gebhart/patrepeval huggingface dataset:
Effects of Radiation Mediating Agents on the Response of a Murine Ependymoma to Proton Irradiation (1966)

Proton radiation is currently employed in a few centers in the United States and Sweden for the treatment of brain tumors in man. There is, however, relatively little quantitative information in the literature on the radiobiological response of experimental brain tumors. Some studies of x-radiation effects on gliomas in mice have been reported (1–3), but the difficulties associated with the use of intracerebral tumors led us to choose a subcutaneously transplantable ependymoma. This test system is a highly malignant neoplasm which transplants readily and grows rapidly. In the normal routine sequential transplants over several years, 100 per cent tumor growth has been obtained (4). We have investigated the in vivo response of this tumor to x and proton radiation under a variety of conditions, in terms of reduction in successful transplantation immediately after irradiation of the tumor-bearing animal. Materials and Methods The two mouse gliomas (Nos. 15 and 48) which we have studied had been induced in C3H mice by intracerebral implantation of methylcholanthrene pellets and then carried by subcutaneous transplantation in male C3H mice six to eight weeks old. The tumors were induced by Perese and Moore2 (5) in 1957 and histologically they have remained unchanged and are both classified as ependymomas. The same general transplantation procedure was employed in the radiation experiments and for routine stock maintenance. Single or bilateral injections of 20 mg of homogenized tumor tissue in a volume of 0.1 ml were made subcutaneously in the flank of the recipient (unirradiated) animals. Tumor growth (“take”) was considered positive when a detectable, palpable mass continued to increase in size. Irradiation Procedure: Proton radiation was administered with a 3∕4-in. diameter beam from the Harvard synchrocyclotron. Absorbers and a water collimator reduced the beam energy to 55 MeV, with a mean linear energy transfer (LET) of 11.5 MeV cm2∕g. The dose calibration was obtained from Faraday cup measurements, and a secondary nitrogen-filled transmission ion chamber was used as integrating monitor. The beam cross-section profile curve at the radiation position was obtained with a silicon diode probe detector (6). The mice were irradiated individually, under light Nembutal anesthesia, with the tumor positioned axially in the beam. Doses in the range of 1,500 to 6,000 rads were given at a dose rate of 1,000 rads∕min. The dose was essentially uniform throughout the tumor volume of approximately 800 cubic millimeters. A smaller series of x irradiations was carried out under comparable conditions. A 2 MeV Van de Graaff accelerator with an x-ray dose rate of 350 rads∕min.
The Role of Stem Cells in Skeletal and Cardiac Muscle Repair (2002)

In postnatal muscle, skeletal muscle precursors (myoblasts) can be derived from satellite cells (reserve cells located on the surface of mature myofibers) or from cells lying beyond the myofiber, e.g., interstitial connective tissue or bone marrow. Both of these classes of cells may have stem cell properties. In addition, the heretical idea that post-mitotic myonuclei lying within mature myofibers might be able to re-form myoblasts or stem cells is examined and related to recent observations for similar post-mitotic cardiomyocytes. In adult hearts (which previously were not considered capable of repair), the role of replicating endogenous cardiomyocytes and the recruitment of other (stem) cells into cardiomyocytes for new cardiac muscle formation has recently attracted much attention. The relative contribution of these various sources of precursor cells in postnatal muscles and the factors that may enhance stem cell participation in the formation of new skeletal and cardiac muscle in vivo are the focus of this review. We concluded that, although many endogenous cell types can be converted to skeletal muscle, the contribution of non-myogenic cells to the formation of new postnatal skeletal muscle in vivo appears to be negligible. Whether the recruitment of such cells to the myogenic lineage can be significantly enhanced by specific inducers and the appropriate microenvironment is a current topic of intense interest. However, dermal fibroblasts appear promising as a realistic alternative source of exogenous myoblasts for transplantation purposes. For heart muscle, experiments showing the participation of bone marrow-derived stem cells and endothelial cells in the repair of damaged cardiac muscle are encouraging.
Activation of p70 Ribosomal Protein S6 Kinase Is an Essential Step in the DNA Damage-dependent Signaling Pathway Responsible for the Ultraviolet B-mediated Increase in Interstitial Collagenase (MMP-1) and Stromelysin-1 (MMP-3) Protein Levels in Human Dermal Fibroblasts (2000)

