gebhart/patrepeval huggingface dataset:
Osteogenic differentiation of purified, culture-expanded human mesenchymal stem cells in vitro (1997)

Human bone marrow contains a population of cells capable of differentiating along multiple mesenchymal cell lineages. Recently, techniques for the purification and culture-expansion of these human marrow-derived Mesenchymal Stem Cells (MSCs) have been developed. The goals of the current study were to establish a reproducible system for the in vitro osteogenic differentiation of human MSCs, and to characterize the effect of changes in the microenvironment upon the process. MSCs derived from 2nd or 3rd passage were cultured for 16 days in various base media containing 1 to 1000 nM dexamethasone (Dex), 0.01 to 4 mM L-ascorbic acid-2-phosphate (AsAP) or 0.25 mM ascorbic acid, and 1 to 10 mM beta-glycerophosphate (beta GP). Optimal osteogenic differentiation, as determined by osteoblastic morphology, expression of alkaline phosphatase (APase), reactivity with anti-osteogenic cell surface monoclonal antibodies, modulation of osteocalcin mRNA production, and the formation of a mineralized extracellular matrix containing hydroxyapatite was achieved with DMEM base medium plus 100 nM Dex, 0.05 mM AsAP, and 10 mM beta GP. The formation of a continuously interconnected network of APase-positive cells and mineralized matrix supports the characterization of this progenitor population as homogeneous. While higher initial seeding densities did not affect cell number of APase activity, significantly more mineral was deposited in these cultures, suggesting that events which occur early in the differentiation process are linked to end-stage phenotypic expression. Furthermore, cultures allowed to concentrate their soluble products in the media produced more mineralized matrix, thereby implying a role for autocrine or paracrine factors synthesized by human MSCs undergoing osteoblastic lineage progression. This culture system is responsive to subtle manipulations including the basal nutrient medium, dose of physiologic supplements, cell seeding density, and volume of tissue culture medium. Cultured human MSCs provide a useful model for evaluating the multiple factors responsible for the step-wise progression of cells from undifferentiated precursors to secretory osteoblasts, and eventually terminally differentiated osteocytes.
Regulating role of STAT3 to HSP27 and c-MYC expression in breast cancer (2006)

AIM: To investigate the regulating role of signal transducer and activator of transcription 3(STAT3) to 27 ku heat shock protein(HSP27) and c-MYC expression in breast cancer.METHODS: Expressions of STAT3,HSP27 and c-MYC were examined in primary breast infiltrating duct carcinoma tissues of 51 patients using immunohistochemistry.Correlations between STAT3 expression and HSP27 or c-MYC expression were analyzed with statistic method.After the transfection of MDA-MB-435S(human) breast carcinoma cells with STAT3 decoy oligodeoxynucleotides(Decoy ODNs),expressions of HSP27 and c-MYC of MDA-MB-435S were semi-quantified by Western blot,the apoptosis and the cell cycle distribution of MDA-MB-435S cells were analyzed with flow cytometry and proliferation of MDA-MB-435S cells was analyzed by MTT assay.RESULTS: In primary breast infiltrating duct carcinoma tissues,STAT3 expression was correlated positively with HSP27 expression and c-MYC expression respectively(r_s0.454,P0.001;r_s0.541,P0.000).As the result of STAT3 inhibition by STAT3 Decoy ODNs in MDA-MB-435S cells,expressions of HSP27 and c-MYC were markedly reduced,which was consistent with STAT3 activation reduction(Both P0.01).The cell cycle progression of MDA-MB-435S cells was significantly inhibited at G0/G1 phase,the apoptosis of those cells was augmented and their proliferation was inhibited((P0.01).) CONCLUSION: Constitutively activated STAT3 may up-regulate HSP27 and c-MYC expression to inhibit breast cancer cell apoptosis and to facilitate their proliferation,thus leading to the malignancy of breast cancer cells.
Overwhelming tPA release, not PAI-1 degradation, is responsible for hyperfibrinolysis in severely injured trauma patients (2015)

Prognostic and epidemiologic study, level II.
Regulatory T Cells and Cancer Therapy: An Old Story with a New Hope (2010)

Accumulating evidence indicates that regulatory T cells (Treg) are a distinct group of immune cells that are essential in maintaining immunologic homeostasis, largely by their ability to suppress responses mediated by other populations of immune cells. In a microbial infection, this suppressive function can be temporally overridden via different mechanisms so that the immune system can mount efficient antimicrobial immunity. However, if Tregs suppressive function is not restored after the elimination of pathogens, the resulting immune hyperactivity would injure self tissues and autoimmune diseases may occur. In case of cancer, the overexpressed self-antigens can induce tumor/self-specific Treg cells that suppress effective antitumor responses. A wealth of evidence clearly shows that some microbes and their products, such as CpG-ODN, OK-432 and BCG, are effective in cancer treatment, most likely by suppression of Tregs function. Therefore, the search for approaches which can override Tregs suppressive functions and trigger an efficient antitumor immunity is crucial to the development of effective cancer immunotherapy.
Protection of nonobese diabetic mice from diabetes by intranasal or subcutaneous administration of insulin peptide B-(9-23). (1996)

