gebhart/patrepeval huggingface dataset:
Preferential outgrowth of central nervous system neurites on astrocytes and Schwann cells as compared with nonglial cells in vitro. (1985)

I have compared central nervous system (CNS) neurite outgrowth on glial and nonglial cells. Monolayers of glial cells (astrocytes and Schwann cells) or nonglial cells (e.g., fibroblasts) were prepared and were shown to be greater than 95% pure as judged by cell type-specific markers. These monolayers were then tested for their ability to support neurite outgrowth from various CNS explants. While CNS neurites grew vigorously on the glial cells, most showed little growth on nonglial cell monolayers. Neurites grew singly or in fine fascicles on the glial cells at rates greater than 0.5 mm/d. The neurite outgrowth on astrocytes was investigated in detail. Scanning and transmission electron microscopy showed that the neurites were closely apposed to the astrocyte surface and that the growth cones were well spread with long filopodia. There was no evidence of significant numbers of explant-derived cells migrating onto the monolayers. Two types of experiments indicated that factors associated with the astrocyte surface were primarily responsible for the vigorous neurite outgrowth seen on these cells: (a) Conditioned media from either astrocytes or fibroblasts had no effect on the pattern of outgrowth on fibroblasts and astrocytes, and conditioned media factors from either cell type did not promote neurite outgrowth when bound to polylysine-coated dishes. (b) When growing CNS neurites encountered a boundary between astrocytes and fibroblasts, they stayed on the astrocytes and did not encroach onto the fibroblasts. These experiments strongly suggest that molecules specific to the surfaces of astrocytes make these cells particularly attractive substrates for CNS neurite outgrowth, and they raise the possibility that similar molecules on embryonic glial cells may play a role in guiding axonal growth during normal CNS development.
Cross‐flow microfiltration with high‐frequency reverse filtration (1995)

Abstract A primary method of reducing membrane fouling during cross‐flow microfiltration is periodic reverse filtration. This in situ method of cleaning the membrane forces clear fluid in the reverse direction through the membrane and readjusts the particle or solute accumulation on the retentate side of the membrane. This work focuses on the design of a high‐frequency, reverse‐filtration strategy to maximize the flux for washed yeast suspensions through 0.2‐ μm cellulose acetate flat sheet membranes. Several experiments were conducted with reverse‐filtration times ranging from 0.5–4 s and forward‐filtration times ranging from 1–40 s. For every back‐filtration time, there exists an optimum forward‐filtration time that gives the maximum global average flux. The optimum average flux increases with decreasing back filtration times and feed concentrations, but shows little dependence on cross‐flow velocity and reverse filtration transmembrane pressure. The optimum flux with rapid backflushing is 20 to 30 times higher than the long‐term flux in the absence of backflushing. A theory presented assumes that cake formation during forward filtration follows dead‐end filtration theory and the cake is instantly removed during reverse filtration. The measured average flux per cycle follows the trends predicted by the theory, but the measured values exceed the predictions, presumably due to brief delays in cake removal and cake formation at the start of reverse and forward filtration, respectively, during each cycle.
IL-4-regulated enteropathy in an intestinal nematode infection (1998)

The relationship between intestinal pathology and immune expulsion of gastrointestinal nematodes remains controversial. Parasite expulsion is associated with intestinal pathology in several model systems and both of these phenomena are T cell dependent. Immune expulsion of gastrointestinal helminth parasites is usually associated with Th2 responses, but the effector mechanisms directly responsible for parasite loss have not been elucidated. In contrast, the intestinal pathology observed in many other disease models closely resembles that seen in helminth infections, but has been attributed to Th1 cytokines. We have used infection with the nematode Trichinella spiralis in mice defective for cytokines or their receptors to investigate cytokine regulation of both immunopathology and parasite rejection. Consistent with previous findings, we found that parasite expulsion is IL-4 dependent. Contrary to expectations, however, the enteropathy is not regulated by IFN-gamma but by IL-4. Moreover, abrogation of severe pathology in TNF receptor-defective animals does not prevent parasite expulsion. TNF is therefore involved in intestinal pathology in nematode infections, apparently under regulation by IL-4- and Th2-mediated responses. This work therefore not only reveals a novel interplay between IL-4 and TNF, but also that the IL-4-dependent protective response against the parasite operates by a mechanism other than merely the gross degradation of the parasite's environment brought about by the immune enteropathy.
Geometric Scaling Effects in Electrical Field Flow Fractionation. 2. Experimental Results (2002)

