gebhart/patrepeval huggingface dataset:
Multianalyte Single-Cell Analysis with Multiple Cell Lines Using a Fiber-Optic Array (2007)

A single-cell drug screening method is described that produces rich single-cell data and discriminates between single-cell responses from clonal populations stimulated with different agonists. Ligand-induced receptor activation is commonly detected by observing intracellular Ca2+ oscillations using high-throughput screening (HTS) methods. In most cases, HTS results in an average signal from several cells and is not sensitive enough to enable the identification of population outliers or population variance. In order to obtain this information, many individual cells must be analyzed simultaneously. We have developed a novel system using a specialized fiber-optic platform and have combined it with statistical analysis, to simultaneously analyze the dynamics of Ca2+ oscillations in a large number of single cells. Mammalian cells ectopically expressing different human GPCR receptors were stimulated, and Ca2+ changes in numerous single cells were recorded over time using a fluorescent microscope and a CCD camera. We determined the percentage of live cells in a population responding to stimuli, the distribution of responses within a population of clonal cells, and the number of outliers. By employing principal component analysis and K-nearest neighbor modeling, we classified the time-resolved Ca2+ traces of single cells as a function of the stimulus type with high certainty for a population of cells. This method is potentially a powerful tool for identifying new drug targets or for investigating the single-cell behavior of an existing target or known receptor. The development of this single-cell drug screening method is presented, and fluorescent and statistical analyses of single-cell dynamic responses are discussed.
β-Glycosphingolipids-mediated lipid raft alteration is associated with redistribution of NKT cells and increased intrahepatic CD8+ T lymphocyte trapping (2008)

The aim of this study was to determine the effect of beta-glycosphingolipids on intra-hepatic natural killer T (NKT) lymphocyte regulatory function and on lymphocyte trapping via alteration of cell membrane lipid rafts. Immune-mediated colitis was induced by intracolonic instillation of trinitrobenzene sulfonic acid. Mice were treated with beta-lactosylceramide (LC), beta-glucosylceramide (GC), beta-galactosylceramide, ceramide, or a combination of both GC and LC (IGL), or solvent alone. Lipid rafts were investigated by fluorescence-activated cell sorting analysis of ganglioside-GM1 and fluorescence microscopy of structure. Administration of beta-glycosphingolipids resulted in an increased intrahepatic/peripheral NKT ratio, increased intrahepatic CD8+ lymphocyte trapping, decreased serum interferon-gamma (IFN-gamma) levels and decreased serum IFN-gamma/interleukin-10 ratio. Administration of GC, LC, or IGL significantly altered the levels of GM1, a key marker of lipid rafts, on NKT regulatory lymphocytes. The immune modulatory effect of beta-glycosphingolipids was associated with increased survival and significant alleviation of colitis as determined by improvement in both the macroscopic and microscopic scores. In conclusion, administration of beta-glycosphingolipids increased NKT regulatory lymphocyte redistribution and intrahepatic CD8(+) T lymphocyte trapping, resulting in alleviation of immune-mediated colitis. The effects of these naturally occurring compounds were associated with modification of the T lymphocyte lipid raft structure, which is a site for immune modulation.
High Speed Homology Search with FPGAs (2001)

We will introduce a way how we can achieve high speed homology search by only adding one off-the-shelf PCI board with one Field Programmable Gate Array (FPGA) to a Pentium based computer system in use. FPGA is a reconfigurable device, and any kind of circuits, such as pattern matching program, can be realized in a moment. The performance is almost proportional to the size of FPGA which is used in the system, and FPGAs are becoming larger and larger following Moore's law. We can easily obtain latest/larger FPGAs in the form off-the-shelf PCI boards with FPGAs, at low costs. The result which we obtained is as follows. The performance is most comparable with small to middle class dedicated hardware systems when we use a board with one of the latest FPGAs and the performance can be furthermore accelerated by using more number of FPGA boards. The time for comparing a query sequence of 2,048 elements with a database sequence of 64 million elements by the Smith-Waterman algorithm is about 34 sec, which is about 330 times faster than a desktop computer with a 1 GHz Pentium III. We can also accelerate the performance of a laptop computer using a PC card with one smaller FPGA. The time for comparing a query sequence (1,024) with the database sequence (64 million) is about 185 sec, which is about 30 times faster than the desktop computer.
Soluble receptors for cytokines and growth factors: generation and biological function (1994)