The observation that overt type I diabetes is often preceded by the appearance of insulin autoantibodies and the reports that prophylactic administration of insulin to biobreeding diabetes-prone (BB-DP) rats, nonobese diabetic (NOD) mice, and human subjects results in protection from diabetes suggest that an immune response to insulin is involved in the process of beta cell destruction. We have recently reported that islet-infiltrating cells isolated from NOD mice are enriched for insulin-specific T cells, that insulin-specific T cell clones are capable of adoptive transfer of diabetes, and that epitopes present on residues 9-23 of the B chain appear to be dominant in this spontaneous response. In the experiments described in this report, the epitope specificity of 312 independently isolated insulin-specific T cell clones was determined and B-(9-23) was found to be dominant, with 93% of the clones exhibiting specificity toward this peptide and the remainder to an epitope on residues 7-21 of the A chain. On the basis of these observations, the effect of either subcutaneous or intranasal administration of B-(9-23) on the incidence of diabetes in NOD mice was determined. The results presented here indicate that both subcutaneous and intranasal administration of B-(9-23) resulted in a marked delay in the onset and a decrease in the incidence of diabetes relative to mice given the control peptide, tetanus toxin-(830-843). This protective effect is associated with reduced T-cell proliferative response to B-(9-23) in B-(9-23)-treated mice.
Post‐translational modifications and activation of p53 by genotoxic stresses (2001)

In unstressed cells, the tumor suppressor protein p53 is present in a latent state and is maintained at low levels through targeted degradation. A variety of genotoxic stresses initiate signaling pathways that transiently stabilize the p53 protein, cause it to accumulate in the nucleus, and activate it as a transcription factor. Activation leads either to growth arrest at the G1/S or G2/M transitions of the cell cycle or to apoptosis. Recent studies point to roles for multiple post-translational modifications in mediating these events in response to genotoxic stresses through several potentially interacting but distinct pathways. The approximately 100 amino-acid N-terminal and approximately 90 amino-acid C-terminal domains are highly modified by post-translational modifications. The N-terminus is heavily phosphorylated while the C-terminus contains phosphorylated, acetylated and sumoylated residues. Antibodies that recognize p53 only when it has been modified at specific sites have been developed, and studies with these reagents show that most known post-translational modifications are induced when cells are exposed to genotoxic stresses. These recent results, coupled with biochemical and genetic studies, suggest that N-terminal phosphorylations are important for stabilizing p53 and are crucial for acetylation of C-terminal sites, which in combination lead to the full p53-mediated response to genotoxic stresses. Modifications to the C-terminus inhibit the ability of this domain to negatively regulate sequence-specific DNA binding; additionally, they modulate the stability, the oligomerization state, the nuclear import/export process and the degree of ubiquitination of p53.
How ERK1/2 activation controls cell proliferation and cell death: Is subcellular localization the answer? (2009)

Extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) are members of the mitogen-activated protein kinase super family that can mediate cell proliferation and apoptosis. The Ras-Raf-MEK-ERK signaling cascade controlling cell proliferation has been well studied but the mechanisms involved in ERK1/2-mediated cell death are largely unknown. This review focuses on recent papers that define ERK1/2 translocation to the nucleus and the proteins involved in the cytosolic retention of activated ERK1/2. Cytosolic retention of ERK1/2 denies access to the transcription factor substrates that are responsible for the mitogenic response. In addition, cytosolic ERK1/2, besides inhibiting survival and proliferative signals in the nucleus, potentiates the catalytic activity of some proapoptotic proteins such as DAP kinase in the cytoplasm. Studies that further define the function of cytosolic ERK1/2 and its cytosolic substrates that enhance cell death will be essential to harness this pathway for developing effective treatments for cancer and chronic inflammatory diseases.
Unconditionally Secure Quantum Bit Commitment is Impossible (1997)

The claim of quantum cryptography has always been that it can provide protocols that are unconditionally secure, that is, for which the security does not depend on any restriction on the time, space, or technology available to the cheaters. We show that this claim does not hold for any quantum bit commitment protocol. Since many cryptographic tasks use bit commitment as a basic primitive, this result implies a severe setback for quantum cryptography. The model used encompasses all reasonable implementations of quantum bit commitment protocols in which the participants have not met before, including those that make use of the theory of special relativity.
ei24, a p53 Response Gene Involved in Growth Suppression and Apoptosis (2000)