Ultraviolet B (UVB) irradiation has been shown to stimulate the expression of matrix-degrading metalloproteinases via generation of DNA damage and/or reactive oxygen species. Matrix-degrading metalloproteinases promote UVB-triggered detrimental long term effects like cancer formation and premature skin aging. Here, we were interested in identifying components of the signal transduction pathway that causally link UVB-mediated DNA damage and induction of matrix-degrading metalloproteinase (MMP)-1/interstitial collagenase and MMP-3/stromelysin-1 in human dermal fibroblasts in vitro. The activity of p70 ribosomal S6 kinase, a downstream target of the FK506-binding protein-12/rapamycin-associated protein kinase (FRAP) kinase (RAFT1, mTOR), was identified to be 4.8 +/- 0.8-fold, and MMP-1 and MMP-3 protein levels 2.4- and 11.5-fold increased upon UVB irradiation compared with mock-irradiated controls. The FRAP kinase inhibitor rapamycin and the DNA repair inhibitor aphidicolin significantly suppressed the UVB-mediated increase in p70 ribosomal S6 kinase activity by 50-65% and MMP-1 and MMP-3 protein levels by 34-68% and 42-88% compared with UVB-irradiated fibroblasts. By contrast, the interleukin-1beta-mediated increase in MMP-1 and MMP-3 protein levels could not be suppressed by rapamycin. Collectively, our data suggest that the FRAP-controlled p70 ribosomal S6 kinase is an essential component of a DNA damage-dependent, but not of the interleukin-1/cell membrane receptor-dependent signaling.
Preparation of Surface Organometallic Catalysts by Gas‐Phase Ligand Stripping and Reactive Landing of Mass‐Selected Ions (2010)

Abstract Organometallic complexes immobilized on surfaces combine the high selectivity of homogeneous catalysts with the ease of separation of catalyst from products attainable with heterogeneous catalysts. Here we report a novel approach for the highly controlled preparation of surface organometallic catalysts by gas‐phase ligand stripping combined with reactive landing of mass‐selected ions onto self‐assembled monolayer surfaces. Collision‐induced dissociation is used to generate highly reactive undercoordinated metal complexes in the gas‐phase for subsequent surface immobilization. Complexes with an open coordination shell around the metal center are demonstrated to show enhanced activity towards reactive landing in comparison to fully ligated species. In situ TOF‐SIMS analysis indicates that the immobilized complexes exhibit behavior consistent with catalytic activity when exposed to gaseous reagents.
Effects of eicosapentaenoic acid on biochemical failure after radical prostatectomy for prostate cancer. (2010)

A longer and/or larger intervention or docosahexaenoic acid supplementation might be necessary to identify significant preventive effects of mega-3 polyunsaturated fatty acids on PSA recurrence.
Stroke recurrence in children with congenital heart disease (2012)

Stroke recurrence was relatively common in neonates and children with CHD. Identified groups of patients at increased risk may require more aggressive secondary prophylaxis, especially in the early poststroke period.
64Cu-labeled folate-conjugated shell cross-linked nanoparticles for tumor imaging and radiotherapy: synthesis, radiolabeling, and biologic evaluation. (2005)

Despite high RES uptake, the evaluated 64Cu-labeled SCKs exhibited long circulation in blood and were able to passively accumulate in tumors. Furthermore, SCK-folate uptake was competitively blocked by excess folate in small-size solid tumors, suggesting interaction with the FR. For these reasons, functionalized SCKs are promising drug-delivery agents for imaging and therapy of early-stage solid tumors.
Polymorphic Sirpa is the genetic determinant for NOD-based mouse lines to achieve efficient human cell engraftment (2013)

Current mouse lines efficient for human cell xenotransplantation are backcrossed into NOD mice to introduce its multiple immunodeficient phenotypes. Our positional genetic study has located the NOD-specific polymorphic Sirpa as a molecule responsible for its high xenograft efficiency: it recognizes human CD47 and the resultant signaling may cause NOD macrophages not to engulf human grafts. In the present study, we established C57BL/6.Rag2(nullIl2rgnull) mice harboring NOD-Sirpa (BRGS). BRGS mice engrafted human hematopoiesis with an efficiency that was equal to or even better than that of the NOD.Rag1(nullIl2rgnull) strain, one of the best xenograft models. Consequently, BRGS mice are free from other NOD-related abnormalities; for example, they have normalized C5 function that enables the evaluation of complement-dependent cytotoxicity of antibodies against human grafts in the humanized mouse model. Our data show that efficient human cell engraftment found in NOD-based models is mounted solely by their polymorphic Sirpa. The simplified BRGS line should be very useful in future studies of human stem cell biology.
<title>Objective quality measurement of integral 3D images</title> (2002)

At De Montfort University the imaging technologies group have developed an integral imaging system capable of real time capture and replay. The system has many advantages compared with other 3D capture and display techniques, however one issue that has not been adequately addressed is the measurement of the fidelity of replayed 3D images where some distortion has occurred. This paper presents a method for producing a viewing angle-dependent PSNR metric based on extraction of optical model data as conventional images. The technique produces image quality measurements which are more relevant to the volume spatial content of an integral image than a conventional fidelity metric applied to the raw, optically encoded spatial distribution. Comparisons of the previous, single metric with the new angle-dependent metric are made when used in assessing the performance of a 3D-DCT based compression scheme, and the utility of the extra information provided by the angle dependent PSNR is considered.
Roles of insulinlike growth factor 1 (IGF-1) and the IGF-1 receptor in epidermal growth factor-stimulated growth of 3T3 cells. (1992)