Research Article| June 01 1994 Soluble receptors for cytokines and growth factors: generation and biological function S Rose-John; S Rose-John 1Institut für Biochemie der Rheinisch-Westfälischen Technischen Hochschule Aachen, Pauwelsstraβe 30, 52057 Aachen, Germany Search for other works by this author on: This Site PubMed Google Scholar P C Heinrich P C Heinrich 1Institut für Biochemie der Rheinisch-Westfälischen Technischen Hochschule Aachen, Pauwelsstraβe 30, 52057 Aachen, Germany Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1994) 300 (2): 281–290. https://doi.org/10.1042/bj3000281 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation S Rose-John, P C Heinrich; Soluble receptors for cytokines and growth factors: generation and biological function. Biochem J 1 June 1994; 300 (2): 281–290. doi: https://doi.org/10.1042/bj3000281 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1994 The Biochemical Society, London1994 Article PDF first page preview Close Modal You do not currently have access to this content.
ETV6-NTRK3 gene fusions and trisomy 11 establish a histogenetic link between mesoblastic nephroma and congenital fibrosarcoma. (1998)

Congenital mesoblastic nephroma (CMN) is an infantile spindle cell tumor of the kidney that is subdivided into "classical" and "cellular" forms based on the degree of cellularity and mitotic activity. The histogenesis of CMN remains obscure, but relationships to other pediatric renal neoplasms have been proposed. However, cellular CMN is virtually identical histologically to congenital fibrosarcoma (CFS), a malignant tumor of fibroblasts in children of the same age group. Moreover, cytogenetic studies have reported common trisomies in CFS and cellular CMN, particularly of chromosome 11. We show here that t(12;15)(p13;q25)-associated ETV6-NTRK3 gene fusions described in CFS are also present in cellular CMN. ETV6-NTRK3 chimeric transcripts were detected in 8 of 9 cellular CMNs and 2 of 2 mixed CMNs. In contrast, all of the four classical CMNs tested were negative, as were cases of Wilms' tumor and clear cell sarcoma of the kidney. Moreover, we found trisomy 11 only in cellular or mixed CMNs with the ETV6-NTRK3 gene fusion. Our studies indicate that classical and cellular CMN have different genetic features and support the concept that cellular CMN is histogenetically related to CFS. They also provide insight into potential mechanisms involved in the transformation of the classical into the cellular form of CMN.
Lyophilized Plasma With Ascorbic Acid Decreases Inflammation in Hemorrhagic Shock (2011)

In this animal model of trauma, hemorrhage and resuscitation, AA decreases IL-6 expression relative to CA and HCl. These findings confirm previous work from our laboratory and suggest that AA is responsible for suppression of dysfunctional inflammation in this model.
Autologous Hematopoietic Stem Cell Transplantation in Severe Multiple Sclerosis. The Brazilian Experience with Two Conditioning Regimes: BEAM and High-Dose Cyclophosphamide. (2007)