Geometric scaling of microelectrical field flow fractionation (micro-EFFF) systems is investigated experimentally and compared to theory and to macroscale EFFF systems. Experimental results are presented to demonstrate that the miniaturized system operates according to the scaling theory associated with the system. Demonstrated improvements in the channels include increased retention and resolution and decreased peak broadening, electrical time constants, relaxation time, power consumption, and sample size. Additionally, scaling effects related to the compression of separation zones in the miniaturized EFFF systems are discussed.
NMR-based metabolomics: translational application and treatment of cancer. (2007)

Cancer cells possess a highly unique metabolic phenotype which is characterized by high glucose uptake, increased glycolytic activity, decreased mitochondrial activity, low bioenergetic expenditure and increased phospholipid turnover. In addition to these general metabolic markers of malignancy, tissue-specific biochemistry has identified specific endogenous metabolites found in particular tumors types. These include N-acetyl aspartate in neuroblastoma, myo-inositol in gliomas and citrate in prostate cancer. Metabolic profiles can be readily assessed to monitor responsiveness and the development of resistance to novel targeted drugs, for example, where a cytostatic effect rather than cytotoxicity occurs. Using modern analytical technologies in combination with statistical approaches, a methodology termed 'metabolomics' has been developed. Metabolomics has been used to generate a global metabolic profile on patient samples, which can then be used to determine treatment response. This review describes existing NMR-based approaches for global metabolic profiling in tissue biopsies and body fluids and the use of non-invasive radiological techniques to assess metabolic biomarkers. In addition, studies on metabolic responses to novel targeted drugs, including tyrosine kinase inhibitors and metabolic modulators, are evaluated.
Human Immunodeficiency Virus (1996)

Mutations in the human immunodeficiency virus (HIV) protease (L90M, G48V, and L90M/G48V) arise when HIV is passaged in the presence of the HIV protease inhibitor saquinavir. These mutations yield a virus with less sensitivity to the drug (L90M > G48V >> L90M/G48V). L90M, G48V, and L90M/G48V proteases have 1/20, 1/160, and 1/1000 the affinity for saquinavir compared to WT protease, respectively. Therefore, the affinity of mutant protease for saquinavir decreased as the sensitivity of the virus to saquinavir decreased. Association rate constants for WT and mutant proteases with saquinavir were similar, ranging from 2 to 4 x 10(7) M-1 s-1. In contrast, the dissociation rate constants for WT, L90M, G48V, and L90M/G48V proteases complexed with saquinavir were 0.0014, 0.019, 0.128, and 0. 54 s-1, respectively. This indicated that the reduced affinity for mutant proteases and saquinavir is primarily the result of larger dissociation rate constants. The increased dissociation rate constants may be the result of a decrease in the internal equilibrium between the bound inhibitor with the protease flaps up and the bound inhibitor with the flaps down. Interestingly, the affinity of these mutant proteases for VX-478, ABT-538, AG-1343, or L-735,524 was not reduced as much as that for saquinavir. Finally, the catalytic constants of WT and mutant proteases were determined for eight small peptide substrates that mimic the viral cleavage sites in vivo. WT and L90M proteases had similar catalytic constants for these substrates. In contrast, G48V and L90M/G48V proteases had catalytic efficiency (kcat/Km) values with TLNF-PISP, RKIL-FLDG, and AETF-YVDG that were 1/10 to 1/20 the value of WT protease. The decreased catalytic efficiencies were primarily the result of increased Km values. Thus, mutations in the protease decrease the affinity of the enzyme for saquinavir and the catalytic efficiency with peptide substrates.
B7-H4 expression in renal cell carcinoma and tumor vasculature: Associations with cancer progression and survival (2006)

