gebhart/patrepeval huggingface dataset:
Activated mouse astrocytes and T cells express similar CD44 variants. Role of CD44 in astrocyte/T cell binding (1993)

The CD44 adhesion molecule is expressed by astrocytes, glial-type cells which exhibit features of accessory cells for immune responses in the central nervous system. In primary cultures of mouse astrocytes, we have observed that surface expression and mRNA levels of CD44 are induced following stimulation with either PMA, or tumor necrosis factor alpha plus gamma interferon. Comparison of CD44 splice variants expressed by astrocytes and a T cell hybridoma shows that upon activation, both cell types express a similar pattern of CD44 transcripts. Thus, in both cell types, CD44 transcripts are produced which contain additional exons, including the exon v6 (known to be expressed by in vivo activated lymphocytes and by metastatic variants of tumor cells) as well as variants of larger size. In the autoimmune disease multiple sclerosis, activated T cells cross the blood-brain barrier and lead to inflammation in the central nervous system. Analysis of mice with experimental allergic encephalomyelitis, frequently used as an animal model of multiple sclerosis, shows that CD44 is induced in vivo on glial cells surrounding inflammatory lesions. Using an in vitro model for adhesion between T cells and astrocytes, we have found a correlation between the activation state of these cells and their adhesion potential. Dose-dependent inhibition of adhesion by hyaluronate and by anti-CD44 monoclonal antibody KM81 shows that CD44 is involved in the adhesive interactions between T cells and astrocytes.
Alterations of the Blood-Brain Barrier and Glial Cells in White-Matter Lesions in Cerebrovascular and Alzheimer's Disease Patients (1996)

Dysfunction of the blood-brain barrier is more prominent in white-matter lesions seen in ischemic CVD than in AD and may have a role in the pathogenesis of cerebrovascular white-matter lesions.
Direct nonradioactive in situ hybridization of somatic cell hybrid DNA to human lymphocyte chromosomes (1990)

Abstract Biotinylated DNA from various human–rodent hybrids was hybridized to human lymphocyte spreads after preannealing of the repeated sequences with sonicated total human DNA. Fluorescent labeling was achieved by successive treatments with fluorescein‐labeled avidin and biotinylated antiavidin antibody. The use of labeled total DNA from hybrids with known chromosome composition permits the fluorescent staining‐(“painting”) of specific chromosomes, or parts thereof, in human lymphocyte metaphases. Alternatively, the human chromosome content of cell hybrids with unknown chromosome composition is directly assessed from the labeling pattern of human lymphocyte spreads using the total hybrid DNA as probe.
The Cystine-Knot Growth-Factor Superfamily (1995)

Four recent crystal structures of growth factors--nerve growth factor, transforming growth factor-beta, platelet-derived growth factor, and human chorionic gonadotropin--from four separate superfamilies revealed that these proteins are structurally related and share a common overall topology. These proteins have very little sequence homology, but they all have an unusual arrangement of six cysteines linked to form a "cystine-knot" conformation. The active forms of these proteins are dimers, either homo- or heterodimers. Despite the overall topological similarity between the monomers, the interfaces used to form the dimer are in each case quite different. Because the surfaces used for dimer formation are mostly hydrophobic, the uniqueness of each dimer accounts for the lack of sequence homology and raises questions about the effectiveness of reverse sequence fitting in this kind of structure as a predictor of structural homology.
Creation of an infectious recombinant Sendai virus expressing the firefly luciferase gene from the 3' proximal first locus. (1997)

A genetic engineering approach was made to generate a recombinant non-segmented negative-strand RNA virus, Sendai virus (SeV) of the family Paramyxoviridae, that expresses firefly luciferase. The DNA construct containing the entire open reading frame (ORF) of the luciferase gene followed by the SeV transcription stop and restart signals connected with the conserved intergenic three nucleotides was inserted immediately before the ORF of the viral 3'-proximal nucleocapsid (N) protein gene in a full-length SeV cDNA copy. After intracellular expression of full-length antigenomic transcripts from the engineered cDNA and of the viral n ucleocapsid protein and RNA polymerase from the respective plasmids, a recombinant SeV expressing luciferase activity at a high level was recovered, although the tendency of this particular reporter gene product to aggregate in cells made it difficult to estimate the maximum level of expression. The increase in genome length brought about by inserting 1728 nucleotides into the 15,384 nucleotide parental SeV was associated with reduced plaque size, slightly slower replication kinetics and a severalfold decrease in yield of the virus. The inserted luciferase gene was stably maintained after numerous rounds of replication by serial passages in chick embryos. These results indicate the potential utility of SeV as a novel expression vector.
Transcriptional and post-transcriptional regulation of soybean seed protein mRNA levels (1986)

