gebhart/patrepeval huggingface dataset:
Morphological and Virological Investigations on Cultured Burkitt Tumor Lymphoblasts (Strain Raji)<xref ref-type="fn" rid="FN2">2</xref> (1966)

Cells of the Raji strain, established in vitro in Nigeria from a Burkitt lymphoma, were maintained and studied between the 16th and 28th months of culture. As judged by their mode of growth in suspension, appearance when stained, and fine structural organization, the cells were undifferentiated lymphoblasts similar to those of other tissue culture strains from Burkitt tumors. Characteristics suggesting a lack of differentiation were the formation of large aggregations containing many hundreds of individuals, a relatively large diameter, irregularly indented nuclei, and a fairly extensive cytoplasm with free ribosomes tending to clump. No virus particles could be found in the cells by electron microscopy, despite intensive searching of 16 separate samples. Although the cells were resistant to vesicular stomatitis virus, this resistance could not be transferred to other normally susceptible test cultures and an interferon-like inhibitor could not be found. The Raji cells could, however, produce interferon when stimulated by Newcastle disease virus. Unlike other cultured Burkitt tumor cells, Raji cells did not respond positively in immunofluorescence tests. The failure to detect virus particles or indirect evidence of virus infection in Raji cells is discussed.
Anti-Cancer Therapies that Utilize Cell Penetrating Peptides (2010)

Cell penetrating peptides (CPPs) are 9-35mer cationic and/or amphipathic peptides that are rapidly internalized across cell membranes. Importantly, they can be linked to a variety of cargo, including anti-cancer therapeutics, making CPPs an efficient, effective and non-toxic mechanism for drug delivery. In this review, we discuss a number of CPP conjugated therapies (CTTs) that are either patented are in the progress of patenting, and show strong promise for clinical efficacy. The CTTs discussed here target a number of different processes specific to cancer progression, including proliferation, survival and migration. In addition, many of these CTTs also increase sensitivity to current anti-cancer therapy modalities, including radiation and other DNA damaging chemotherapies, thereby decreasing the toxic dosage required for effective treatment. Mechanistically, these CTTs function in a dominant-negative manner by blocking tumorspecific protein-protein interactions with the CPP-conjugated peptide or protein. The treatment of both cell lines and mouse models demonstrates that this method of molecular targeting results in equal if not greater efficacy than current standards of care, including DNA damaging agents and topoisomerase inhibitors. For the treatment of invasive carcinoma, these CTTs have significant clinical potential to deliver highly targeted therapies without sacrificing the patients quality of life.
Various kinds of lipoamino acids including a novel serine‐containing lipid in an opportunistic pathogen Flavobacterium (1988)

Lipoamino acids were found to represent 60% of the total extractable cellular lipids in Flavobacterium meningosepticum and F. indologenes which are known to be opportunistic pathogens. The structures of the lipoamino acids were resolved by chemical and physicochemical methods. Three kinds of lipoamino acids were included in the lipid of Flavobacterium: 3-hydroxyisoheptadecanoic acid amide-linked to serine and esterified to isopentadecanoic acid, and 3-hydroxyisoheptadecanoic acid amide-linked to ornithine and esterified to isopentadecanoic acid or 2-hydroxyisopentadecanoic acid. This type of serine-containing lipid is a novel, rare substance and exhibited high hemagglutinating activity (minimum hemagglutinating concentration was 0.25-0.5 micrograms/ml) with very good, stable dispersion of its liposomes. We called the serine-containing lipid 'flavolipin', based on the genus name of the bacteria. Of the two types of the ornithine-containing lipids, the one that had a nonpolar terminal fatty acid showed higher hemagglutinating activity than the one that had a polar terminal fatty acid. The reconstituted liposomes whose lipid composition was similar to that of the original bacterial cell membrane exhibited definite hemagglutinating activity. As soon as a terminal fatty acid of the lipoamino acids was lost, their biological activity on erythrocytes changed from hemagglutinating to hemolytic, being accompanied by the disappearance of animal species specificity. The mechanism of both the hemagglutination and the hemolysis was discussed.
The next-generation Endeavor Resolute stent: 4-month clinical and angiographic results from the Endeavor Resolute first-in-man trial. (2007)