DNA damage and/or hyperproliferative signals activate the wild-type p53 tumor suppressor protein, which induces a G(1) cell cycle arrest or apoptosis. Although the mechanism of p53-mediated cell cycle arrest is fairly well defined, the p53-dependent pathway regulating apoptosis is poorly understood. Here we report the functional characterization of murine ei24 (also known as PIG8), a gene directly regulated by p53, whose overexpression negatively controls cell growth and induces apoptotic cell death. Ectopic ei24 expression markedly inhibits cell colony formation, induces the morphological features of apoptosis, and reduces the number of beta-galactosidase-marked cells, which is efficiently blocked by coexpression of Bcl-X(L). The ei24/PIG8 gene is localized on human chromosome 11q23, a region frequently altered in human cancers. These results suggest that ei24 may play an important role in negative cell growth control by functioning as an apoptotic effector of p53 tumor suppressor activities.
Cyclin‐dependent protein kinases: Key regulators of the eukaryotic cell cycle (1995)

Passage through the cell cycle requires the successive activation of different cyclin-dependent protein kinases (CDKs). These enzymes are controlled by transient associations with cyclin regulatory subunits, binding of inhibitory polypeptides and reversible phosphorylation reactions. To promote progression towards DNA replication, CDK/cyclin complexes phosphorylate proteins required for the activation of genes involved in DNA synthesis, as well as components of the DNA replication machinery. Subsequently, a different set of CDK/cyclin complexes triggers the phosphorylation of numerous proteins to promote the profound structural reorganizations that accompany the entry of cells into mitosis. At present, much research is focused on elucidating the links between CDK/cyclin complexes and signal transduction pathways controlling cell growth, differentiation and death. In future, a better understanding of the cell cycle machinery and its deregulation during oncogenesis may provide novel opportunities for the diagnostic and therapeutic management of cancer and other proliferation-related diseases.
THE ROLE OF MENTORING IN THE FIELD OF CONTACT DERMATITIS (2005)

Aims & Scope | The leading peer-reviewed scientific journal in contact dermatitis, and the only journal in its field that publishes leading research in atopic, contact, occupational, environmental, and drug dermatitis.
Endoplasmic Reticulum Stress-Induced Formation of Transcription Factor Complex ERSF Including NF-Y (CBF) and Activating Transcription Factors 6α and 6β That Activates the Mammalian Unfolded Protein Response (2001)

The levels of molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) are controlled by a transcriptional induction process termed the unfolded protein response (UPR). The mammalian UPR is mediated by the cis-acting ER stress response element (ERSE), the consensus sequence of which is CCAAT-N(9)-CCACG. We recently proposed that ER stress response factor (ERSF) binding to ERSE is a heterologous protein complex consisting of the constitutive component NF-Y (CBF) binding to CCAAT and an inducible component binding to CCACG and identified the basic leucine zipper-type transcription factors ATF6alpha and ATF6beta as inducible components of ERSF. ATF6alpha and ATF6beta produced by ER stress-induced proteolysis bind to CCACG only when CCAAT is bound to NF-Y, a heterotrimer consisting of NF-YA, NF-YB, and NF-YC. Interestingly, the NF-Y and ATF6 binding sites must be separated by a spacer of 9 bp. We describe here the basis for this strict requirement by demonstrating that both ATF6alpha and ATF6beta physically interact with NF-Y trimer via direct binding to the NF-YC subunit. ATF6alpha and ATF6beta bind to the ERSE as a homo- or heterodimer. Furthermore, we showed that ERSF including NF-Y and ATF6alpha and/or beta and capable of binding to ERSE is indeed formed when the cellular UPR is activated. We concluded that ATF6 homo- or heterodimers recognize and bind directly to both the DNA and adjacent protein NF-Y and that this complex formation process is essential for transcriptional induction of ER chaperones.
Completely ES Cell-Derived Mice Produced by Tetraploid Complementation Using Inner Cell Mass (ICM) Deficient Blastocysts (2014)

Tetraploid complementation is often used to produce mice from embryonic stem cells (ESCs) by injection of diploid (2n) ESCs into tetraploid (4n) blastocysts (ESC-derived mice). This method has also been adapted to mouse cloning and the derivation of mice from induced pluripotent stem (iPS) cells. However, the underlying mechanism(s) of the tetraploid complementation remains largely unclear. Whether this approach can give rise to completely ES cell-derived mice is an open question, and has not yet been unambiguously proven. Here, we show that mouse tetraploid blastocysts can be classified into two groups, according to the presence or absence of an inner cell mass (ICM). We designate these as type a (presence of ICM at blastocyst stage) or type b (absence of ICM). ESC lines were readily derived from type a blastocysts, suggesting that these embryos retain a pluripotent epiblast compartment; whereas the type b blastocysts possessed very low potential to give rise to ESC lines, suggesting that they had lost the pluripotent epiblast. When the type a blastocysts were used for tetraploid complementation, some of the resulting mice were found to be 2n/4n chimeric; whereas when type b blastocysts were used as hosts, the resulting mice are all completely ES cell-derived, with the newborn pups displaying a high frequency of abdominal hernias. Our results demonstrate that completely ES cell-derived mice can be produced using ICM-deficient 4n blastocysts, and provide evidence that the exclusion of tetraploid cells from the fetus in 2n/4n chimeras can largely be attributed to the formation of ICM-deficient blastocysts.
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures (2012)

