gebhart/patrepeval huggingface dataset:
An In Vitro Model for Neuroscience: Differentiation of SH-SY5Y Cells into Cells with Morphological and Biochemical Characteristics of Mature Neurons (2010)

Neuroscience, including research on Alzheimer's disease, is hampered by the lack of suitable in vitro models to study the human nervous system. To counteract this, many attempts to differentiate cell lines into more neuron-like cells have been performed, resulting in partial expression of neuronal features. Furthermore, it has been reported that neuroblastoma cell lines lack mature isoforms of tau. Our aim was to develop an improved in vitro model, generating sustainable cells with morphology and biochemistry of human, mature neurons. To obtain cells with neuronal differentiation and function, we investigated the effect of combining three-dimensional culturing of SH-SY5Y cells in extracellular matrix (ECM) gel with several factors reported to have neuro-differentiating effects. This resulted in cells with apparent neuronal morphology with long, extensively branched neurites. Further investigation revealed expression of several neurospecific markers including synapse protein Sv2 and nuclear marker NeuN, as well as the presence of synapses and axonal vesicle transport. In addition, these cells expressed mature tau isoforms, and tau protein expression was significantly increased compared to undifferentiated cells, reaching levels found in adult human brain. In conclusion, we found that pre-treatment with retinoic acid followed by ECM gel culturing in combination with brain derived neurotrophic factor, neuregulin beta1, nerve growth factor, and vitamin D3 treatment generated sustainable cells with unambiguous resemblance to adult neurons. These cells also expresses adult splicing forms of tau with neuronal localization, making this cellular in vitro model useful in many areas of neuroscience research, particularly the Alzheimer's disease field.
A proposal of hierarchical chordal ring network topology for WDM networks (2005)

This paper presents a hierarchical chordal ring network topology (HCRN) as a regular logical topology for multihop WDM networks. In order to minimize the traffic increase and the transmission delay through the network due to packet relays or hops on intermediate nodes in the multihop network, the network topology is hierarchically constructed in HCRN, so that more lightpaths are assigned to connections between nearby nodes than those for distant nodes, while the maximum hop between any pair of nodes is restrained. This hierarchical topology is also beneficial to reduce the number of required wavelengths through increasing their reuses by multiple lightpaths, which is important for cost-conscious metropolitan area networks. Through comparisons on the network diameter and the number of required wavelengths with the original chordal ring network topology, we show the effectiveness of our proposed HCRN.
Facilitation of polyoma tumor growth in rats by blocking sera and tumor eluate (1972)

Abstract It has been shown previously that sera of tumor‐bearing individuals are capable of blocking specifically the lymphocyte cytotoxicity in vitro against the tumor cells in question. The present investigation demonstrates that blocking material, in the form of sera of rats carrying progressively growing polyoma tumors and low p H eluates of polyoma tumor tissue inoculated into polyoma isografted rats, cause an enhanced tumor growth. Corresponding serum from rats carrying an MCA‐induced sarcoma and eluate from such tumor tissue had no significant enhancing effect. The administered blocking activity was detectable in the sera of the recipients for 3 days after inoculation. No delay or decrease in the level of cell‐mediated anti‐tumor immunity could be detected by in vitro tests for lymphocyte cytotoxicity against polyoma tumor cells. This indicates that the mechanism of the facilitated tumor growth in vitro is akin to a central or an efferent type of enhancement.
Demonstration of specific C5a receptor on intact human polymorphonuclear leukocytes. (1978)

Human C5a, a complement-derived anaphylatoxin, is a potent mediator of human leukocyte chemotaxis. Using a homogeneous preparation of C5a that was 125I-labeled, we have demonstrated the presence of a specific cellular receptor for this glycoprotein on intact human polymorphonuclear leukocytes. Cellular uptake of the radiolabeled ligand occurred rapidly and the rate of dissociation was extremely slow. Cellular binding was saturable with respect to 125I-labeled C5a, and half-saturation occurred at a concentration of 3-7 X 10(-9) M. The number of C5a binding sites per cell was estimated as 1-3 X 10(5). The ligand (C5a) displays specific structural features that are required for binding because analogs of C5a such as C5ades Arg or a yeast carboxypeptidase-digested C5a derivative C5a-(I-69) inhibited the binding but C3a anaphylatoxin, which resembles C5a chemically, did not. Both C5a-mediated leukocyte chemotaxis and C5a-induced lysosomal enzyme release from cytochalasin B-treated cells closely paralleled uptake of the ligand, clearly indicating that it is a receptor-C5a interaction that leads to stimulation of these cellular responses.
Planar Waveguides as High-Performance Sensing Platforms for Fluorescence-Based Multiplexed Oligonucleotide Hybridization Assays (1999)

