gebhart/patrepeval huggingface dataset:
Identification of metastasis-related microRNAs in hepatocellular carcinoma (2008)

MicroRNAs (miRNAs) have been used as cancer-related biomarkers. Hepatocellular carcinoma (HCC) is an aggressive cancer with a dismal outcome largely due to metastasis and postsurgical recurrence. We investigated whether the expression of certain miRNAs are associated with HCC metastasis. We examined the miRNA expression profiles of 482 cancerous and noncancerous specimens from radical resection of 241 patients with HCC. Using a supervised algorithm and a clinically well-defined cohort of 131 cases, we built a unique 20-miRNA metastasis signature that could significantly predict (P < 0.001) primary HCC tissues with venous metastases from metastasis-free solitary tumors with 10-fold cross-validation. However, significant miRNAs could not be identified from the corresponding noncancerous hepatic tissues. A survival risk prediction analysis revealed that a majority of the metastasis-related miRNAs were associated with survival. Furthermore, the 20-miRNA tumor signature was validated in 110 additional cases as a significant independent predictor of survival (P = 0.009) and was significantly associated with both survival and relapse in 89 cases of early stage HCC (P = 0.022 and 0.002, respectively). These 20 miRNAs may provide a simple profiling method to assist in identifying patients with HCC who are likely to develop metastases/recurrence. In addition, functional analysis of these miRNAs may enhance our biological understanding of HCC metastasis.
Specific inhibition of the reverse transcriptase of human immunodeficiency virus type 1 and the chimeric enzymes of human immunodeficiency virus type 1 and type 2 by nonnucleoside inhibitors (1993)

We have studied the effects of four nonnucleoside inhibitors, including the novel natural product inhibitor calanolide A, on molecular chimeras containing complementary segments of human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) reverse transcriptases (RTs). All four compounds specifically inhibited the DNA polymerase activity of HIV-1 RT but had no apparent effect on the RNase H activity of this enzyme or on the DNA polymerase or RNase H activity of HIV-2 RT. Three of these compounds showed the generally expected patterns of resistance and susceptibility with the various chimeric RTs. However, the inhibition patterns of the chimeric RTs by calanolide A provided evidence that there is a segment between residues 94 and 157 in HIV-1 RT that is critical for inhibition. However, the data also suggest that there may be a second segment located between amino acids 225 and 427 in HIV-1 RT that is also important for specifying susceptibility to the drug.
Mesenchymal stem cells contribute to the renal repair of acute tubular epithelial injury (2004)

Acute renal failure (ARF) is a common disease with high morbidity and mortality. Recovery from ARF is dependent on the replacement of necrotic tubular cells with functional tubular epithelium. Recent advancement in developmental biology led to the discovery of immature mesenchymal stem cells (MSCs) in bone marrow and several established organs and to the definition of their potential in the recovery from tissue injury. We investigated the effect of MSCs infusion on the recovery from ARF induced by intramuscle injection of glycerol in C57/BL6 mice. In this model, ARF is associated with an extensive necrosis of tubular epithelial cells due to myoglobin- and hemoglobin-induced injury. MSCs were obtained from bone marrow of transgenic mice expressing green fluorescent protein (GFP). MSC GFP-positive cells (MSC-GFP(+)) injected intravenously homed to the kidney of mice with glycerol-induced ARF but not to the kidney of normal mice. MSC-GFP(+) localized in the context of the tubular epithelial lining and expressed cytokeratin, indicating that MSCs engrafted in the damaged kidney, differentiated into tubular epithelial cells and promoted the recovery of morphological and functional alterations. Moreover, MSCs enhanced tubular proliferation as detected by the increased number of proliferating cell nuclear antigen (PCNA) positive cells. A significant contribution of the engrafted MSCs in the regeneration of tubular epithelial cells was shown by the presence of a consistent number of GFP(+) tubular cells 21 days after the induction of injury. In conclusion, these results indicated a tropism of MSCs for the injured kidney and a potential contribution of these cells to tubular regeneration and to the recovery from ARF.
Bombesin, vasopressin, and endothelin rapidly stimulate tyrosine phosphorylation in intact Swiss 3T3 cells. (1991)

