gebhart/patrepeval huggingface dataset:
Direct demonstration of elevated aldehyde dehydrogenase in human hematopoietic progenitor cells (1990)

Relative levels of cytoplasmic aldehyde dehydrogenase (ALDH) were determined in selected subpopulations of normal human bone marrow cells using a flow cytometric assay that simultaneously detects a cell surface antigen (as a marker of cell lineage and developmental stage) and the level of ALDH. The intracellular level of this enzyme has been shown to be directly related to cellular resistance to activated cyclophosphamide and is believed to be important in the survival of cells capable of repopulating marrow in autologous bone marrow transplant procedures. Western blot analysis and flow cytometric analysis of four murine cell lines with known ALDH levels were used to establish the relation between ALDH content and fluorescence with an affinity-purified anti-mouse ALDH antibody. An affinity purified anti-human ALDH antibody, characterized by immunoblotting of cytosolic extracts of cell lines with known ALDH content, was used to determine relative ALDH levels in the marrow subpopulations. We found that hematopoietic progenitor cells express the highest level of ALDH, while lymphocytes express the lowest level. Immature erythroid cells express ALDH at a level intermediate between progenitor cells and lymphocytes.
Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix (2006)

Mechanisms leading to fibroblast accumulation during pulmonary fibrogenesis remain unclear. Although there is in vitro evidence of lung alveolar epithelial-to-mesenchymal transition (EMT), whether EMT occurs within the lung is currently unknown. Biopsies from fibrotic human lungs demonstrate epithelial cells with mesenchymal features, suggesting EMT. To more definitively test the capacity of alveolar epithelial cells for EMT, mice expressing beta-galactosidase (beta-gal) exclusively in lung epithelial cells were generated, and their fates were followed in an established model of pulmonary fibrosis, overexpression of active TGF-beta1. beta-gal-positive cells expressing mesenchymal markers accumulated within 3 weeks of in vivo TGF-beta1 expression. The increase in vimentin-positive cells within injured lungs was nearly all beta-gal-positive, indicating epithelial cells as the main source of mesenchymal expansion in this model. Ex vivo, primary alveolar epithelial cells cultured on provisional matrix components, fibronectin or fibrin, undergo robust EMT via integrin-dependent activation of endogenous latent TGF-beta1. In contrast, primary cells cultured on laminin/collagen mixtures do not activate the TGF-beta1 pathway and, if exposed to active TGF-beta1, undergo apoptosis rather than EMT. These data reveal alveolar epithelial cells as progenitors for fibroblasts in vivo and implicate the provisional extracellular matrix as a key regulator of epithelial transdifferentiation during fibrogenesis.
Complement factor H and the hemolytic uremic syndrome (2007)

Immune recognition is coupled to powerful proinflammatory effector pathways that must be tightly regulated. The ancient alternative pathway of complement activation is one such proinflammatory pathway. Genetic susceptibility factors have been identified in both regulators and activating components of the alternative pathway that are associated with thrombotic microangiopathies, glomerulonephritides, and chronic conditions featuring debris deposition. These observations indicate that excessive alternative pathway activation promotes thrombosis in the microvasculature and tissue damage during debris accumulation. Intriguingly, distinct genetic changes in factor H (FH), a key regulator of the alternative pathway, are associated with hemolytic uremic syndrome (HUS), membranoproliferative glomerulonephritis (dense deposit disease), or age-related macular degeneration (AMD). A mouse model of HUS designed to mirror human mutations in FH has now been developed, providing new understanding of the molecular pathogenesis of complement-related endothelial disorders.
A regulatory system for target gene expression (1998)