16-Mer and 22-mer oligonucleotide capture probes with an amino function at the 5‘-end were covalently immobilized on (3-glycidoxypropyl)trimethoxysilane (GOPTS) silanized planar waveguides in “checkerboard”-style 2-dimensional arrays by means of ink-jet printing in order to demonstrate the potential of multiplexed planar waveguide biosensing. The laser-induced fluorescence was collected by a CCD camera, providing quantitative information regarding the intensity of individual sensing pads. In model hybridization assays with Cy5-labeled complementary oligonucleotides, sample concentrations down to 50 fM were successfully detected within 12 min. The overall spot-to-spot variability of the ink-jet immobilization in combination with amino functionalized oligonucleotides and GOPTS silanized waveguides was found to be about 12% and almost independent of the formation of an equilibrium between the labeled analyte and capture probes. Both pipet-made and ink-jet-made oligonucleotide spots showed comparable assay performances.
22.4-Gb/s OFDM Transmission over 1000 km SSMF using Polarization Multiplexing with Direct Detection (2009)

In this paper, we experimentally demonstrate 22.4-Gb/s optical OFDM transmission over 1000km SSMF with polarization multiplexing (POLMUX) and direct detection. To the best of our knowledge, this is the longest reach directly-detected POLMUX-OFDM experiment reported.
Suicide gene therapy with an adenovirus expressing the fusion gene CD::UPRT in human glioblastomas: different sensitivities correlate with p53 status (2004)

Our study has shown that p53 status is important for CD::UPRT/5-FC treatment. Moreover, this study demonstrated that the three-dimensional spheroid model is a more stringent in vitro model for suicide gene therapy evaluation than are monolayer cultures.
Confounding Effect of Obstructive Jaundice in the Interpretation of Proteomic Plasma Profiling Data for Pancreatic Cancer (2008)

It is well established that variation in sampling, processing and storage protocols can alter the levels of potential biomarkers in serum and plasma. Here, using pancreatic cancer as an example, we demonstrate that consideration of clinical parameters related to the patient's illness is equally important when seeking cancer-specific biomarkers. Bile duct-obstruction is a feature of pancreatic disease that can cause jaundice. Comparing patients with pancreatic cancer, chronic pancreatitis or biliary duct obstruction, we observed that the plasma levels of apolipoprotein A1, transthyretin, and apolipoprotein E, when examined in isolation, were each associated with pancreatic cancer. However, when the effect of bile duct obstruction was considered, only transthyretin levels were independently associated with cancer likelihood. Our results demonstrate the importance of accounting for disease-related confounding factors when analyzing data for the detection of cancer biomarkers.
[Transdermal therapeutic systems (TTS)]. (1988)

The technique, pharmacokinetics, and advantages and disadvantages of transdermal drug delivery systems (TDS) are discussed. Special emphasis is laid on the dermatological problems arising during use of the TDS, such as irritation, sensitization, and the effects of occlusion, dermatoses, skin microflora and epidermal metabolism.
Using encryption for authentication in large networks of computers (1978)

Use of encryption to achieve authenticated communication in computer networks is discussed. Example protocols are presented for the establishment of authenticated connections, for the management of authenticated mail, and for signature verification and document integrity guarantee. Both conventional and public-key encryption algorithms are considered as the basis for protocols.
Therapeutic potential of target of rapamycin inhibitors (2004)