The mitogenic neuropeptides bombesin and vasopressin markedly increased tyrosine and serine phosphorylation of multiple substrates in quiescent Swiss 3T3 fibroblasts, including two major bands of Mr 90,000 and 115,000. Tyrosine phosphorylation of these proteins was increased as judged by immunoprecipitation of 32Pi-labeled cells and immunoblotting of unlabeled cells with monoclonal antiphosphotyrosine antibodies, elution with phenyl phosphate, and phospho amino acid analysis. Phosphotyrosyl proteins generated by bombesin and vasopressin did not correspond either by apparent molecular weight or by immunological and biochemical criteria to several known tyrosine kinase substrates, including phospholipase C gamma, the microtubule-associated protein 2 kinase, GTPase-activating protein, or phosphatidylinositol kinase. The effect was rapid (within seconds), concentration dependent, and inhibited by specific receptor antagonists for both bombesin and vasopressin. The endothelin-related peptide, vasoactive intestinal contractor, also elicited a rapid and concentration-dependent tyrosine/serine phosphorylation of a similar set of substrates. These results demonstrate that neuropeptides, acting through receptors linked to GTP-binding proteins, stimulate tyrosine phosphorylation of a common set of substrates in quiescent Swiss 3T3 cells and suggest the existence of an additional signal transduction pathway in neuropeptide-induced mitogenesis.
GATA Transcription Factors and Cancer (2010)

It has been almost a quarter century since it was first appreciated that a class of oncogenes contained in rapidly transforming avian retroviruses encoded DNA-binding transcription factors. As with other oncogenes, genetic recombination with the viral genome led to their overexpression or functional alteration. In the years that followed, alterations of numerous transcription factors were shown to be causatively involved in various cancers in human patients and model organisms. Depending on their normal cellular functions, these factors were subsequently categorized as proto-oncogenes or tumor suppressor genes. This review focuses on the role of GATA transcription factors in carcinogenesis. GATA factors are zinc finger DNA binding proteins that control the development of diverse tissues by activating or repressing transcription. GATA factors thus coordinate cellular maturation with proliferation arrest and cell survival. Therefore, a role of this family of genes in human cancers is not surprising. Prominent examples include structural mutations in GATA1 that are found in almost all megakaryoblastic leukemias in patients with Down syndrome; loss of GATA3 expression in aggressive, dedifferentiated breast cancers; and silencing of GATA4 and GATA5 expression in colorectal and lung cancers. Here, we discuss possible mechanisms of carcinogenesis vis-à-vis the normal functions of GATA factors as they pertain to human patients and mouse models of cancer.
Genome-wide analysis of organ-preferential metastasis of human small cell lung cancer in mice. (2003)

Although a number of molecules have been implicated in the process of cancer metastasis, the organ-selective nature of cancer cells is still poorly understood. To investigate this issue, we established a metastasis model in mice with multiple organ dissemination by i.v. injection of human small cell lung cancer (SBC-5) cells. We analyzed gene-expression profiles of 25 metastatic lesions from four organs (lung, liver, kidney, and bone) using a cDNA microarray representing 23,040 genes and extracted 435 genes that seemed to reflect the organ specificity of the metastatic cells and the cross-talk between cancer cells and microenvironment. Furthermore, we discovered 105 genes that might be involved in the incipient stage of secondary-tumor formation by comparing the gene-expression profiles of metastatic lesions classified according to size (<1 or >2 mm) as either "micrometastases" or "macrometastases." This genome-wide analysis should contribute to a greater understanding of molecular aspects of the metastatic process in different microenvironments, and provide indicators for new strategies to predict and prevent metastasis.
The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches (2006)