We investigated soybean seed protein gene transcription during development. We found that seed protein genes are transcriptionally activated and then repressed during embryogenesis and that these genes are either inactive or transcribed at low levels in the mature plant. We further observed that genes encoding mRNAs with vastly different prevalences are transcribed at similar rates. DNA gel blot studies showed that transcriptionally active and inactive seed protein genes have indistinguishable methylation patterns. We conclude that both transcriptional and posttranscriptional processes regulate seed protein mRNA levels in the absence of detectable DNA methylation changes.
Development of Cationic Polymer Coatings to Regulate Foreign‐Body Responses (2011)

A library of cationic polymers, poly(beta-amino alcohols) with a great chemical diversity are synthesized using combinatorial polymerization. These polymers, when immobilized on a surface, drastically affect the behavior of monocyte/macrophage cells in vitro and early inflammatory reactions in vivo. Certain polymers are found capable of mitigating the foreign-body responses.
Treatment with retinoid X receptor agonist IRX4204 ameliorates experimental autoimmune encephalomyelitis. (2016)

Retinoid x receptors (RXRs) are master regulators that control cell growth, differentiation, and survival and form heterodimers with many other family members. Here we show that treatment with the RXR agonist IRX4204 enhances the differentiation of CD4(+) T cells into inducible regulatory T cells (iTreg) and suppresses the development of T helper (Th) 17 cells in vitro. Furthermore in a murine model of multiple sclerosis (experimental autoimmune encephalomyelitis (EAE)), treatment with IRX4204 profoundly attenuates both active and Th17-mediated passive disease. In the periphery, treatment with IRX4204 is associated with decreased numbers of CD4(+) T cells that produce pro-inflammatory cytokines. In addition, CD4(+) T cells express decreased levels of Ki-67 and increased expression of CTLA-4. Our findings demonstrate IRX4204 treatment during EAE results in immune modulation and profound attenuation of disease severity.
Recursive data structure profiling (2005)

As the processor-memory performance gap increases, so does the need for aggressive data structure optimizations to reduce memory access latencies. Such optimizations require a better understanding of the memory behavior of programs. We propose a profiling technique called Recursive Data Structure Profiling to help better understand the memory access behavior of programs that use recursive data structures (RDS) such as lists, trees, etc. An RDS profile captures the runtime behavior of the individual instances of recursive data structures. RDS profiling differs from other memory profiling techniques in its ability to aggregate information pertaining to an entire data structure instance, rather than merely capturing the behavior of individual loads and stores, thereby giving a more global view of a program's memory accesses.This paper describes a method for collecting RDS profile without requiring any high-level program representation or type information. RDS profiling achieves this with manageable space and time overhead on a mixture of pointer intensive benchmarks from the SPEC, Olden and other benchmark suites. To illustrate the potential of the RDS profile in providing a better understanding of memory accesses, we introduce a metric to quantify the notion of stability of an RDS instance. A stable RDS instance is one that undergoes very few changes to its structure between its initial creation and final destruction, making it an attractive candidate to certain data structure optimizations.
Determination of Cell Surface Membrane Antigens Common to Both Human Neuroblastoma and Leukemia-Lymphoma Cell Lines by a Panel of 38 Monoclonal Antibodies<xref ref-type="fn" rid="FN2">2</xref> (1984)