Temporally-regulated expression of endogenous genes is a desirable goal in stable cell line and transgenic animal systems, as well as in clinical gene therapy. Protocols for introducing genes into stable cell lines and experimental animals are often unsatisfactory due to the constitutive expression of such transgenes. To circumvent this problem we have demonstrated specific and temporally regulable expression of a target gene in vivo effected by a chimeric regulator in response to an orally-administered, non-toxic chemical. This regulatory system utilizes a chimeric regulator GLVP, consisting of a mutated human progesterone receptor ligand binding domain (PRLBD-delta) fused to the yeast GAL4 DNA binding domain (DBD) and the HSV VP16 transcriptional activation domain and whose activity is solely regulable by non-physiological doses of RU486 but not by progesterone or other endogenous progestins. Replacing the activation domain of the chimeric regulator with a transcriptional repression domain results in inducible repression of target gene expression in vitro. Our regulatory system functions in transient and stable transfections as well as in transgenic animals, and will have a wide variety of potential applications.
Annexin-1 and Peptide Derivatives Are Released by Apoptotic Cells and Stimulate Phagocytosis of Apoptotic Neutrophils by Macrophages (2007)

The resolution of inflammation is a dynamically regulated process that may be subverted in many pathological conditions. Macrophage (Mphi) phagocytic clearance of apoptotic leukocytes plays an important role in the resolution of inflammation as this process prevents the exposure of tissues at the inflammatory site to the noxious contents of lytic cells. It is increasingly appreciated that endogenously produced mediators, such as lipoxins, act as potent regulators (nanomolar range) of the phagocytic clearance of apoptotic cells. In this study, we have investigated the intriguing possibility that apoptotic cells release signals that promote their clearance by phagocytes. We report that conditioned medium from apoptotic human polymorphonuclear neutrophils (PMN), Jurkat T lymphocytes, and human mesangial cells promote phagocytosis of apoptotic PMN by Mphi and THP-1 cells differentiated to a Mphi-like phenotype. This prophagocytic activity appears to be dose dependent, sensitive to the caspase inhibitor zVAD-fmk, and is associated with actin rearrangement and release of TGF-beta1, but not IL-8. The prophagocytic effect can be blocked by the formyl peptide receptor antagonist Boc2, suggesting that the prophagocytic factor(s) may interact with the lipoxin A(4) receptor, FPRL-1. Using nanoelectrospray liquid chromatography mass spectrometry and immunodepletion and immunoneutralization studies, we have ascertained that annexin-1 and peptide derivatives are putative prophagocytic factors released by apoptotic cells that promote phagocytosis of apoptotic PMN by M[phi] and differentiated THP-1 cells. These data highlight the role of annexin-1 and peptide derivatives in promoting the resolution of inflammation and expand on the therapeutic anti-inflammatory potential of annexin-1.
Only One Splice Variant of the Human TAZ Gene Encodes a Functional Protein with a Role in Cardiolipin Metabolism (2003)

Barth syndrome (BTHS) is an X-linked recessive disorder caused by mutations in the TAZ gene and is characterized by cardiomyopathy, short stature, neutropenia, and 3-methylglutaconic aciduria. Recently it was found that BTHS patients exhibit a profound cardiolipin deficiency although the biosynthetic capacity to synthesize this lipid from its precursor phosphatidylglycerol is entirely normal. Like BTHS patients, a Saccharomyces cerevisiae strain, in which the yeast orthologue of the human TAZ gene has been disrupted, exhibits an abnormal cardiolipin profile as determined by tandem mass spectrometry. Additionally, this yeast strain grows poorly on non-fermentable carbon sources. We have used both properties of this yeast disruptant as a read-out system to test the physiological functionality of each of 12 different splice variants that have been reported for the human TAZ gene. Our results demonstrate that only the splice variant lacking exon 5 was able to complement the retarded growth of the yeast disruptant on selective plates and restore the cardiolipin profile to the wild type pattern. We conclude that this splice variant most likely represents the only physiologically important mRNA, at least with regard to cardiolipin metabolism.
Photoluminescence from nanosize gold clusters (1998)

We have observed visible light emission from nanosize gold clusters. Liquid chromatographic analysis of the metal clusters shows that relatively intense photoluminescence occurs only when the size of the metal nanocluster is sufficiently small (&amp;lt;5 nm). The emission is strongly Stokes shifted and is assigned to radiative recombination of Fermi level electrons and sp- or d-band holes. The electron and/or hole states are perturbed by surface states, as indicated by the dependence of the emission spectrum on the nature of the cluster surface. Finally, we found that large, nonemitting gold clusters can also be made luminescent by partial dissolution using KCN.
Context-Aware Computing: The CyberDesk Project (1998)