The 4 month results in this subset of Endeavor Resolute patients demonstrated excellent procedural and device success when deployed in lesions up to 27 mm of length. The Endeavor Resolute stent, in this subset, was associated with a low in-stent late lumen loss and a minimal amount of neointimal hyperplastic in-growth.
Tissue expression and developmental regulation of chicken cathelicidin antimicrobial peptides (2012)

Cathelicidins are a major family of antimicrobial peptides present in vertebrate animals with potent microbicidal and immunomodulatory activities. Four cathelicidins, namely fowlicidins 1 to 3 and cathelicidin B1, have been identified in chickens. As a first step to understand their role in early innate host defense of chickens, we examined the tissue and developmental expression patterns of all four cathelicidins. Real-time PCR revealed an abundant expression of four cathelicidins throughout the gastrointestinal, respiratory, and urogenital tracts as well as in all primary and secondary immune organs of chickens. Fowlicidins 1 to 3 exhibited a similar tissue expression pattern with the highest expression in the bone marrow and lung, while cathelicidin B1 was synthesized most abundantly in the bursa of Fabricius. Additionally, a tissue-specific regulatory pattern was evident for all four cathelicidins during the first 28 days after hatching. The expression of fowlicidins 1 to 3 showed an age-dependent increase both in the cecal tonsil and lung, whereas all four cathelicidins were peaked in the bursa on day 4 after hatching, with a gradual decline by day 28. An abrupt augmentation in the expression of fowlicidins 1 to 3 was also observed in the cecum on day 28, while the highest expression of cathelicidin B1 was seen in both the lung and cecal tonsil on day 14. Collectively, the presence of cathelicidins in a broad range of tissues and their largely enhanced expression during development are suggestive of their potential important role in early host defense and disease resistance of chickens.
Interleukin-17 (1998)

The particular interest of IL-17, a homodimeric cytokine of about 32 kDa, is the strict requirement for an activation signal to induce its expression from a rather restricted set of cells, human memory T cells or mouse alpha beta TCR+CD4-CD8- thymocytes. In contrast with the tightly controlled expression pattern of this gene, the IL-17 receptor, a novel cytokine receptor, is ubiquitously distributed but apparently more abundant in spleen and kidney. In addition to its capture by the T lymphotropic Herpesvirus Saimiri (HVS), this cytokine is inducing the secretion of IL-6, IL-8, PGE2, MCP-1 and G-CSF by adherent cells like fibroblasts, keratinocytes, epithelial and endothelial cells. IL-17 is also able to induce ICAM-1 surface expression, proliferation of T cells, and growth and differentiation of CD34+ human progenitors into neutrophils when cocultured in presence of irradiated fibroblasts. In vitro, IL-17 synergizes with other proinflammatory signals like TNF alpha for GM-CSF induction, and with CD40-ligand for IL-6, IL-8, RANTES and MCP-1 secretion from kidney epithelial cells. In vivo, injection of IL-17 induces a neutrophilia, except in IL-6-KO mice. The involvement of IL-17 in rejection of kidney graft has also been demonstrated. The role of this T cell secreted factor in various inflammatory processes is presently investigated.
Quantitative Automated Microscopy (QuAM) Elucidates Growth Factor Specific Signalling in Pain Sensitization (2010)

QuAM is a suitable if not necessary tool to analyze activation of endogenous signalling in heterogeneous cultures. NGF, GDNF and EGF stimulation of DRG-neurons shows differential Erk1/2 activation responses and a corresponding differential behavioral phenotype. Thus, in addition to expression-markers also signalling-activity can be taken for functional subgroup differentiation and as predictor of behavioral outcome. The anti-nociceptive function of EGF is an intriguing result in the context of tissue damage but also for understanding pain resulting from EGF-receptor block during cancer therapy.
Structures of the Apo and FAD‐Bound Forms of 2‐Hydroxybiphenyl 3‐monooxygenase (HbpA) Locate Activity Hotspots Identified by Using Directed Evolution (2015)