So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population. In the present study eight metagenomic samples from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to existing algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a 100 times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt).
Prenatal Diagnosis of β-Thalassemia (1983)

We investigated a method employing synthetic oligonucleotides for the prenatal diagnosis of beta-thalassemia due to a single nucleotide mutation. The beta 0 thalassemia we tested is produced by a nonsense mutation and is commonly found in Sardinia and other parts of the Mediterranean. In this DNA lesion, the glutamine codon CAG at the beta 39 position is mutated to TAG, which results in a stop codon and premature termination of the beta-globin chain. We synthesized two oligonucleotides: one homologous to the normal beta A gene and the other to the beta 0 thalassemia gene at the beta 39 location. The oligonucleotides were labeled with 32P and used as hybridization probes for normal and thalassemic DNA. The beta A probe hybridized only to the normal DNA, and the beta-thalassemia probe only to thalassemic DNA, thus providing a technique for direct demonstration of the mutation. The method is sensitive enough to be applied directly to DNA that is isolated from uncultured cells obtained from only 20 ml of amniotic fluid as early as the 16th gestational week.
Molecular cloning and exon‐intron mapping of the gene encoding human transmembrane secretory component (the poly‐Ig receptor) (1992)

Secretory component (SC or the poly-Ig receptor) plays a crucial role in mucosal immunity by translocating polymeric IgA and IgM through secretory epithelial cells into external body fluids. Labeled restriction fragments from human SC cDNA were used to screen a human genomic leukocyte library. Three overlapping clones, spanning a total of 19 kb of the human SC gene, including 3 kb of the 5' flanking region, were characterized. The putative TATA box candidate, preceded by a CAAT-like box, was found 329 nucleotides upstream of the first exon. Altogether 11 exons covering the entire coding region were identified. The exon size ranged from 59 to 657 nucleotides and exon-intron junctions followed known consensus sequences. Three of the five extracellular Ig-related domains (D1, D4 and D5) were confined to one exon each (E3, E5 and E6), whereas D2 and D3 were encoded by the same exon (E4). The latter exon corresponds to that involved in alternate splicing of rabbit SC. The membrane-spanning segment was confined to part of one exon (E8). The cytoplasmic tail was encoded by four exons (E8-E11), whose boundaries encompassed fairly well the structural determinants proposed to be responsible for intracellular sorting of SC in the rabbit. The polymorphic restriction site reported earlier for Pvu II was localized to the third intron.
Predictive value of the EphA2 receptor tyrosine kinase in lung cancer recurrence and survival. (2003)

Underestimation of disease severity is a major problem confronting the successful clinical management of non-small cell lung cancer. Recent advances in molecular biological substaging may provide an opportunity to identify those patients with the most aggressive forms of the disease, but there is a continuing need for accurate markers of disease relapse and survival.In our present study, immunohistochemical analyses of a retrospective database of pathologic specimens were used to demonstrate that the EphA2 receptor kinase is frequently overexpressed in NSCLC.Initial presentation with high levels of EphA2 predicts subsequent survival, overall relapse, and site of relapse. Specifically, high levels of EphA2 in the primary tumor predict brain metastases, whereas low levels of EphA2 relate to disease-free survival or contralateral lung metastasis.These data suggest that EphA2 may provide a molecular marker to identify and predict patients who have isolated brain metastases. Moreover, the high levels of EphA2 in lung cancer may provide an opportunity for therapeutic targeting.
A Review of Polyamines and Cancer (2003)

The first research publication describing polyaminated compounds in cancer tissues occurred in 1958 in the Proceedings of the National Acadamy of Japan (1). In those early years, polyaminated molecules and substances were identified in all forms of life – bacteria, fungus, plants, and all types of eukaroytic cells. They were determined to be critical for all types of cellular proliferation, and indeed for the continuation of life in all currently known cell types. Immediately, research on polyamines expanded very rapidly. Between 1960 and 1985, there were more than 5,000 research publications about polyaminated small molecules and compounds, including 11 multi-chapter research review books (2-12) and six extensive review publications (averaging more than 50 pages per review) just by the Tabors alone (1318). It was anticipated that knowledge and/or control of intracellular polyamine systems would have unlimited industrial and medical/clinical applications. However, now 45 years later, these great expections have not proven to be “exactly” correct.