The surface membrane antigens of 7 neuroblastoma and 91 leukemia-lymphoma cell lines were studied with the use of a total of 36 murine monoclonal antibodies (MoAb) primarily developed against hematopoietic cells and 2 MoAb developed against human fetal brain. Five of the MoAb against hematopoietic cells (BA-1, BA-2, DU-ALL-1, J-5, and BA-3) consistently bound to common acute lymphoblastic leukemia cell lines, and 2 others (MCS-2 and OKM-1) reacted uniformly with acute myeloblastic-acute monoblastic leukemia cell lines. However, these 7 MoAb also reacted with 1-7 neuroblastoma cell lines. All the human neuroblastoma cell lines bound MoAb BA-2 and DU-ALL-1. Six of the 7 lines reacted with BA-1. Only 1 neuroblastoma cell line (SJ-N-CG) gave positive staining with J-5 and BA-3, and another line (SK-N-AS) bound MoAb MCS-2 and OKM-1. Anti-fetal brain MoAb (UJ-13A and UJ-127-11) were highly positive for all the neuroblastoma cell lines. By contrast, 4 of 43 leukemia-lymphoma cell lines tested bound these anti-fetal brain antibodies. Both B3/25 and OKT-9, anti-transferrin receptor antibodies, reacted with all of the hematopoietic and neuroblastoma cell lines. These results demonstrate that neuroblastoma and hematopoietic cell lines possess common antigenic determinants despite their different embryologic origins. The neuroblastoma cell lines may be classified into subgroups on the basis of phenotype profiles determined by the MoAb. MoAb may be useful in characterization and classification of neuroblastoma cells, as has already proved to be the case for cells of the hematopoietic lineages.
Adeno-Associated Virus (AAV) Vectors in the CNS (2011)

Adeno-associated virus (AAV) vectors exhibit a number of properties that have made this vector system an excellent choice for both CNS gene therapy and basic neurobiological investigations. In vivo, the preponderance of AAV vector transduction occurs in neurons where it is possible to obtain long-term, stable gene expression with very little accompanying toxicity. Promoter selection, however, significantly influences the pattern and longevity of neuronal transduction distinct from the tropism inherent to AAV vectors. AAV vectors have successfully manipulated CNS function using a wide variety of approaches including expression of foreign genes, expression of endogenous genes, expression of antisense RNA and expression of RNAi. With the discovery and characterization of different AAV serotypes, as well as the creation of novel chimeric serotypes, the potential patterns of in vivo vector transduction have been expanded substantially, offering alternatives to the more studied AAV 2 serotype. Furthermore, the development of specific AAV chimeras offers the potential to further refine targeting strategies. These different AAV serotypes also provide a solution to the immune silencing that proves to be a realistic likelihood given broad exposure of the human population to the AAV 2 serotype. These advantageous CNS properties of AAV vectors have fostered a wide range of clinically relevant applications including Parkinsons disease, lysosomal storage diseases, Canavans disease, epilepsy, Huntingtons disease and ALS. In many cases the proposed therapies have progressed to phase I/II clinical trials. Each individual application, however, presents a unique set of challenges that must be solved in order to attain clinically effective gene therapies.
Molecular characterization and functional analysis of the leukocyte surface protein CD31. (1990)

The CD31 Ag is a surface glycoprotein of 130 kDa with a broad cellular distribution. We show that among peripheral human blood cells, it is expressed on monocytes, granulocytes, platelets, and a subpopulation of lymphocytes. Activation of granulocytes leads to down-regulation of CD31 molecule expression. Sequence analysis and quantitative measurements of the relatedness of the CD31 molecule to other known proteins demonstrate that it consists of six Ig constant domains and that each domain bears substantial similarity to Fc gamma R domains. We find, however, that the CD31 molecule does not bind Ig Fc domains. On human monocytes we demonstrate that CD31 mAb recognizing certain epitopes of the CD31 molecule induce the generation of reactive oxygen metabolites. No such effect was seen with human granulocytes. By using two CD31 mAb, termed 1B5 and 7E4, we analyzed the requirements for activation of the monocyte respiratory burst via CD31 Ag in more detail. We show that signal transduction occurs via formation of a CD31 Ag-mAb-Fc gamma R complex involving either Fc gamma RI (CD64) or Fc gamma RII (CDw32) molecules.
Characterization of Cementum Derived Growth Factor as an Insulin-Like Growth Factor-I Like Molecule (1997)