B7-H4 is a recently described B7 family coregulatory ligand that has been implicated as an inhibitor of T cell-mediated immunity. Although expression of B7-H4 is typically limited to lymphoid cells, aberrant B7-H4 expression has also been reported in several human malignancies. To date, associations of B7-H4 with clinical outcomes for cancer patients are lacking. Therefore, we examined B7-H4 expression in fresh-frozen tumor specimens from 259 renal cell carcinoma (RCC) patients treated with nephrectomy between 2000 and 2003 and performed correlative outcome analyses. We report that 153 (59.1%) RCC tumor specimens exhibited B7-H4 staining and that tumor cell B7-H4 expression was associated with adverse clinical and pathologic features, including constitutional symptoms, tumor necrosis, and advanced tumor size, stage, and grade. Patients with tumors expressing B7-H4 were also three times more likely to die from RCC compared with patients lacking B7-H4 (risk ratio = 3.05; 95% confidence interval = 1.51-6.14; P = 0.002). Additionally, 211 (81.5%) specimens exhibited tumor vasculature endothelial B7-H4 expression, whereas only 6.5% of normal adjacent renal tissue vessels exhibited endothelial B7-H4 staining. Based on these findings, we conclude that B7-H4 has the potential to be a useful prognostic marker for patients with RCC. In addition, B7-H4 represents a target for attacking tumor cells as well as tumor neovasculature to facilitate immunotherapeutic treatment of RCC tumors. Last, we demonstrate that patients with RCC tumors expressing both B7-H4 and B7-H1 are at an even greater risk of death from RCC.
Generation of hypoimmunogenic human pluripotent stem cells (2019)

Polymorphic HLAs form the primary immune barrier to cell therapy. In addition, innate immune surveillance impacts cell engraftment, yet a strategy to control both, adaptive and innate immunity, is lacking. Here we employed multiplex genome editing to specifically ablate the expression of the highly polymorphic HLA-A/-B/-C and HLA class II in human pluripotent stem cells. Furthermore, to prevent innate immune rejection and further suppress adaptive immune responses, we expressed the immunomodulatory factors PD-L1, HLA-G, and the macrophage "don't-eat me" signal CD47 from the <i>AAVS1</i> safe harbor locus. Utilizing in vitro and in vivo immunoassays, we found that T cell responses were blunted. Moreover, NK cell killing and macrophage engulfment of our engineered cells were minimal. Our results describe an approach that effectively targets adaptive as well as innate immune responses and may therefore enable cell therapy on a broader scale.
Efficacy of multi-electrode linear irreversible electroporation (2020)

Epicardial multi-electrode linear application of IRE pulses is effective in creating continuous deep lesions.
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (2016)

Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use.
Biosynthesis and attachment of novel bacterial polyketide synthase starter units (2001)

The biosynthesis and mode of attachment of a wide range of polyketide synthase (PKS) starter units in bacteria are covered in this review. Natural, unnatural, and engineered starter units associated with type I and type II PKSs are reported. The literature through early 2001 is reviewed, and 240 references cited.
Optimal depth buffer for low-cost graphics hardware (1999)

3D applications using hardware depth buffers for visibility testing are confronted with multiple choices of buffer types, sizes and formats. Some of the options are not exposed through 3D API or may be used by the driver without application's knowledge. As a result, it becomes increasingly diffkult to select depth buffer optimal for desired balance between performance and precision.
Aromatic Ring‐Fused Carborane‐Based Luminescent π‐Conjugated Polymers (2010)

A series of π-conjugated polymers linked by benzocarborane (1,2-(buta-1',3'-diene-1',4'-diyl)-1,2-dicarbadodecaborane) were synthesized via Sonogashira-Hagihara polycondensation reaction. The opened molecular structure of diiodo monomer containing benzocarborane resulted in fast polymerization and high molecular weights. The obtained polymers were fully characterized by (1) H, (13) C, and (11) B NMR spectroscopies. UV-vis absorption and photoluminescence studies revealed the acceptor-profile of benzocarborane. Unlike the polymers linked by o-carborane, these polymers exhibited strong luminescence in the solution state, presumably because the inductive effect of carborane is dominant, rather than cage-π interactions.
Copy number of a human type I alpha 2 collagen gene. (1982)