Target of rapamycin (TOR) functions within the cell as a transducer of information from various sources, including growth factors, energy sensors, and hypoxia sensors, as well as components of the cell regulating growth and division. Blocking TOR function mimics amino acid, and to some extent, growth factor deprivation and has a cytostatic effect on proliferating cells in vivo. Inhibition of TOR in vivo, utilising its namesake rapamycin, leads to immunosuppression. This property has been exploited successfully with the use of rapamycin and its derivatives as a therapeutic agent in the prevention of organ rejection after transplantation with relatively mild side effects when compared to other immunosuppressive agents. The cytostatic effect of TOR on vascular smooth muscle cell proliferation has also recently been exploited in the therapeutic application of rapamycin to drug eluting stents for angioplasty. These stents significantly reduce the amount of arterial reblockage that results from proliferating vascular smooth muscle cells. In cancer, the effect of blocking TOR function on tumour growth and disease progression is currently of major interest and is the basis for a number of ongoing clinical trials. However, different cell types and tumours respond differently to TOR inhibition, and TOR is clearly not cytostatic for all types of cancer cells in vitro or in vivo. As the molecular details of how TOR functions and the targets of TOR activity are further elucidated, tumour and tissue specific functions are being identified that implicate TOR in angiogenesis, apoptosis, and the reversal of some forms of cellular transformation. This review will describe our current understanding of TOR function, describe the current strategies for employing TOR inhibitors in clinical and preclinical development, and outline future strategies for appropriate targets of TOR inhibitors in the treatment of disease.
The skeletal muscle secretome: an emerging player in muscle–bone crosstalk (2012)

In vitro and in vivo studies provide evidence that a variety of growth factors and cytokines are actively secreted by muscle tissue. Muscle can therefore function as an endocrine and paracrine organ. These peptides characterize the muscle secretome, and many muscle-derived factors such as insulin-like growth factor-1, basic fibroblast growth factor, interleukin-15, myostatin and secreted protein acidic and rich in cysteine (osteonectin) are also known to have significant effects on bone metabolism. The factors secreted by muscle may vary according to muscle activity, in that muscle contraction, muscle atrophy or traumatic muscle injury can alter the type and relative abundance of particular factors released from muscle cells. The molecular and cellular pathways by which muscle-derived factors affect different types of bone cells (for example, osteoblasts, osteoclasts and osteocytes) are, however, poorly understood. Nevertheless, these findings further underscore the complex nature of muscle-bone interactions, and highlight the importance of integrating muscle biology and physiology into our understanding of bone growth, development and aging.
Properties of a Novel Pleiotropic Bacteriophage-Resistant Mutant of Staphylococcus aureus H (1969)

A phage-resistant mutant of Staphylococcus aureus H (Sm(R)), S. aureus 52A5, was previously shown to lack polymeric teichoic acid. This paper characterizes other phenotypic differences between the strains. In broth cultures the mutant cells grew more slowly, were larger, and formed much larger clumps than the parent strain. The clumps of cells appeared to be covalently linked and could only be separated by mild sonic energy-a process which yielded viable cells. Mutant and parent cells autolyzed at equal rates, whereas isolated cell walls of the mutant strain autolyzed faster than the wild type. Nevertheless, the specific activity of the autolytic enzyme in the wild type soluble fraction was much higher than in the mutant. In contrast to the parent, strain 52A5 failed to accumulate nucleotide-bound murein precursors when treated with penicillin. Mutant strains with these characteristics were repeatedly isolated both spontaneously and by chemical mutagenesis. Strain 52A5 was shown to be fully revertible. Thus, it appears to be a pleiotropic mutation, and the possible nature of the defect which causes these varied effects is discussed.
Type 1 Capsule Genes of Staphylococcus aureus Are Carried in a Staphylococcal Cassette Chromosome Genetic Element (2002)