Cementum is the thin calcified outer layer through which tooth-root surfaces are anchored to soft periodontal connective tissues. A variety of growth factors and adhesion molecules are sequestered in the extracellular matrix of cementum, and we have purified and characterized one of the growth factors. This growth factor, the cementum derived growth factor (CGF), was purified from bovine cementum by acetic acid extraction followed by heparin affinity chromatography and HPLC using cation exchange, molecular sieve, and reverse-phase columns. NaDodSO4-polyacrylamide gel electrophoresis of purified CGF preparation revealed the presence of two major protein bands migrating with Mr 18,000-22,000 and 14,000-16,000. The latter was associated with the major part of the mitogenic activity. The activity of CGF was inhibited by antibodies to insulin-like growth factor-I (IGF-I) and IGF-I receptor. Both CGF and IGF-I were mitogenic to human gingival fibroblasts and alveolar bone cells, but the bone cells responded better to CGF than to IGF-I. The IGF-I did not bind to heparin-sepharose, while CGF bound to it and was eluted with 0.6M NaCl from heparin-sepharose columns. Heparin-sepharose 0.2M NaCl fractions of cementum extracts contained IGF-I migrating with Mr 7,500, but its mobility was not affected by N-glycosidase treatment. Western analysis using anti-IGF-I antibodies showed that CGF preparations contained cross-reacting species migrating with Mr 18,000-22,000, 14,000-16,000 and 11,000-12,000, however after treatment with N-glycosidase the Mr 18,000-22,000 component was absent. Internal amino acid sequences of six tryptic peptides of CGF were determined by microsequencing. The sequence of one 15-amino acid long peptide was the same as the receptor binding domain of IGF-I, and another 9-amino acid peptide had 78 % homology to a sequence derived from an untranslated region of sheep IGF-I exon 1. Four other peptides had no apparent homology with IGF-I. From these results we conclude that the CGF is an IGF-I like molecule.
Gene Duplications at the Chemokine Locus on Mouse Chromosome 4: Multiple Strain-Specific Haplotypes and the Deletion of Secondary Lymphoid-Organ Chemokine and EBI-1 Ligand Chemokine Genes in the plt Mutation (2001)

The murine paucity of lymph node T cell (plt) mutation leads to abnormalities in leukocyte migration and immune response. The causative defect is thought to be a loss of secondary lymphoid-organ chemokine (SLC) expression in lymphoid tissues. We now find that the plt defect is due to the loss of both SLC and EBI-1 ligand chemokine (ELC) expression in secondary lymphoid organs. In an examination of the plt locus, we find that commonly used inbred mouse strains demonstrate at least three different haplotypes. Polymorphism at this locus is due to duplications of at least four genes, three of them encoding chemokines. At least two cutaneous T cell-attracting chemokine (CTACK), three SLC, and four ELC genes or pseudogenes are present in some haplotypes. All haplotypes share a duplication that includes two SLC genes, which demonstrate different expression patterns, a single functional ELC gene, and an ELC pseudogene. The plt mutation represents a deletion that includes the SLC gene expressed in secondary lymphoid organs and the single functional ELC gene, leaving only an SLC gene that is expressed in lymphatic endothelium and an ELC pseudogene. This lack of CCR7 ligands in the secondary lymphoid organs of plt mice provides a basis for their severe abnormalities in leukocyte migration and immune response.
Cytotoxic Activity toward KB Cells of 2-Substituted Naphtho[2,3-b]furan-4,9-diones and Their Related Compounds (2006)

We investigated the cytotoxic activity of 2-substituted naphtho[2,3-b]furan-4,9-diones. We have previously synthesized 33 types of 2-substituted and related compounds, and the cytotoxic activity of these compounds was then examined by a KB cell culture assay. 2-(3-Furanoyl)benzoic acids and 1,4-naphthoquinones had no activity. 2-Acetyl-4,9-dimethoxynaphtho[2,3-b]furan 4 showed low activity. However, parent naphtho[2,3-b]furan-4,9-dione 2 and most 2-substituted derivatives exhibited cytotoxic activity. The parent structure was therefore for cytotoxicity. 2-Formylnaphtho[2,3-b]furan-4,9-dione 11 had particularly potent activity (ED50=0.09 microg/ml).
CD4 immunoadhesin, but not recombinant soluble CD4, blocks syncytium formation by human immunodeficiency virus type 2-infected lymphoid cells (1990)