HpCl, a Charon 4A bacteriophage containing a 16.3-kilobase insert of human genomic DNA, has been identified as representing the 3' portion of the human alpha 2(I) collagen gene by hybrid selected translation and cross-reactivity with characterized sheep and chick collagen genes. Evaluation of HpCl by restriction endonuclease mapping and alpha 2(I) mRNA hybridization demonstrated that the alpha 2(I) mRNA coding regions are separated by noncoding regions including one of 2.7 kilobase pairs near the 3' end of the mRNA coding region. In addition, a 1.8-kilobase XbaI-BamHI fragment containing the 2' a 1.8-kilobase XbaI-BamHI fragment containing the 3' end of the alpha 2(I) mRNA coding region includes a region of DNA that is repeated many times throughout the human genome. Quantification of alpha 2(I) gene number, using the technique of DNA dot hybridization, with two EcoRI fragments from HpClo as probes, demonstrated that HpCl is represented once in the human genome. In this context, it is unlikely that human alpha 2(I) collagen chain production is modulated by differential transcription of multiple alpha 2(I) genes.
Hybridization of Oligonucleotide-Modified Silver and Gold Nanoparticles in Aqueous Dispersions and on Gold Films (2004)

Functionalization of silver and gold nanoparticles by 12mer-thiolated homo-oligonucleotides, SA and ST (containing only adenine or thymine, respectively), and their hybridization and dehybridization in aqueous dispersions have been described. In addition, ST and SA were self-assembled onto gold films and hybridized with their complementary pairs, unlabeled or labeled by gold and silver nanoparticles. The base pairing between DNA strands and the types of oligonucleotides (adenine or thymine) attached to the nanoparticles was detected by Polarization Modulated Fourier Transform Infrared Reflection Absorption Spectroscopy (PM-FTIRRAS).
Sparsity in higher order methods for unconstrained optimization (2011)

In this paper, we introduce data structures for storing the third derivative (tensor) of a multivariate scalar function when the second and third derivatives of the function are sparse. We consider solving unconstrained optimization problems using methods of the Halley class. The gradient, Hessian matrix and the tensor of the objective function are required for the methods and they have a third-order rate of convergence. However, these methods require the solution of two linear systems of equations at each iteration. Solving the linear systems using a factorization will cause fill-ins. The impact of these fill-ins will be discussed and we give the number of arithmetic operations of the methods of the Halley class compared to Newton's method. Finally, we will give some preliminary numerical results showing that including the time to compute the derivatives, the ratios of elapsed time of methods in the Halley class and Newton's method are close to the ratios of arithmetic operations.
CLINICAL OBSERVATIONS ON THE USE OF HYALURONIDASE (1949)

The use of hyaluronidase was observed in 116 infants and children in such procedures as hypodermoclysis, phthalein excretion test and urography. Eight tenths of a milligram (0.8 mg.) of the dry substance dissolved in 1 ml. of distilled water was used as a standard amount of the enzyme for all procedures. Hyaluronidase provided an effective expedient to fluid diffusion in subcutaneous therapy. From clinical observations, the speed of flow in any one case is dependent upon: 1. general development of the patient, 2. state of hydration of the patient, 3. activity of the patient, 4. position of the needles in the skin, 5. original speed of the flow and 6. type and amount of fluid given. There was no significant change either in dye excretion or total renal fluid excretion when hyaluronidase was used in the phthalein excretion test. Hyaluronidase reduced the amount of dye necessary when given subcutaneously to secure adequate visualization in urography. Repeated urinalyses in many of the procedures showed no evidence of renal pathology. There were no instances of thermal reaction, spread of infection, or reactivation of infection that could be attributed to the use of the enzyme.
Transmission System Evaluation for Two-Way Cable (1979)

The installation and operation of a two-way cable system in London, Ontario is discussed.
Rice‐bran Treatment for Calcium Stone Formers with Idiopathic Hypercalciuria (1986)

The efficacy of rice-bran therapy was studied in patients with hypercalciuria who were suffering from calcium stones. The frequency of stone episodes was reduced dramatically, especially in "active recurrent stone formers". Urinary calcium excretion was considerably reduced, while urinary phosphate and oxalate were slightly increased. Urinary magnesium, uric acid, serum calcium, phosphate, magnesium and uric acid were not affected. There were no changes in serum iron, copper and zinc even when patients were treated for long periods. The treatment was tolerated well and there were no serious side effects. Rice-bran therapy is particularly useful in patients with hyperabsorptive hypercalciuria and it is effective in the prevention of recurrent urinary stone disease.
Complementary DNA sequence and deduced peptide sequence for CD59/MEM-43 antigen, the human homologue of murine lymphocyte antigen Ly-6C (1989)