The FAD-dependent monooxygenase HbpA from Pseudomonas azelaica HBP1 catalyses the hydroxylation of 2-hydroxybiphenyl (2HBP) to 2,3-dihydroxybiphenyl (23DHBP). HbpA has been used extensively as a model for studying flavoprotein hydroxylases under process conditions, and has also been subjected to directed-evolution experiments that altered its catalytic properties. The structure of HbpA has been determined in its apo and FAD-complex forms to resolutions of 2.76 and 2.03 Å, respectively. Comparisons of the HbpA structure with those of homologues, in conjunction with a model of the reaction product in the active site, reveal His48 as the most likely acid/base residue to be involved in the hydroxylation mechanism. Mutation of His48 to Ala resulted in an inactive enzyme. The structures of HbpA also provide evidence that mutants achieved by directed evolution that altered activity are comparatively remote from the substrate-binding site.
The proatherogenic properties of lipoprotein(a) may be enhanced through the formation of circulating immune complexes containing Chlamydia pneumoniae -specific IgG antibodies (2000)

The proatherogenic effects of Lp(a) may be enhanced and/or partly mediated through the formation of circulating immune complexes containing C. pneumoniae -specific IgG antibodies. The connection between chronic C. pneumoniae infections and atherosclerosis may, at least in part, be explained by an interaction with Lp(a) through the formation of circulating immune complexes.
Class II HLA-DC beta-chain DNA restriction fragments differentiate among HLA-DR2 individuals in insulin-dependent diabetes and multiple sclerosis. (1984)

HLA-DR2 allele is negatively associated with insulin-dependent diabetes and positively associated with multiple sclerosis (MS). A 2.2-kilobase-pair EcoRI DNA restriction fragment detected with a beta-chain HLA-DC cDNA probe was found to be strongly correlated with HLA-DR2 in the normal population, but was absent in HLA-DR2 insulin-dependent diabetic patients. This fragment was found in HLA-DR2 multiple sclerosis patients with the same frequency as in controls. A beta-chain HLA-DC 12-kilobase-pair BamHI fragment might differentiate multiple sclerosis patients from healthy individuals.
Decision Forest:  Combining the Predictions of Multiple Independent Decision Tree Models (2003)

The techniques of combining the results of multiple classification models to produce a single prediction have been investigated for many years. In earlier applications, the multiple models to be combined were developed by altering the training set. The use of these so-called resampling techniques, however, poses the risk of reducing predictivity of the individual models to be combined and/or over fitting the noise in the data, which might result in poorer prediction of the composite model than the individual models. In this paper, we suggest a novel approach, named Decision Forest, that combines multiple Decision Tree models. Each Decision Tree model is developed using a unique set of descriptors. When models of similar predictive quality are combined using the Decision Forest method, quality compared to the individual models is consistently and significantly improved in both training and testing steps. An example will be presented for prediction of binding affinity of 232 chemicals to the estrogen receptor.
[Correlation between expression of metastasis-related genes and lymph node metastasis in testicular cancer]. (2000)

To investigate the factors related to lymph node metastasis of testicular germ cell tumors, we first established a seminoma orthotopic model with lymph node metastasis in SCID mice by inoculating small fragments from subcutaneous xenografts. Second, we compared the expression patterns of metastasis-related genes of the seminoma xenografts and of the TCam-2 cells which were established as a seminoma cell line from a primary testicular seminoma. Third, we immunohistochemically analyzed human germ cell tumors (25 seminomas, 17 nonseminomas) using monoclonal antibodies to CD34, VEGF, VEGF-C, Flt-4, MMP-2 and E-cadherin. Testicular seminoma xenografts grew in 32/32 (100%) of the inoculated mice, of which 15 (47%) developed macroscopic metastasis to the renal hilar lymph node. Circulating tumor cells were detectable by using a PCR assay for the human beta-globin gene in 25/32 (78%) mice, although metastatic foci were not histologically evident in the visceral organs, including lungs, liver, kidneys and spleen. This may reflect the lymphophilic characteristics of the seminoma cells used. Regarding mRNA expression of metastasis-related genes, an increased expression of MMP-2 and VEGF compared with that in the s.c. xenografts was demonstrated by RT-PCR assay in the testicular seminoma xenografts. In addition, uPAR, MMP-1, MMP-2, MT1-MMP and MT3-MMP showed a a stronger expression and PAI-2 a weaker expression in the seminoma xenografts than did TCam-2 cells. These results suggest a higher metastatic potential of the seminoma xenografts, especially testicular xenografts, as compared with TCam-2 cells. In the immunohistochemical study, a significant correlation was found between MMP-2 expression and lymph node metastasis, which is compatible with the results for the metastasis-related gene expression from the seminoma xenografts.
Mice Deficient in Complement Receptors 1 and 2 Lack a Tissue Injury-Inducing Subset of the Natural Antibody Repertoire (2002)