Abstract Introduction: Multiple sclerosis (MS) is a chronic, inflammatory and demyelinating disease of the central nervous system (CNS) leading to gradual axonal degeneration. It is a classical auto-immune disease, thus high-dose chemotherapy followed by autologous hematopoietic stem cell transplantation (AHSCT) could “reset” the immune disorder by controlling autoreactive clones and by restoring self-tolerance after immunological recovery. Objectives: Describe the experience of the Brazilian Cooperative Group of AHSCT for Autoimmune Diseases in 41 MS patients followed-up to five years. Methods: Stem cells were mobilized from the bone marrow with Cy (2g/m2) and Filgrastim (10μg/kg/d SC), collected by leukapheresis and cryopreserved. Patients were conditioned with BEAM (BCNU 300 mg/m2, cytarabine 200 mg/m2, etoposide 200 mg/m2 ×4, melphalan 140 mg/m2) and horse antilymphocyte globulin (ATG) 90 mg/kg) or cyclophosphamide (CY) 50 mg/kg ×4 and rabbit ATG (rATG) 4.5 mg/kg, followed by stem cell infusion. Quality of life was assessed by the Short Form-36 Health Survey Questionnaire (SF-36). Results: Between January 2001 and June 2006, 21 patients received BEAM/ATG and 20 received CY/ATG. Medium age was 42 years (27–53 years), 24 (58.5%) were females, 33 (80.4%) had secondary progressive MS form, 80.95% had EDSS (Expanded Disability Status Scale) 6.0 or higher. No significant difference was seen between the groups regarding age, sex, disease presentation and EDSS. The mean number of CD34+ infused cells was 8.8×106/kg (2,5– 25.13×106/kg). Mean engraftment was 9,3 days (7–10 days) for neutrophils and 13 days (7–24 days) for platelets. 18 patients (46%) had neutropenic fever, 8 (20.0%) had pneumonia and 5 (12.5%) had allergic reactions to lymphoglobulin. Three patients (14.3%) died in the BEAM group due to conditioning regiment toxicity, sepsis and alveolar hemorrhage. Mean hospital stay was 35.47 days (20–168 days) in the BEAM group and 20.15 days (14–32 days) in the CY group (p&lt;0,0001). EDSS-based disease progress in six months to a year was similar in both groups (p = 0.54). Disease worsening was detected in 6/18 patients in the BEAM group and 4/14 in the Cy group. Median follow-up was 17 months. Disease-free survival 4 years post-transplant was 65%. 31/41 patients completed SF-36 after transplantation and they exhibited improvement in their general health status at 100 days post-transplant (p = 0.02). Conclusion: In our study, a less intensive conditioning regimen (CY + rATG) was associated with similar neurological outcomes but also with less toxicity when compared to BEAM regimen. The majority of patients had an improvement in their quality of live. Longer follow-up is required to assess the therapeutic effectiveness of both regimens in MS progression.
A CD200R-CD28 fusion protein appropriates an inhibitory signal to enhance T-cell function and therapy of murine leukemia (2017)

Acute myeloid leukemia (AML), the most common adult acute leukemia in the United States, has the poorest survival rate, with 26% of patients surviving 5 years. Adoptive immunotherapy with T cells genetically modified to recognize tumors is a promising and evolving treatment option. However, antitumor activity, particularly in the context of progressive leukemia, can be dampened both by limited costimulation and triggering of immunoregulatory checkpoints that attenuate T-cell responses. Expression of CD200 (OX2), a negative regulator of T-cell function that binds CD200 receptor (CD200R), is commonly increased in leukemia and other malignancies and is associated with poor prognosis in leukemia patients. To appropriate and redirect the inhibitory effects of CD200R signaling on transferred CD8<sup>+</sup> T cells, we engineered CD200R immunomodulatory fusion proteins (IFPs) with the cytoplasmic tail replaced by the signaling domain of the costimulatory receptor, CD28. An analysis of a panel of CD200R-CD28 IFP constructs revealed that the most effective costimulation was achieved in IFPs containing a dimerizing motif and a predicted tumor-T-cell distance that facilitates localization to the immunological synapse. T cells transduced with the optimized CD200R-CD28 IFPs exhibited enhanced proliferation and effector function in response to CD200<sup>+</sup> leukemic cells in vitro. In adoptive therapy of disseminated leukemia, CD200R-CD28-transduced leukemia-specific CD8 T cells eradicated otherwise lethal disease more efficiently than wild-type cells and bypassed the requirement for interleukin-2 administration to sustain in vivo activity. The transduction of human primary T cells with the equivalent human IFPs increased proliferation and cytokine production in response to CD200<sup>+</sup> leukemia cells, supporting clinical translation. This trial was registered at www.clinicaltrials.gov as #NCT01640301.
Design, fabrication and initial results of a 2g autonomous glider (2005)