Localized proliferation of lateral roots in NO(3)(-)-rich patches is a striking example of the nutrient-induced plasticity of root development. In Arabidopsis, NO(3)(-) stimulation of lateral root elongation is apparently under the control of a NO(3)(-)-signaling pathway involving the ANR1 transcription factor. ANR1 is thought to transduce the NO(3)(-) signal internally, but the upstream NO(3)(-) sensing system is unknown. Here, we show that mutants of the NRT1.1 nitrate transporter display a strongly decreased root colonization of NO(3)(-)-rich patches, resulting from reduced lateral root elongation. This phenotype is not due to lower specific NO(3)(-) uptake activity in the mutants and is not suppressed when the NO(3)(-)-rich patch is supplemented with an alternative N source but is associated with dramatically decreased ANR1 expression. These results show that NRT1.1 promotes localized root proliferation independently of any nutritional effect and indicate a role in the ANR1-dependent NO(3)(-) signaling pathway, either as a NO(3)(-) sensor or as a facilitator of NO(3)(-) influx into NO(3)(-)-sensing cells. Consistent with this model, the NRT1.1 and ANR1 promoters both directed reporter gene expression in root primordia and root tips. The inability of NRT1.1-deficient mutants to promote increased lateral root proliferation in the NO(3)(-)-rich zone impairs the efficient acquisition of NO(3)(-) and leads to slower plant growth. We conclude that NRT1.1, which is localized at the forefront of soil exploration by the roots, is a key component of the NO(3)(-)-sensing system that enables the plant to detect and exploit NO(3)(-)-rich soil patches.
Deconvolution of Combinatorial Libraries for Drug Discovery:  Experimental Comparison of Pooling Strategies (1996)

An experimental evaluation of several different pooling strategies for combinatorial libraries was conducted using a library of 810 compounds and an enzyme inhibition assay (phospholipase A2). The library contained compounds with varying degrees of activity as well as inactive compounds. The compounds were synthesized in groups of three and pooled together in various formats to realize different pooling strategies. With one exception, all iterative deconvolution strategies and position scanning resulted in identification of the same compound. The results are in good agreement with the predicted outcome from theoretical and computational methods. These data support the tenet that active compounds for pharmaceutically relevant targets can be successfully identified from combinatorial libraries organized in mixtures.
From Deformations to Parts: Motion-based Segmentation of 3D Objects (2012)

We develop a method for discovering the parts of an articulated object from aligned meshes of the object in various three-dimensional poses. We adapt the distance dependent Chinese restaurant process (ddCRP) to allow nonparametric discovery of a potentially unbounded number of parts, while simultaneously guaranteeing a spatially connected segmentation. To allow analysis of datasets in which object instances have varying 3D shapes, we model part variability across poses via affine transformations. By placing a matrix normal-inverse-Wishart prior on these affine transformations, we develop a ddCRP Gibbs sampler which tractably marginalizes over transformation uncertainty. Analyzing a dataset of humans captured in dozens of poses, we infer parts which provide quantitatively better deformation predictions than conventional clustering methods. 1
CD98, a novel marker of transient amplifying human keratinocytes (2005)

Identification of plasma membrane markers of basal keratinocytes is essential for sorting basal cells and, subsequently, adult epidermal stem cells. In this study, we isolated caveolin-1-enriched microdomains from human HaCaT keratinocytes and identified proteins representing potential cell surface markers of the epidermis by a proteomic approach. The purification of this caveolae domain allowed us to characterize 53 proteins of which 26% were transmembrane and 32% associated-membrane proteins. One of them, CD98, was found to be co-localized with beta1 integrin at the plasma membrane of the basal keratinocytes of healthy human epidermis. We then isolated CD98-positive keratinocytes from fresh skin biopsies. Using clonogenic assays, we demonstrate that CD98 may be considered as a marker of transient amplifying human keratinocytes.
Graft-through Synthesis and Assembly of Janus Bottlebrush Polymers from A-Branch-B Diblock Macromonomers (2016)

We report the synthesis of Janus bottlebrush block copolymers by graft-through polymerization of branched diblock macromonomers. Self-assembly of the bottlebrushes was characterized by small-angle X-ray scattering, atomic force microscopy, and scanning electron microscopy. Phase separation and packing models of the bottlebrushes were computed, and their self-assembly behavior was corroborated experimentally in bulk and in thin films. Lamellar, hexagonal cylinder, and gyroid phases were observed and modeled. The A-branch-B Janus bottlebrush structure provides several unique advantages in the context of bottlebrush polymer assembly, including access to the first examples of gyroid phases.
The development of T and non-T cell lineages from CD34+ human thymic precursors can be traced by the differential expression of CD44. (1995)