Intestinal ischemia-reperfusion (IR) injury is initiated when natural Abs recognize neoantigens that are revealed on ischemic cells. Cr2(-/-) mice, deficient in complement receptors (CR)1 and CR2, demonstrate defects in T-dependent B-2 B cell responses to foreign Ags and have also been suggested to manifest abnormalities of the B-1 subset of B lymphocytes. To determine whether these CRs might play a role in the generation of the natural Abs that initiate intestinal IR injury, we performed experiments in Cr2(-/-) and control Cr2(+/+) mice. We found that Cr2(-/-) mice did not demonstrate severe intestinal injury that was readily observed in control Cr2(+/+) mice following IR, despite having identical serum levels of IgM and IgG. Pretreatment of Cr2(-/-) mice before the ischemic phase with IgM and IgG purified from the serum of wild-type C57BL/6 mice reconstituted all key features of IR injury, demonstrating that the defect involves the failure to develop this subset of natural Abs. Pretreatment with IgM and IgG individually demonstrates that each contributes to unique features of IR injury. In sum, CR2/CR1 play an unanticipated but critical role in the development of a subset of the natural Ab repertoire that has particular importance in the pathogenesis of IR injury.
A Natural Disruption of the Secretory Group II Phospholipase A2 Gene in Inbred Mouse Strains (1995)

The synovial fluid or group II secretory phospholipase A2 (sPLA2) has been implicated as an important agent involved in a number of inflammatory processes. In an attempt to determine the role of sPLA2 in inflammation, we set out to generate sPLA2-deficient mice. During this investigation, we observed that in a number of inbred mouse strains, the sPLA2 gene was already disrupted by a frameshift mutation in exon 3. This mutation, a T insertion at position 166 from the ATG of the cDNA, terminates out of frame in exon 4, resulting in the disruption of the calcium binding domain in exon 3 and loss of both activity domains coded by exons 4 and 5. The mouse strains C57BL/6, 129/Sv, and B10.RIII were found to be homozygous for the defective sPLA2 gene, whereas outbred CD-1:SW mice had variable genotype at this locus. BALB/c, C3H/HE, DBA/1, DBA/2, NZB/BIN, and MRL lpr/lpr mice had a normal sPLA2 genotype. The sPLA2 mRNA was expressed at very high levels in the BALB/c mouse small intestine, whereas in the small intestine of the sPLA2 mutant mouse strains, sPLA2 mRNA was undetectable. In addition, PLA2 activity in acid extracts of the small intestine were approximately 40 times higher in BALB/c than in the mutant mice. Transcription of the mutant sPLA2 gene resulted in multiple transcripts due to exon skipping. None of the resulting mutant mRNAs encoded an active product. The identification of this mutation should not only help define the physiological role of sPLA2 but also has important implications in mouse inflammatory models developed by targeted mutagenesis.
Maximum weight matching via max-product belief propagation (2005)

The max-product "belief propagation" algorithm is an iterative, local, message passing algorithm for finding the maximum a posteriori (MAP) assignment of a discrete probability distribution specified by a graphical model. Despite the spectacular success of the algorithm in many application areas such as iterative decoding and computer vision which involve graphs with many cycles, theoretical convergence results are only known for graphs which are tree-like or have a single cycle. In this paper, we consider a weighted complete bipartite graph and define a probability distribution on it whose MAP assignment corresponds to the maximum weight matching (MWM) in that graph. We analyze the fixed points of the max-product algorithm when run on this graph and prove the surprising result that even though the underlying graph has many short cycles, the maxproduct assignment converges to the correct MAP assignment. We also provide a bound on the number of iterations required by the algorithm
Vascular Smooth Muscle Cell Senescence Promotes Atherosclerosis and Features of Plaque Vulnerability (2015)

We conclude that plaque VSMC senescence in atherosclerosis is associated with loss of TRF2. VSMC senes cence promotes both atherosclerosis and features of plaque vulnerability, identifying prevention of senescence as a potential target for intervention.
Nucleation and crystallization process of silicon using Stillinger-Weber potential (2004)