Recombinant soluble CD4 (rCD4) has been shown to be an effective inhibitor of human immunodeficiency virus type 1 (HIV-1) and HIV-2 infection of lymphoid cells in vitro. In this report, we characterized the effects of rCD4, the V1V2 fragment of CD4, and the immunoadhesin CD4-immunoglobulin G on syncytium formation between lymphoid cells infected by HIV-1 or HIV-2 and uninfected cells. All three molecules blocked HIV-1-mediated syncytium formation, but only CD4-immunoglobulin G blocked HIV-2-mediated syncytium formation. rCD4 and the V1V2 fragment of CD4 enhanced HIV-2-mediated syncytium formation. These results suggest that the process of cell fusion is significantly different between HIV-1- and HIV-2-infected cells.
Randomized Trial of Complete Versus Lesion-Only Revascularization in Patients Undergoing Primary Percutaneous Coronary Intervention for STEMI and Multivessel Disease (2015)

In patients presenting for P-PCI with multivessel disease, index admission complete revascularization significantly lowered the rate of the composite primary endpoint at 12 months compared with treating only the IRA. In such patients, inpatient total revascularization may be considered, but larger clinical trials are required to confirm this result and specifically address whether this strategy is associated with improved survival.
SCRAMSAC: Improving RANSAC's efficiency with a spatial consistency filter (2009)

Geometric verification with RANSAC has become a crucial step for many local feature based matching applications. Therefore, the details of its implementation are directly relevant for an application's run-time and the quality of the estimated results. In this paper, we propose a RANSAC extension that is several orders of magnitude faster than standard RANSAC and as fast as and more robust to degenerate configurations than PROSAC, the currently fastest RANSAC extension from the literature. In addition, our proposed method is simple to implement and does not require parameter tuning. Its main component is a spatial consistency check that results in a reduced correspondence set with a significantly increased inlier ratio, leading to faster convergence of the remaining estimation steps. In addition, we experimentally demonstrate that RANSAC can operate entirely on the reduced set not only for sampling, but also for its consensus step, leading to additional speed-ups. The resulting approach is widely applicable and can be readily combined with other extensions from the literature. We quantitatively evaluate our approach's robustness on a variety of challenging datasets and compare its performance to the state-of-the-art.
Parallel-Coupled Transmission-Line-Resonator Filters (1958)

This paper describes the synthesis of band-pass transmission-line filters consisting of series of half-wavelength resonant conductors such as strips. The design differs from the usual end-coupled strip configuration in that successive strips are parallel coupled along a distance of a quarter-wavelength. The resulting coupling between resonators is partly electric and partly magnetic. Several important advantages are gained by this arrangement: 1) the length of the filter is approximately half that of the end-coupled type; 2) the gaps are larger and therefore less critical; and 3) the insertion-Ioss curve is symmetrical on a frequency scale with the first spurious response occurring at three times the center frequency of the pass band. Formulas are derived for the parallel-coupled-resonator transmission-line filter that permit accurate design for Tchebycheff, maximally flat, or any other physically realizable response. The formulas are theoretically exact in the limit of zero bandwidth, but frequency-response calculations show them to give good results for band widths up to about 30 per cent. An experimental strip-line filter of this type has been constructed, and the data given in this paper show that excellent performance has been obtained.
A Study of Automated Custom Fit: Readiness of the Technology for the Apparel Industry (2006)

Sophisticated new technologies are available to the apparel industry to create automated custom-fitted clothing; research and development of necessary data and proceduresfor implementing these programs must be within reach of apparel companies to successfully implement custom.fit. This study explores issues in setting up a custom apparel patternmaking process using 3D body scanning and software designed to automate patternmaking. Questions related to measurement reliability and validity, data and knowledge needed to create and test required system variables, andfit preference issues were addressed in this study. A system for generating custom-fitted outerwearjackets was developedfor an industry collaborator, Log House Designs, and tested on ten participants. The.fit of the prototype custom jackets was compared to thefit of a set of ready-to-wearjackets. Seven of the ten participants preferred thefit of the prototype custom jacket; the remaining three were equally satisfied with both jackets.
The pro-apoptotic Bcl-2 family member tBid localizes to mitochondrial contact sites (2001)

Immunoelectron tomography with statistical analysis confirmed the preferential association of tBid with mitochondrial contact sites. These findings link these sites with cardiolipin in tBid targeting and suggest a role for Bcl-2 family members in regulating the activity of contact sites in relation to apoptosis. We propose a mechanism whereby Bcl-2 proteins alter mitochondrial function by disrupting cardiolipin containing contact site membranes.