995) at the dynamic range from 0.5 to 40 μM. The detection limit is 0.2 μM. The method shows an excellent stability of 2.2% relative standard deviation (RSD) and a good repeatability of 5.5% RSD. Our results have successfully demonstrated the capability of selective and quantitative analysis of cell-based drug absorption and metabolites with high stability, sensitivity, and repeatability on the chip-ESI-MS system. Consequently, the present device shows promise as a high-throughput, low-cost, and online platform for cell metabolism studies and drug screening processes.
Multipotent stromal cells induce human regulatory T cells through a novel pathway involving skewing of monocytes toward anti-inflammatory macrophages (2013)

Multipotent stromal cells (MSC) have been shown to possess immunomodulatory capacities and are therefore explored as a novel cellular therapy. One of the mechanisms through which MSC modulate immune responses is by the promotion of regulatory T cell (Treg) formation. In this study, we focused on the cellular interactions and secreted factors that are essential in this process. Using an in vitro culture system, we showed that culture-expanded bone marrow-derived MSC promote the generation of CD4(+) CD25(hi) FoxP3(+) T cells in human PBMC populations and that these populations are functionally suppressive. Similar results were obtained with MSC-conditioned medium, indicating that this process is dependent on soluble factors secreted by the MSC. Antibody neutralization studies showed that TGF-β1 mediates induction of Tregs. TGF-β1 is constitutively secreted by MSC, suggesting that the MSC-induced generation of Tregs by TGF-β1 was independent of the interaction between MSC and PBMC. Monocyte-depletion studies showed that monocytes are indispensable for MSC-induced Treg formation. MSC promote the survival of monocytes and induce differentiation toward macrophage type 2 cells that express CD206 and CD163 and secrete high levels of IL-10 and CCL-18, which is mediated by as yet unidentified MSC-derived soluble factors. CCL18 proved to be responsible for the observed Treg induction. These data indicate that MSC promote the generation of Tregs. Both the direct pathway through the constitutive production of TGF-β1 and the indirect novel pathway involving the differentiation of monocytes toward CCL18 producing type 2 macrophages are essential for the generation of Tregs induced by MSC.
A Converse 4-1BB and CD40 Ligand Expression Pattern Delineates Activated Regulatory T Cells (Treg) and Conventional T Cells Enabling Direct Isolation of Alloantigen-Reactive Natural Foxp3+ Treg (2012)

Natural regulatory T cells (nTreg) play a central role in the induction and maintenance of immunological tolerance. Experimental transplant models and recent clinical trials demonstrate that nTreg can control alloreactivity. To upgrade Treg-based cell therapies to a selective suppression of undesired immune reactions, only the transfer of Ag-specific nTreg represents the appropriate therapeutic option. However, Ag-specific nTreg are present at extremely low frequencies in the periphery, and so far appropriate surface markers for their precise identification are missing. In this study, we demonstrate that activated nTreg and activated conventional T cells differ in their 4-1BB and CD40 ligand (CD40L) expression signatures, allowing a clear dissection from each other. Based on the expression of 4-1BB and absence of CD40L expression, human alloantigen-reactive Foxp3(+) nTreg can be directly isolated from MLR cultures with high purity. Alloantigen-reactive 4-1BB(+)CD40L(-) nTreg were characterized by a completely demethylated Treg-specific demethylated region and showed alloantigen-specific suppressive properties superior to polyclonal Treg. Importantly, isolated 4-1BB(+)CD40L(-) nTreg maintain the nTreg phenotype and alloantigen-reactivity after in vitro expansion. Our results offer the possibility to simultaneously analyze Ag-specific nTreg and conventional T cells, and to establish cellular therapies with Ag-specific nTreg aiming at a specific inhibition of unwanted immunity.
Template Matching Techniques in Computer Vision: Theory and Practice (2009)

The detection and recognition of objects in images is a key research topic in the computer vision community. Within this area, face recognition and interpretation has attracted increasing attention owing to the possibility of unveiling human perception mechanisms, and for the development of practical biometric systems. This book and the accompanying website, focus on template matching, a subset of object recognition techniques of wide applicability, which has proved to be particularly effective for face recognition applications. Using examples from face processing tasks throughout the book to illustrate more general object recognition approaches, Roberto Brunelli: examines the basics of digital image formation, highlighting points critical to the task of template matching;presents basic and advanced template matching techniques, targeting grey-level images, shapes and point sets;discusses recent pattern classification paradigms from a template matching perspective;illustrates the development of a real face recognition system;explores the use of advanced computer graphics techniques in the development of computer vision algorithms. Template Matching Techniques in Computer Vision is primarily aimed at practitioners working on the development of systems for effective object recognition such as biometrics, robot navigation, multimedia retrieval and landmark detection. It is also of interest to graduate students undertaking studies in these areas.
The Visual Analog Scale for Pain (2001)

When pain is an outcome measure in research studies, grouping final VAS scores into a small number of categories provides greater clinical relevance for comparisons than using the full spectrum of measured values or changes in value. Seeing an earlier VAS form has no apparent influence on later values.
Biomedical Microsystems for Minimally Invasive Diagnosis and Treatment (2004)