In addition to T-lineage cells, a small proportion of hematopoietic non-T cells are present in the human postnatal thymus. However, the origin of this minor non-T cell thymic compartment is presently unknown. In this study we have analyzed the developmental potential of the earliest human intrathymic precursors, characterized as CD34+ cells expressing intermediate levels of CD44. We show that these CD34+CD44int thymocytes cultured with interleukin 7 were able to develop simultaneously into both T- and non-T (monocytes and dendritic cells) -lineage cells. Both developmental pathways progress through a CD1+CD4+ intermediate stage, currently believed to be the immediate precursor of double positive thymocytes. However, separate progenitors for either T or non-T cells could be characterized within CD1+CD4+ thymocytes by their opposite expression of CD44. Downregulated levels of CD44 identified CD1+CD4+ T-lineage precursors, whereas CD44 upregulation occurred on CD1+CD4+ intermediates that later differentiated into non-T cells. Therefore, commitment of human early intrathymic precursors to either T or non-T cell lineages can be traced by the differential expression of the CD44 receptor.
Fibroblast aggregation by suspension with conjugates of poly(ethylene glycol) and RGD (1996)

Cell aggregates may be useful components of artificial organs and mammalian cell bioreactors, but many cells do not naturally aggregate. In a previous report,4 we described a method for promoting neural cell aggregation by addition of water-soluble conjugates of cell adhesion peptides, containing the three amino acid sequence Arg-Gly-Asp (RGD), and poly(ethylene glycol) (PEG). Here, we examined the mechanism of conjugate-induced aggregation using fibroblasts and a variety PEG-peptide conjugates. Aggregation was monitored during rotation culture of fibroblasts in the presence of unconjugated GRGDY and PEG; monofunctional (PEG-GRGDY) and bifunctional (GRGDY-PEG-GRGDY) conjugates; and bifunctional conjugates produced with a similar, but non-cell-binding, peptide (GRGEY-PEG-GRGEY). GRGDY-PEG-GRGDY conjugates induced rapid and pronounced fibroblast aggregation that was dose-dependent; at the highest concentration tested (5 mg/mL GRGDY-PEG-GRGDY), cell aggregates were produced more quickly (∼1 h) and were significantly larger at 24 h (mean radius ∼66 μm) than at slightly lower concentrations (1.7 and 3.3 mg/mL). Aggregation with GRGDY-PEG-GRGDY was completely inhibited by dissolved GRGDY (1.7 mg/mL). Neither unmodified GRGDY, unmodified PEG, PEG-GRGDY, nor GRGEY-PEG-GRGEY conjugates led to significant aggregation. The extent of aggregation depended on PEG molecular weight: conjugates with 3400 Mw PEG produced aggregates with significantly larger mean radius than conjugates with 20,000 Mw PEG. When 1N-8A fibroblasts, genetically engineered to produce recombinant nerve growth factor (NGF), were aggregated with GRGDY-PEG-GRGDY, aggregated cells produced more NGF per cell than nonaggregated cells. Aggregation of cells may lead to improved cell function, such as the increase in NGF production observed here, which could be useful in large-scale cell culture and construction of artificial organs or tissue transplants for tissue engineering. © 1996 John Wiley & Sons, Inc.
Mode of Action of the Antibacterial Compound Dequalinium Acetate (1969)

Dequalinium acetate is taken up rapidly by bacterial cells. Unlike the membrane-active drugs exemplified by cetrimide or chlorhexidine, its capacity for damaging the plasma membrane is low. The drug appears to penetrate quite rapidly into the cytoplasm where its effect seems to be exerted. A review of the evidence obtained in this study suggests that nucleic acid-containing components of the cell may be the prime target of this compound.
α-Synuclein propagates from mouse brain to grafted dopaminergic neurons and seeds aggregation in cultured human cells (2011)

Post-mortem analyses of brains from patients with Parkinson disease who received fetal mesencephalic transplants show that α-synuclein-containing (α-syn-containing) Lewy bodies gradually appear in grafted neurons. Here, we explored whether intercellular transfer of α-syn from host to graft, followed by seeding of α-syn aggregation in recipient neurons, can contribute to this phenomenon. We assessed α-syn cell-to-cell transfer using microscopy, flow cytometry, and high-content screening in several coculture model systems. Coculturing cells engineered to express either GFP- or DsRed-tagged α-syn resulted in a gradual increase in double-labeled cells. Importantly, α-syn-GFP derived from 1 neuroblastoma cell line localized to red fluorescent aggregates in other cells expressing DsRed-α-syn, suggesting a seeding effect of transmitted α-syn. Extracellular α-syn was taken up by cells through endocytosis and interacted with intracellular α-syn. Next, following intracortical injection of recombinant α-syn in rats, we found neuronal uptake was attenuated by coinjection of an endocytosis inhibitor. Finally, we demonstrated in vivo transfer of α-syn between host cells and grafted dopaminergic neurons in mice overexpressing human α-syn. In summary, intercellularly transferred α-syn interacts with cytoplasmic α-syn and can propagate α-syn pathology. These results suggest that α-syn propagation is a key element in the progression of Parkinson disease pathology.
Semiconductor Nanocrystals as Fluorescent Biological Labels (1998)