Journal Article Complementary DNA sequence and deduced peptide sequence for CD59/MEM-43 antigen, the human homologue of murine lymphocyte antigen Ly-6C Get access Ritsuko Sawada, Ritsuko Sawada Search for other works by this author on: Oxford Academic PubMed Google Scholar Kensaku Ohashi, Kensaku Ohashi Search for other works by this author on: Oxford Academic PubMed Google Scholar Kiyoshi Okano, Kiyoshi Okano Search for other works by this author on: Oxford Academic PubMed Google Scholar Masakazu Hattori, Masakazu Hattori 1Department of Veterinary Medicine, Hokkaido UniversitySapporo 060 Search for other works by this author on: Oxford Academic PubMed Google Scholar Nagahiro Minato, Nagahiro Minato 2Division of Clinical Immunology, Jichai Medical SchoolTochigi 329-04, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Masanobu Naruto Masanobu Naruto * *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 16, 25 August 1989, Page 6728, https://doi.org/10.1093/nar/17.16.6728 Published: 25 August 1989 Article history Received: 25 July 1989 Published: 25 August 1989
Animal models for X-linked sideroblastic anemia. (2000)

Erythroid 5-aminolevulinate synthase (ALAS-E) catalyzes the first step of heme biosynthesis in erythroid cells. Several lines of evidence suggest that the expression of ALAS-E is important for the process of erythroid differentiation, which requires a large amount of heme for hemoglobin production. Mutation of human ALAS-E causes the disorder X-linked sideroblastic anemia (XLSA). More than 25 unrelated ALAS-E mutations in XLSA patients have been reported. Most XLSA cases are of the pyridoxine-responsive type, but molecular diagnosis of 1 pyridoxine-refractory type XLSA has also been reported. To examine the roles heme plays during hematopoiesis and to create animal models of XLSA, we disrupted the mouse ALAS-E gene. A chemically induced zebrafish mutant (sau) that lacks ALAS-E has also been isolated. Analysis of these ALAS-E mutants unequivocally demonstrated that ALAS-E is the principal isozyme contributing to erythroid heme biosynthesis In ALAS-E-null mutant mouse embryos, erythroid differentiation was arrested, and an abnormal hematopoietic cell fraction emerged that accumulated a large amount of iron diffusely in the cytoplasm. This accumulation of iron was in contrast to that in XLSA patients, as typical ring sideroblasts accumulated iron primarily in mitochondria. These observations suggest that the mode of iron accumulation caused by the lack of ALAS-E is different in primitive and definitive erythroid cells. Thus ALAS-E, and hence heme supply, is necessary for erythroid cell differentiation and iron metabolism.
Raf-1/bcl-2 phosphorylation: a step from microtubule damage to cell death. (1997)

Recent studies have shown that paclitaxel leads to activation of Raf-1 kinase and have suggested that this activation is essential for bcl-2 phosphorylation and apoptosis. In the present study, we demonstrate that, in addition to paclitaxel, other agents that interact with tubulin and microtubules also induce Raf-1/bcl-2 phosphorylation, whereas DNA-damaging drugs, antimetabolites, and alkylating agents do not. Activation of Raf-1 kinase by paclitaxel is linked to tubulin polymerization; the effect is blunted in paclitaxel-resistant cells, the tubulin of which does not polymerize following the addition of paclitaxel. In contrast, vincristine and vinblastine, drugs to which the paclitaxel-resistant cells retain sensitivity were able to bring about Raf-1 phosphorylation. The requirement for disruption of microtubules in this signaling cascade was strengthened further using paclitaxel analogues by demonstrating a correlation between tubulin polymerization, Raf-1/bcl-2 phosphorylation, and cytotoxicity. Inhibition of RNA or protein synthesis prevents Raf-1 activation and bcl-2 phosphorylation, suggesting that an intermediate protein(s) acts upstream of Raf-1 in this microtubule damage-activating pathway. A model is proposed that envisions a pathway of Raf-1 activation and bcl-2 phosphorylation following disruption of microtubular architecture, serving a role similar to p53 induction following DNA damage.