The cap1 genes are required for the synthesis of type 1 capsular polysaccharide (CP1) in Staphylococcus aureus. We previously showed that the cap1 locus was associated with a discrete genetic element in S. aureus M. In this report, we defined the boundaries of the cap1 element by comparing its restriction pattern to that of a corresponding region from the CP1-negative strain Becker. The element was located in the SmaI-G chromosomal fragment of the standard mapping strain NCTC8325. The sequences of the entire cap1 element and the flanking regions were determined. We found that there were two additional cap1 genes not previously identified. The cap1 operon was located in a staphylococcal cassette chromosome (SCC) element similar to the resistance island SCCmec recently described for methicillin resistance in S. aureus. Notably, the SCCcap1 element was located at the same insertion site as all the SCCmec elements in the staphylococcal chromosome. The excision of SCCcap1 could be demonstrated only in the presence of the recombinase genes from an SCCmec element, verifying that SCCcap1 is a genuine SCC element but defective in mobilization. A novel enterotoxin gene, whose transcript was detected by Northern blotting, was found next to the SCCcap1 locus. We propose that the enterotoxin gene and SCCcap1 were inserted into this locus at the juxtaposition by independent events. Sequence comparison revealed numerous DNA rearrangements and mutations in SCCcap1 and the left flanking region, suggesting that the SCCcap1 had been inserted at the SCC attC site a long time ago. In addition, most genes in this region were incomplete, with the exception of the 15 cap1 genes, implying that the cap1 genes confer a survival advantage on strain M.
Proteins, Peptides and Amino Acids SourceBook (2002)

Explosive growth in the number of biological reagents available for sale to the research community has significantly complicated the process of finding a particular chemical or locating a suitable replacement for one that is no longer sold. Building on the success of their SourceBook of Enzymes, John and Dorothy Chong White have assembled an exhaustive catalog of over 26,000 commercially available proteins, peptides, and amino acids, all arranged alphabetically and by sequence for fast access, and each replete with technical details and vendor information. Compounds can be easily located by either directly searching the appropriate section by chemical name, or by consulting the general index by name, synonym, or derivative formula. Peptides with known sequences may be found alphabetically by basic sequence (no modification) or by consulting the Sequences Index. A Glossary of Abbreviations and Acronyms makes it possible to quickly find compounds by their common names.
Characterization of a human homologue of the murine peripheral lymph node homing receptor. (1989)

Lymphocyte trafficking is a fundamental aspect of the immune system that allows B and T lymphocytes with diverse antigen recognition specificities to be exposed to various antigenic stimuli in spatially distinct regions of an organism. A lymphocyte adhesion molecule that is involved with this trafficking phenomenon has been termed the homing receptor. Previous work (Lasky, L., T. Yednock, M. Singer, D. Dowbenko, C. Fennie, H. Rodriguez, T. Nguyen, S. Stachel, and S. Rosen. 1989. Cell. 56:1045-1055) has characterized a cDNA clone encoding a murine homing receptor that is involved in trafficking of lymphocytes to peripheral lymph nodes. This molecule was found to contain a number of protein motifs, the most intriguing of which was a carbohydrate binding domain, or lectin, that is apparently involved in the adhesive interaction between murine lymphocytes and peripheral lymph node endothelium. In this study, we have used the murine cDNA clone to isolate a human homologue of this peripheral lymph node-specific adhesion molecule. The human receptor was found to be highly homologous to the murine receptor in overall sequence, but showed no sequence similarity to another surface protein that may be involved with human lymphocyte homing, the Hermes glycoprotein. The extracellular region of the human receptor contained an NH2 terminally located carbohydrate binding domain followed by an EGF-like domain and a domain containing two repeats of a complement binding motif. Transient cell transfection assays using the human receptor cDNA showed that it encoded a surface glycoprotein that cross reacted with a polyclonal antibody directed against the murine peripheral lymph node homing receptor. Interestingly, the human receptor showed a high degree of sequence homology to another human cell adhesion glycoprotein, the endothelial cell adhesion molecule ELAM.
Physicochemical Characterization and Tube-like Structure Formation of a Novel Amino Acid-Based Zwitterionic AmphiphileN-(2-Hydroxydodecyl)-l-valine in Water (2008)