Semiconductor nanocrystals were prepared for use as fluorescent probes in biological staining and diagnostics. Compared with conventional fluorophores, the nanocrystals have a narrow, tunable, symmetric emission spectrum and are photochemically stable. The advantages of the broad, continuous excitation spectrum were demonstrated in a dual-emission, single-excitation labeling experiment on mouse fibroblasts. These nanocrystal probes are thus complementary and in some cases may be superior to existing fluorophores.
Surgical Removal of Primary Tumor Reverses Tumor-Induced Immunosuppression Despite the Presence of Metastatic Disease (2004)

Immunotherapy is a promising approach for the management of malignancies. It may be particularly useful for tumors that do not respond to conventional therapies, such as many metastatic cancers. The efficacy of immunotherapy will depend on many factors, one of which is the immunocompetence of the host. Patients with large primary tumors frequently are immunosuppressed, making them poor candidates for immunotherapy. Although a few studies have reported that surgical removal of primary tumor reverses immunosuppression, it is not known whether metastatic disease in postsurgery patients inhibits this recovery. To determine the role of metastatic disease, we examined tumor-free mice versus mice with primary tumor and metastatic disease versus mice whose primary tumors were removed surgically but who had metastatic disease. We have used the mouse 4T1 mammary carcinoma, a BALB/c-derived transplantable tumor that shares many characteristics with human breast cancer and is an established model for spontaneous, metastatic cancer. Cell-mediated and humoral adaptive immunity, as measured by rejection of allogeneic tumor, antigen-specific T-cell proliferation, and antigen-specific antibody responses, was suppressed in 4T1-bearing nonsurgery mice relative to tumor-free mice. Surgical removal of primary tumor resulted in rebounding of antibody and cell-mediated responses, even in mice with metastatic disease. Macrophage activity, as measured by lipopolysaccharide responsiveness, and dendritic cell function, as measured by nominal and alloantigen presentation, were not suppressed in tumor-bearing mice. Therefore, the presence of primary tumor suppresses T-cell and antibody responses; however, surgical removal of primary tumor restores immunocompetence even when disseminated metastatic disease is present.
Role of four major cellulases in triggering of cellulase gene expression by cellulose in Trichoderma reesei (1997)

The relative contributions of four major cellulases of Trichoderma reesei (1,4-beta-D-glucan cellobiohydrolase I [CBH I], CBH II, endo-1,4-beta-D-glucanase I [EG I], and EG II) to the generation of the cellulase inducer from cellulose were studied with isogenic strains in which the corresponding genes (cbh1, cbh2, egl1, and egl2) had been deleted by insertion of the Aspergillus nidulans amdS marker gene. During growth on lactose (a soluble carbon source provoking cellulase gene expression), these strains showed no significant alterations in their ability to express the respective other cellulase genes, with the exception of the strain containing delta cbh1, which exhibited an increased steady-state level of cbh2 mRNA. On crystalline cellulose as the only carbon source, however, significant differences were apparent: strains in which cbh2 and egl2, respectively, had been deleted showed no expression of the other cellulase genes, whereas strains carrying the cbh1 or egl1 deletion showed these transcripts. The delta cbh1-containing strain also showed enhanced cbh2 mRNA levels under these conditions. A strain in which both cbh1 and cbh2 had been deleted, however, was unable to initiate growth on cellulose. Addition of 2 mM sophorose, a putative inducer of cellulase gene expression, to such cultures induced the transcription of egl1 and egl2 and restored the ability to grow on cellulose. We conclude that CBH II and EG II are of major importance for the efficient formation of the inducer from cellulose in T. reesei and that removal of both cellobiohydrolases renders T. reesei unable to attack crystalline cellulose.