We study the homogeneous nucleation process in Stillinger-Weber silicon in the NVT ensemble. A clear first-order transition from the liquid to crystal phase is observed thermodynamically with kinetic and structural evidence of the transformation. At 0.75 T_m, the critical cluster size is about 175 atoms. The lifetime distribution of clusters as a function of the maximum size their reach follows an inverse gaussian distribution as was predicted recently from the classical theory of nucleation (CNT). However, while there is a qualitative agreement with the CNT, the free energy curve obtained from the simulations differs significantly from the theoretical predictions, suggesting that the low-density liquid phase found recently could play a role in the nucleation process.
The Lebanese allele at the low density lipoprotein receptor locus. Nonsense mutation produces truncated receptor that is retained in endoplasmic reticulum. (1987)

We here describe a mutant low density lipoprotein receptor gene that produces a shortened receptor protein lacking three domains: the region of clustered O-linked carbohydrates, the membrane-spanning region, and the cytoplasmic tail. The defect is attributable to a single nucleotide substitution that creates a premature termination codon at amino acid 660, eliminating 180 residues from the mature protein. The truncated protein retains only two domains: a complete ligand-binding region (residues 1-292) and a partial epidermal growth factor precursor homology region (residues 293-659). The termination codon occurs in the middle of a cysteine-rich sequence that is part of the epidermal growth factor precursor homology domain. The mutant protein is present in markedly reduced amounts and may be translated at a reduced rate. After synthesis, most of the receptor remains within the cell for several hours with its N-linked carbohydrate in an unprocessed endoglycosidase H-sensitive form. This finding suggests that the shortened receptor leaves the endoplasmic reticulum at an abnormally slow rate, which is likely attributable to abnormal folding of the truncated protein. The mutation creates a new restriction site for the enzyme HinfI, thus permitting diagnosis by Southern blotting of genomic DNA. Two copies of this mutant gene were present in each of four unrelated Arab patients with homozygous familial hypercholesterolemia (three from Lebanon and one from Syria). We believe that this mutation, hereafter referred to as the "Lebanese allele," is responsible for the extraordinarily high incidence of familial hypercholesterolemia in Lebanon.
Control and image decoding software for portable gamma-ray imaging system with coded aperture (2003)

The Coded Mask Gamma Vision Camera is an experimental computer controlled prototype of a portable device for gamma-ray imaging. The imaging with this system is based on using of coded aperture and combined detector, which includes a scintillator plate and image intensifiers and CCD-camera for signal readout. As coded aperture the hexagonal URA and MURA masks of ranks 6, 9, 11 and 13 are used. The software package makes the following operations: control of all systems of the imager and acquisition of shadow pictures, reconstruction of the initial gamma-image and work with images obtained earlier. The software allowing simulation of shadowgram acquisition with real devices based on a combined detector is briefly described. With this package some configurations of new devices, which may be interesting from a practical point of view were studied.
Complete coding sequence and deduced primary structure of the human cartilage large aggregating proteoglycan, aggrecan. Human-specific repeats, and additional alternatively spliced forms. (1991)

We have obtained the complete coding sequence of the large aggregating chondroitin sulfate proteoglycan of human cartilage (aggrecan) from a combination of cDNA and genomic exon sequencing. We screened a human costal chondrocyte cDNA library, using rat aggrecan cDNA probes, and obtained three nonoverlapping clones totaling 6.2 kilobases in length. These clones were sequenced, and the sequence of the gaps between clones was obtained from genomic exon fragments and polymerase chain reaction-amplified cDNA. The composite sequence is 7137 nucleotides long, encoding 2316 amino acids. The human and rat aggrecan amino acid sequences are about 75% identical, with domains ranging from 100% to about 60% of conserved amino acids. The human sequence contains two regions of highly conserved repeats not found in rat aggrecan: 11 repeats of a hexameric sequence in the keratan sulfate attachment domain, E-E-P-(S,F)-P-S; and a 19-amino acid sequence reiterated 19 times, in the CS-1 portion of the serine-glycine-containing region. There are at least three forms of aggrecan transcripts, generated by alternative exon usage, and the form reported here is the shortest and also the most prevalent, lacking both the epidermal growth factor-like domain, and the complement regulatory protein-like sequence.
Embedded micromechanical devices for the monolithic integration of MEMS and CMOS (1995)

Short communication.