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is known to interact with a cytosolic receptor and, in turn, activate transcription of the mouse P1(450) gene. Various lengths of DNA upstream of the P1(450) gene were inserted into the pSV0-cat expression vector, with and without addition of the Harvey murine sarcoma virus (Ha-MSV) 72-bp repeat enhancer element. The constructs were cotransfected with pSV2-neo into mouse hepatoma wild-type cells and two variant cell lines. One variant is believed to result from a mutation in the P1(450) structural gene and expresses high levels of P1(450) mRNA constitutively; the other variant has a defect in nuclear translocation of the inducer-receptor complex. After selection in G418, the cells were treated with control medium, TCDD, cycloheximide, or TCDD plus cycloheximide and then assayed for chloramphenicol acetyltransferase (CAT) activity. The data are consistent with the presence of several functional regions within the upstream sequence: a promoter region, a region that is negatively autoregulated, possible repressor-binding and inducer-receptor complex-binding sites, and an upstream activation element that is required for transcriptional activation by TCDD. The Ha-MSV enhancer can substitute for this upstream activation element.
Coping with multiple sclerosis: a music therapy viewpoint (2005)

This article introduces coping theory, from the health sociology literature, to the setting of music therapy with people experiencing the chronic degenerative neurological condition, Multiple Sclerosis (MS). Three factors influencing whether a person copes successfully are their (a) style of coping used, (b) perception of control over life events, and (c) sense of self (Updegraff and Taylor, 2000). Factors relevant to the coping process were identified in the literature about music therapy with those experiencing MS. Three case vignettes describing music therapy with women experiencing severe, secondary progressive MS are examined for evidence of coping processes. Coping strategies identified within sessions included active, avoidant, and acceptance and positive interpretation styles (Updegraff, 2000). Music therapy sessions also addressed factors of patient control and sense of self, which are crucial for functional coping. Music therapists are encouraged to investigate the coping with chronic illness literature, recognise the use of particular coping styles in their clients, and integrate this knowledge into existing music therapy practice. (author abstract)
TSG‐6 interacts with hyaluronan and aggrecan in a pH‐dependent manner via a common functional element: implications for its regulation in inflamed cartilage (1998)

Cartilage matrix is stabilised by the interactions of proteins with hyaluronan (HA). We compare the pH dependences of HA binding by aggrecan, link protein and TSG-6. Aggrecan and link protein exhibit maximal binding across a wide pH range (6.0-8.0). TSG-6, a protein that is only produced during inflammation, binds maximally at about pH 6.0 but shows a dramatic loss of function with increasing pH. TSG-6 also interacts with aggrecan, with a similar pH dependence, and this can be inhibited by HA. Thus, a common binding surface on TSG-6 may be involved in HA and aggrecan binding. We propose that TSG-6 is involved in matrix dissociation and that this is regulated by pH gradients in cartilage.
Zirconium-89 Labeled Antibodies: A New Tool for Molecular Imaging in Cancer Patients (2014)

Antibody based positron emission tomography (immuno-PET) imaging is of increasing importance to visualize and characterize tumor lesions. Additionally, it can be used to identify patients who may benefit from a particular therapy and monitor the therapy outcome. In recent years the field is focused on (89)Zr, a radiometal with near ideal physical and chemical properties for immuno-PET. In this review we will discuss the production of (89)Zr, the bioconjugation strategies, and applications in (pre-)clinical studies of (89)Zr-based immuno-PET in oncology. To date, (89)Zr-based PET imaging has been investigated in a wide variety of cancer-related targets. Moreover, clinical studies have shown the feasibility for (89)Zr-based immuno-PET to predict and monitor treatment, which could be used to tailor treatment for the individual patient. Further research should be directed towards the development of standardized and robust conjugation methods and improved chelators to minimize the amount of released Zr(4+) from the antibodies. Additionally, further validation of the imaging method is required. The ongoing development of new (89)Zr-labeled antibodies directed against novel tumor targets is expected to expand applications of (89)Zr-labeled immuno-PET to a valuable method in the medical imaging.
Vaginal Mucosal Vaccine for Recurrent Urinary Tract Infections in Women: Results of a Phase 2 Clinical Trial (2007)