Surface activity and aggregation behavior of an amino acid-based zwitterionic amphiphile N-(2-hydroxydodecyl)-L-valine were studied in aqueous solutions (pH 13). The self-assembly formation was investigated by use of a number of techniques including surface tension, conductivity, viscosity, fluorescence spectroscopy, dynamic light scattering, and transmission electron microscopy. The amphiphile exhibits two breaks in the surface tension vs concentration plot indicating stepwise aggregate formation and thus results in two values of critical aggregation concentration. The amphiphile was found to be very surface active compared to fatty acid soaps. The average hydrodynamic diameter and size distribution of the aggregates were obtained from DLS measurements. Conductivity measurements suggested formation of vesicles or closed tubules. TEM pictures revealed the existence of spherical vesicles, separated tubules, and tubules with multiple Y-type junctions in going from dilute to moderately concentrated solution. However, in concentrated solution, the junctions break to form separate tubular structures which upon further increase of concentration are converted to rod-like micelles. The mechanism of branched tubule formation is discussed in light of the experimental observations.
In vitro cytotoxic targeting by human mononuclear cells and bispecific antibody 2B1, recognizing c-erbB-2 protooncogene product and Fc gamma receptor III. (1992)

Bispecific murine monoclonal antibody 2B1, possessing dual specificity for the human c-erbB-2 protooncogene product and human Fc gamma receptor III (CD16) was evaluated for the ability to promote specific lysis of c-erbB-2-positive tumor cells in vitro. In short-term 51Cr release assays with human mononuclear cells as effectors and SK-Br-3 human breast cancer cells as targets, neither parental antibody of 2B1 mediated significant specific lysis, but bispecific antibody was as active as a chemical heteroconjugate, with 5 ng/ml of 2B1 causing half-maximal lysis at an effector/target ratio of 20:1 and 2 ng/ml 2B1 causing half-maximal lysis at an E/T ratio of 40:1. The cytotoxic targeting activity of 2B1 F(ab')2 fragment was the same as that of whole bispecific antibody, and the activity of whole 2B1 was not reduced when assays were performed in 100% autologous human serum, indicating that 2B1 binds effector cells through the CD16-binding site derived from parental antibody 3G8 rather than through its Fc portion. Variable inhibition of 2B1-mediated lysis was observed when autologous polymorphonuclear leukocytes from different donors were added to mononuclear effector cells at a 2:1 ratio; this inhibition was overcome at higher antibody concentration. 2B1 bispecific monoclonal antibody was also able to mediate targeted cytolysis using whole human blood as a source of effector cells or using effector or target cells derived from ovarian cancer patients.
Engineering Antibody Molecules (2000)

Advances in PCR techniques and the increase of the antibody V region sequences in the database have boosted developments in the field of antibody engineering. The V region genes can be amplified from hybridomas (1), preimmunized donors (2), naive donors (3), or from the cells expressing antibodies.
Histidyl–tRNA Synthetase and Asparaginyl–tRNA Synthetase, Autoantigens in Myositis, Activate Chemokine Receptors on T Lymphocytes and Immature Dendritic Cells (2002)

Autoantibodies to histidyl-tRNA synthetase (HisRS) or to alanyl-, asparaginyl-, glycyl-, isoleucyl-, or threonyl-tRNA synthetase occur in approximately 25% of patients with polymyositis or dermatomyositis. We tested the ability of several aminoacyl-tRNA synthetases to induce leukocyte migration. HisRS induced CD4(+) and CD8(+) lymphocytes, interleukin (IL)-2-activated monocytes, and immature dendritic cells (iDCs) to migrate, but not neutrophils, mature DCs, or unstimulated monocytes. An NH(2)-terminal domain, 1-48 HisRS, was chemotactic for lymphocytes and activated monocytes, whereas a deletion mutant, HisRS-M, was inactive. HisRS selectively activated CC chemokine receptor (CCR)5-transfected HEK-293 cells, inducing migration by interacting with extracellular domain three. Furthermore, monoclonal anti-CCR5 blocked HisRS-induced chemotaxis and conversely, HisRS blocked anti-CCR5 binding. Asparaginyl-tRNA synthetase induced migration of lymphocytes, activated monocytes, iDCs, and CCR3-transfected HEK-293 cells. Seryl-tRNA synthetase induced migration of CCR3-transfected cells but not iDCs. Nonautoantigenic aspartyl-tRNA and lysyl-tRNA synthetases were not chemotactic. Thus, autoantigenic aminoacyl-tRNA synthetases, perhaps liberated from damaged muscle cells, may perpetuate the development of myositis by recruiting mononuclear cells that induce innate and adaptive immune responses. Therefore, the selection of a self-molecule as a target for an autoantibody response may be a consequence of the proinflammatory properties of the molecule itself.