Utilizing the core technologies of emerging microrobotic structures, the rapid design and prototyping of a passive micro air vehicle with the final goal of locating an audio source while avoiding hazardous obstacles is presented. The airfoil and control surfaces are optimized empirically to maximize lift and maneuverability while minimizing drag. Bimorph piezoelectric bending cantilevers actuate the control surfaces. Since such actuators require high voltages, an efficient boost circuit is presented along with appropriate high voltage electronics. To locate audio sources, a pair of acoustic sensors is designed and prototyped using a phase detection algorithm while a custom optic flow sensor is developed to avoid obstacles and give estimates of object distances and velocities. Finally, each subsystem is demonstrated and the complete glider is integrated to demonstrate initial open loop control performance.
A Cysteine-rich Domain Defined by a Novel Exon in aSlo Variant in Rat Adrenal Chromaffin Cells and PC12 Cells (1997)

cDNA libraries from rat chromaffin cells and PC12 cells were screened for homologs to the mouse mSlo gene that encodes a large conductance, calcium (Ca2+)- and voltage-activated potassium channel (BK channel). One Slo variant contained sequence encoding a cysteine-rich, 59-amino acid insert for a previously described site of alternative splicing. This insert is reminiscent of zinc-finger domains. The exon was found in RNA from pancreas, anterior pituitary, cerebellum, and hippocampus. Expression in Xenopus oocytes of a Slo construct containing this exon conferred a -30 to -20 mV shift of the conductance-voltage curve. A previously uncharacterized alternative splice junction near the C-terminal end of Slo was also identified. In contrast to BK channels in rat chromaffin cells, none of the Slo variants exhibited inactivation when expressed in Xenopus oocytes. PCR screening of chromaffin cell RNA failed to reveal a homolog of an accessory beta subunit known to influence Slo channel function. Furthermore, a beta-subunit-dependent Slo channel activator, dehydrosoyasaponin I, was without effect on chromaffin cell BK current. The results argue that an accessory subunit may not be a required component of the native chromaffin cell BK channel.
Chilled ammonia process for CO2 capture (2009)

The chilled ammonia process absorbs the CO2 at low temperature (2–10 ∘C). The heat of absorption of carbon dioxide by ammonia is significantly lower than for amines. In addition, degradation problems can be avoided and a high carbon dioxide capacity is achieved. Hence, this process shows good perspectives for decreasing the energy requirement. However, a scientific understanding of the processes is required. The properties of the NH3- CO2- H2O system were described using the Extended UNIQUAC electrolyte model developed by Thomsen and Rasmussen in a temperature range from 0 to 110 ∘C and pressure up to 100 bars [1]. The results show that solid phases consisting of ammonium carbonate and bicarbonate are formed in the absorber. The energy requirements in the absorber and in the desorber have been studied. The enthalpy calculations show that an energy requirement for the desorber lower than 2 GJ/ton CO2 can be reached.
Secure and efficient access to outsourced data (2009)

Providing secure and efficient access to large scale outsourced data is an important component of cloud computing. In this paper, we propose a mechanism to solve this problem in owner-write-users-read applications. We propose to encrypt every data block with a different key so that flexible cryptography-based access control can be achieved. Through the adoption of key derivation methods, the owner needs to maintain only a few secrets. Analysis shows that the key derivation procedure using hash functions will introduce very limited computation overhead. We propose to use over-encryption and/or lazy revocation to prevent revoked users from getting access to updated data blocks. We design mechanisms to handle both updates to outsourced data and changes in user access rights. We investigate the overhead and safety of the proposed approach, and study mechanisms to improve data access efficiency.
Stability and Activity of Vancomycin in Corneal Storage Media (1993)

Gentamicin is the only antibiotic currently added to commercially available corneal storage media. To reduce the potential for bacterial dissemination from donor corneal tissue to the recipient eye, we evaluated the addition of vancomycin to corneal storage media. When added to Dexsol at a concentration of 200 micrograms/ml, vancomycin levels were maintained, showing a 7% decrease in vancomycin concentration per month, measured < or = 90 days after its addition. Human corneas were stored in gentamicin-free Dexsol (Chiron Ophthalmics, Inc., Irvine, CA, U.S.A.) containing 150 micrograms/ml vancomycin. Corneal tissue levels of vancomycin determined by agar diffusion bioassay were 201, 226, 292 micrograms/ml at 1, 3, and 7 days of storage respectively, suggesting that corneal tissue concentrates vancomycin with time. No differences in endothelial cell count or cell death were seen in corneas stored in Dexsol (containing gentamicin) or Dexsol plus vancomycin when followed for < or = 14 days. Vancomycin added to corneal storage media should reduce the potential for endophthalmitis due to gentamicin-resistant organisms.
Affinity capture of cell culture-derived influenza virus particles (2009)