Great significant progress has been made in the development of biomedical microdevices in recent years, and these devices are now playing an important role in diagnosis and therapy. This paper presents a review of applications of microelectromechanical systems (MEMS) devices for in vivo diagnosis and therapy, and endoscopic- and catheter-based interventions. MEMS technology has enabled the further development of advanced biomedical microdevices for use in the human body by integration of sensors, actuators, and electronics into small medical devices for use in the body. In this paper, we discuss three categories of such devices: navigation systems, sensors and actuators for catheters and endoscopes, and other minimally invasive techniques. A brief introduction to principles, device structures, packaging, and related issues is presented.
Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model (2011)

Massively parallel sequencing is a powerful tool for studying posttransplantation chimerism. Plasma DNA molecules exhibit a distinct fragmentation pattern, with the nonhematopoietically derived molecules being shorter than the hematopoietically derived ones.
COX‐2 Inhibitors: A New Class of Antiangiogenic Agents (1999)

ABSTRACT The formation of new blood vessels by angiogenesis to provide adequate blood supply is a key requirement for the growth of many tumors. While normal blood vessels expressed the COX‐1 enzyme, new angiogenic endothelial cells expressed the inducible COX‐2. We evaluated the role of COX inhibitors in the mouse corneal micropocket assay in which angiogenesis is driven by the addition of a Hydron pellet containing basic fibroblast growth factor (bFGF). Neovascular areas were measured with a slit lamp five days after pellet implantation into the corneal stroma. All animals containing implants with bFGF (90 ng) developed intensive areas of neovascularization, whereas the controls implanted with the Hydron pellet alone did not. Indomethacin (a nonselective COX‐1/COX‐2 inhibitor) and SC‐236 (a COX‐2‐selective inhibitor) inhibited angiogenesis in a dose‐dependent manner. Importantly, the indomethacin‐treated mice developed severe gastrointestinal toxicity at the efficacious dose of 3 mg/kg/day. By contrast, gastrointestinal lesions were not observed, and platelet COX‐ 1 activity was unaffected, at anti‐angiogenic doses of SC‐236 (1–6 mg/kg/day). Furthermore, a COX‐1‐selective inhibitor, SC‐560, was ineffective at doses up to 10 mg/kg, a dose that completely blocked platelet COX‐1 activity in these mice. SC‐236 was also effective in reducing angiogenesis driven by bFGF, vascular endothelium growth factor (VEGF), or carrageenan in the matrigel rat model. Finally, in several tumor models, SC‐236 consistently and effectively inhibited tumor growth and angiogenesis. This novel antiangiogenic activity of COX‐2 inhibitors indicates their potential therapeutic utility in several types of cancer.
A rapid, reliable method of evaluating growth and viability of intraerythrocytic protozoan hemoparasites using fluorescence flow cytometry (1992)

Fluorescence flow cytometry was employed to assess the potential of a vital dye, hydroethidine, for use in the detection and monitoring of the viability of hemoparasites in infected erythrocytes, using Babesia bovis as a model parasite. The studies demonstrated that hydroethidine is taken up by B. bovis and metabolically converted to the DNA binding fluorochrome, ethidium. Following uptake of the dye, erythrocytes containing viable parasites were readily distinguished and quantitated. Timed studies with the parasiticidal drug, Ganaseg, showed that it is possible to use the fluorochrome assay to monitor the effects of the drug on the rate of replication and viability of B. bovis in culture. The assay provides a rapid method for evaluation of the in vitro effect of drugs on hemoparasites and for analysis of the effect of various components of the immune response, such as lymphokines, monocyte products, antibodies, and effector cells (T, NK, LAK, ADCC) on the growth and viability of intraerythrocytic parasites.
Lectins facilitate calcium‐induced fusion of phospholipid vesicles containing glycosphingolipids (1984)

Ca2+-induced fusion of phospholipid vesicles containing globoside (GL-4) or disialoganglioside (GDla) is several-fold slower than the fusion of the pure phospholipid vesicles. Lectins specific for these glycosphingolipids, soybean agglutinin and wheat germ agglutinin, respectively, enhance the rate of fusion when added to the vesicle suspension before the introduction of Ca2+. The enhancement depends on the lectin concentration and the time of preincubation with the lectin. We propose that lectins facilitate membrane fusion by inducing intermembrane contact, which is the first step in the overall process of membrane fusion, or by laterally phase separating the inhibitory glycolipids.
Toward an artificial cell based on gene expression in vesicles (2005)

We present a new experimental approach to build an artificial cell using the translation machinery of a cell-free expression system as the hardware and a DNA synthetic genome as the software. This approach, inspired by the self-replicating automata of von Neumann, uses cytoplasmic extracts, encapsulated in phospholipid vesicles, to assemble custom-made genetic circuits to develop the functions of a minimal cell. Although this approach can find applications, especially in biotechnology, the primary goal is to understand how a DNA algorithm can be designed to build an operating system that has some of the properties of life. We provide insights on this cell-free approach as well as new results to transform step by step a long-lived vesicle bioreactor into an artificial cell. We show how the green fluorescent protein can be anchored to the membrane and we give indications of a possible insertion mechanism of integral membrane proteins. With vesicles composed of different phospholipids, the fusion protein alpha-hemolysin-eGFP can be expressed to reveal patterns on the membrane. The specific degradation complex ClpXP from E. coli is introduced to create a sink for the synthesized proteins. Perspectives and subsequent limitations of this approach are discussed.