This study demonstrated the efficacy of vaginal mucosal immunization with a multivalent vaccine in reducing recurrence of E. coli urinary tract infections. The results suggest that the vaccine may provide the most benefit to sexually active women in the 20 to 50-year-old age group.
The integrin alpha IIb-beta 3, platelet glycoprotein IIb-IIIa, can form a functionally active heterodimer complex without the cysteine-rich repeats of the beta 3 subunit. (1994)

Integrin alpha IIb-beta 3 binds fibrinogen via the recognition sequence Arg-Gly-Asp-Ser (RGDS). We have used the baculovirus/insect cell expression system to study the structural requirements for the formation of a functionally active fragment of alpha IIb-beta 3. A tandem baculovirus transfer vector was constructed containing the cDNA coding for the heavy chain of human alpha IIb (alpha IIbH, amino acids 1-874) and the cDNA coding for a truncated form of human beta 3 (t beta 3; amino acids 1-469). Sf9 insect cells were infected with the corresponding baculovirus, and the produced soluble recombinant proteins were purified using an RGD-like affinity column. The bound receptor fragments were specifically eluted with RGDS and existed as a heterodimeric complex (rec alpha IIbH-t beta 3) with an apparent M(r) of 160,000. In an immunocapture assay, the monoclonal antibody pl-55, which only recognizes the functionally active form of alpha IIb-beta 3, bound to the purified complex. Rec alpha IIbH-t beta 3 specifically bound 125I-fibrinogen with an affinity comparable with that of purified platelet alpha IIb-beta 3. Electron micrographs of rotary-shadowed rec alpha IIbH-t beta 3 showed that the complex had the characteristic globular head, but the two rodlike tails were 4-6 nm shorter than those found in intact alpha IIb-beta 3. Thus, the cysteine-rich repeats of beta 3 are not required for assembly, stability, and functional activity of this integrin.
Childhood cerebral form of adrenoleukodystrophy: short-term effect of bone marrow transplantation on brain MR observations. (1994)

Bone marrow transplantation can affect brain MR observations in childhood-onset cerebral adrenoleukodystrophy. Although brain MR findings do not typically resolve, they do seem to stabilize, which is an improvement over the natural MR history of the disease.
Hydrophobic surfactant-associated polypeptides: SP-C is a lipopeptide with two palmitoylated cysteine residues, whereas SP-B lacks covalently linked fatty acyl groups. (1990)

Pulmonary surfactant contains two hydrophobic polypeptides, SP-B and SP-C, with known amino acid sequences and with truncated subforms lacking the N-terminal residues. Treatment of SP-C with KOH releases fatty acids (palmitic acid to more than 85%) in molar ratios of 1.8-2.0 relative to the polypeptide. Furthermore, plasma-desorption mass spectrometry shows native SP-C of both the intact and truncated types to be monomers with masses about 500 units higher than those expected for the polypeptide chains. After treatment with KOH, trimethylamine, or dithioerythritol, the polypeptide masses are obtained. These results prove that native SP-C is a lipopeptide with two palmitoyl groups covalently linked to the polypeptide chain. The deacylation conditions, the presence of two cysteine residues in the polypeptide, and the absence of other possible attachment sites establish that the palmitoyl groups are thioester-linked to the two adjacent cysteine residues. In contrast, the major form of porcine SP-B is a dimer without fatty acid components. That SP-C is a true lipopeptide with covalently bound palmitoyl groups suggests possibilities for functional interactions. It gives a direct physical link between SP-C and surfactant phospholipid components. Long-chain acylation may constitute a means for association of proteins with membranes and could conceivably modulate the stability and biological activity of surfactant films.
New synonymy and new species of American bark beetles (Coleoptera: Scolytidae), Part III (1976)