Human influenza vaccines are traditionally produced in embryonated chicken eggs. However, due to several disadvantages of this method, mammalian cell culture based influenza vaccine production processes are currently being established demanding new virus purification methods. \nOur study provides comprehensive results from three different strategies to capture Madin-Darby canine kidney (MDCK) cell culture-derived influenza virus particles (A/Wisconsin/67/2005, A/Puerto Rico/8/34, B/Malaysia/2506/2004) based on affinity and pseudo-affinity adsorption.\n\n\nFirst, an affinity based capture step, lectin-affinity chromatography (LAC), was developed. This method was investigated concerning the selection of lectins and matrices, viral recoveries and contaminant depletion as well as process robustness. LAC showed a high degree of contaminant reduction, in particular host cell dsDNA depletion. The results from LAC represent a high potential of an affinity capture step at the beginning of a downstream process for production of viral vaccines. \n\nInfluenza viruses have an affinity to sulfated carbohydrates, such as heparin or sulfated cellulose. Hence, column based Cellufine® sulfate is often used in industrial influenza virus purification. The main disadvantage of this method is the limited flow rate, due to high back pressure, leading to suboptimal process productivity. To overcome this drawback, we have developed a second capturing method for influenza viruses based on sulfated reinforced cellulose membranes (SCM). \nCompared to commercially available cation exchange membrane adsorbers and column based Cellufine® sulfate resin, these membrane adsorbers achieved high product recoveries and contaminant reduction. In addition, the SCM allow an increased flow rate during capturing leading to superior productivity compared to conventional bead chromatography. Hence, this method is an economic alternative for industrial influenza vaccine production.\n\nThe third purification strategy was capturing of influenza viruses by immobilized metal affinity chromatography (IMAC) using zinc modified membrane adsorbers. This method shows valuable purification results for the influenza virus strain A/Puerto Rico/8/34. However, IMAC depends highly on the primary structure of viral envelope proteins as well as the accessibility of certain amino acids. Hence, IMAC is an interesting capturing method of A/Puerto Rico/8/34 in a laboratory scale, but is only of limited interest for industrial vaccine production processes.
Vascular basement membrane components and the lesions of Alzheimer's disease: Light and electron microscopic analyses (1994)

Alzheimer's disease (AD) is one of several systemic and cerebral diseases that involve the abnormal deposition of fibrillar proteins called amyloids. All amyloids share conformational and staining characteristics, as well as an association with resident tissue macrophages and two extracellular matrix components [heparan sulfate proteoglycan (HSPG) and amyloid P component]. Vascular, glomerular, and Schwann cell basement membrane pathologies have been documented in many forms of amyloidosis, and often amyloid fibrils fuse to and project from the basement membrane in these diseases. The present report demonstrates the vascular basement membrane (VBM) alterations in AD autopsy samples, and details the methodologies used. Electron microscopy reveals the fusion of amyloid fibrils with the VBM and the alteration of the VBM in the absence of amyloid accumulation. Double-labelling and pre-embed immuno-electron microscopy techniques demonstrate the colocalization of amyloid P component and VBM components with amyloid, and also reveal that amyloid P component is not localized to the cerebral VBM. Finally, a novel correlative light/electron microscopy technique demonstrates the association between amyloid P component and cerebral resident tissue macrophages, the microglia. Taken together, these data suggest that the physicochemical processes of amyloid formation, rather than amyloid deposition, may be responsible for VBM pathology.
Preparation of hydroxytelechelic poly(butadiene) via ring-opening metathesis polymerization employing a well-defined metathesis catalyst (1993)

In this paper we show that ring-opening metathesis polymerization (ROMP) using a discrete metal alkylidene catalyst offers another alternative polymerization technique that is applicable to the synthesis of well-defined HTPBD.