New synonomy is proposed as follows: Metacorthylus Blandford ( = Paracorthylus Wood), Corthylus spinifer Schwarz (= Corthylus tomentosus Schedl), Cryptocarinus brevicollis Eggers ( = Cryptocarenus coronatus Wood), Dendrocranulus guatemalensis (Hopkins), n. comb. (= Dendrocranulus parallelus Schedl), Dendroterus mexicanus Blandford (=Conophthocranulus umbratus Schedl), Hypothenemus cylindricus (Hopkins) (= Hypothenemus guadeloupensis Schedl), Hypothenemus erectus LeConte (= Stephanoderes discedens Schedl), Hypothenemus javanus (Eggers) (= Stephanoderes pistor Schedl, Stephanoderes prosper Schedl), Xyleborus pseudotenuis Schedl (= Xyleborus tenuis Schedl), and Xyleborus villosulus Blandford (= Xyleborus coccotrypoides Eggers, villosus Schedl). Scolytodes punctiferus n. n. is proposed for Scolytodes punctifer Wood, 1971 (nec Wood 1969). The following species are named as new to science: Amphicranus argutus, A. fulgidus, A. micans, Pityophthorus inops, P. debilis, P. strictus. P. galeritus. P. sobrinus, P. laetus, P. lenis, P. conspectus P. medialis (Costa Rica), P. perexiguus (Costa Rica and Panama), P. scitulus (Panama), P. costatulus, P. costabilis, P. detentus, P. nebulosus, P. melanurus, P. indigens, P. burserae, P. molestus, P. diligens, P. corruptus (Mexico), P. tenax, P. nugalis, P. minutalis (Guatemala), P. nemoralis, P. morosus, P. hermosus (Honduras), Araptus gracilens (Mexico).
Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria (2010)

Mucolytic bacteria are present in healthy humans, where they are an integral part of the mucosa-associated bacterial consortium. The disproportionate increase in R. gnavus and R. torques could explain increased total mucosa-associated bacteria in IBD.
Production and characterization of a murine/human chimeric anti-idiotype antibody that mimics ganglioside. (1992)

The VL and VH from a murine anti-idiotypic antibody that mimics ganglioside have been cloned, sequenced, and expressed as a chimeric mouse/human IgG1 antibody. The chimeric antibody retained a binding specificity indistinguishable from the original murine antibody. The VH was a member of Vgam 3.8 family. The sequences are discussed in terms of ways in which proteins may mimic ganglioside epitopes.
Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA hairpin structure (1998)

Using an in vitro selection approach we have previously isolated oligodeoxy aptamers that can bind to a DNA hairpin structure without disrupting the double-stranded stem. We report here that these oligomers can bind to the RNA version of this hairpin, mostly through pairing with a designed 6 nt anchor. The part of the aptamer selected against the DNA hairpin did not increase stability of the RNA-aptamer complex. However, it contributed to the binding site for Escherichia coli RNase H, leading to very efficient cleavage of the target RNA. In addition, a 2'- O -methyloligoribonucleotide analogue of one selected sequence selectively blocked in vitro translation of luciferase in wheat germ extract by binding to the hairpin region inserted upstream of the initiation codon of the reporter gene. Therefore, non-complementary oligomers can exhibit antisense properties following hybridization with the target RNA. Our study also suggests that in vitro selection might provide a means to extend the repertoire of sequences that can be targetted by antisense oligonucleotides to structured RNA motifs of biological importance.
Paclitaxel in cancer therapy (2002)

The last decade witnessed the introduction of exciting new chemotherapeutic agents. Among these, paclitaxel emerged as one of the most powerful compounds. Paclitaxel promotes the polymerisation of tubulin, thereby causing cell death by disrupting the normal microtubule dynamics required for cell division and vital interphase processes. Mechanisms of acquired resistance to paclitaxel include alterations of tubulin structure and the amplification of membrane phosphoglycoproteins that function as drug-efflux pumps. Toxicities associated with paclitaxel include hypersensitivity reaction, neurotoxicity and haematological toxicities. Toxicities may be both dose- and schedule-dependent. Paclitaxel has activity against a broad band of tumour types, including breast, ovarian, lung, head and neck cancers. Paclitaxel also has activity in other malignancies that are refractory to conventional chemotherapy, including previously-treated lymphoma and small cell lung cancers and oesophageal, gastric endometrial, bladder and germ cell tumours. Paclitaxel is also active against AIDS-associated Kaposi's sarcoma.