BALB/c3T3 cells are exquisitely growth regulated and require platelet-derived growth factor, epidermal growth factor (EGF), and insulinlike growth factor 1 (IGF-1) for growth. When BALB/c3T3 cells are transfected with plasmids constitutively expressing both EGF and the human IGF-1 receptor mRNAs, the cells are capable of growing in serum-free medium without the addition of any exogenous growth factor. These cells, called p5 cells, can grow for prolonged periods in serum-free medium. BALB/c3T3 cells transfected with only the IGF-1 receptor expression plasmid (p6 cells) do not grow in serum-free medium but do grow if IGF-1 (or insulin in supraphysiological concentrations) is added. p6 cells also grow in response to EGF, confirming that the combination of EGF and an overexpressed IGF-1 receptor is sufficient for the growth of 3T3 cells. We have found that in EGF-stimulated p6 cells there is an increase in the expression of IGF-1 mRNA, that IGF-1 is secreted into the medium, and that the growth of p5 cells and EGF-stimulated p6 cells is inhibited by exposure to antisense oligodeoxynucleotides to IGF-1 receptor RNA. Finally, while cells constitutively expressing both EGF and EGF receptor RNAs grow, albeit modestly, in serum-free medium, their growth is also inhibited by an antisense oligodeoxynucleotide to IGF-1 receptor RNA. In contrast, in cells overexpressing the IGF-1 receptor, IGF-1-mediated cell growth occurs independently of the platelet-derived growth factor and EGF receptors (Z. Pietrzkowski, R. Lammers, G. Carpenter, A. M. Soderquist, M. Limardo, P. D. Phillips, A. Ullrich, and R. Baserga, Cell Growth Differ. 3:199-205, 1992, and this paper). These data indicate that an important role for EGF is participation in the activation of an autocrine loop based on the IGF-1-IGF-1 receptor interaction, which is obligatory for the proliferation of 3T3 cells.
Counting Dependence Predictors (2008)

Modern processors rely on memory dependence prediction to execute load instructions as early as possible, speculating that they are not dependent on an earlier, unissued store. To date, the most sophisticated dependence predictors, such as Store Sets, have been tightly coupled to the fetch and execution streams, requiring global knowledge of the in-flight stream of stores to synchronize loads with specific stores. This paper proposes a new dependence predictor design, called a Counting Dependence Predictor (CDP). The key feature of CDPs is that the prediction mechanism predicts some set of events for which a particular dynamic load should wait, which may include some number of matching stores. By waiting for local events only, this dependence predictor can work effectively in a distributed microarchitecture where centralized fetch and execution streams are infeasible or undesirable. We describe and evaluate a distributed Counting Dependence Predictor and protocol that achieves 92% of the performance of perfect memory disambiguation. It outperforms a load-wait table, similar to the Alpha 21264, by 11%. Idealized, centralized implementations of Store Sets and the Exclusive Collision Predictor, both of which would be difficult to implement in a distributed microarchitecture, achieve 97% and 94% of oracular performance, respectively.
Role of Microbial Enzymes in the Bioremediation of Pollutants: A Review (2011)

A large number of enzymes from bacteria, fungi, and plants have been reported to be involved in the biodegradation of toxic organic pollutants. Bioremediation is a cost effective and nature friendly biotechnology that is powered by microbial enzymes. The research activity in this area would contribute towards developing advanced bioprocess technology to reduce the toxicity of the pollutants and also to obtain novel useful substances. The information on the mechanisms of bioremediation-related enzymes such as oxido-reductases and hydrolases have been extensively studied. This review attempts to provide descriptive information on the enzymes from various microorganisms involved in the biodegradation of wide range of pollutants, applications, and suggestions required to overcome the limitations of their efficient use.
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases (2014)

baesau@snu.ac.kr or jskim01@snu.ac.kr.
Characterization of adhesion and differentiation markers of osteogenic marrow stromal cells (2004)

Marrow stroma cells (MSC) play a major role in osteogenesis. The potential of the MSC to differentiate to bone-forming cells relies upon molecular regulation. This study analyzed MBA-15 cells for the expression of genes and proteins that are key regulators of osteoblast differentiation. These cells express Cbfa1 and c-fos transcription factors (TF) of osteoprogenitor proliferating cells. RT-PCR and immunohistochemistry were used to demonstrate the message and protein expression of extracellular matrix proteins that are a prerequisite for matrix formation and mineralization, including alkaline phosphatase (ALP), osteocalcin, osteopontin, biglycan, and bone sialoprotein (BSP). The activity of ALP was correlated at various cell densities with co-expression of osteocalcin or osteopontin. Adhering cells must attach to the appropriate matrix to enable survival and differentiation. Using attachment assays, we demonstrated that MBA-15 cells adhered to collagenous matrix and the effect on survival measured by changes in intracellular calcium (Ca) levels. The cells' adhesion to matrix is mediated via cell surface molecules. We quantified the expression of cells surface molecules that are important players in mediating cell-matrix interaction. Flow cytometry analysis (FACS) was used to determine the expression of CD-31 (36%), and lower levels were identified for CD-62E and CD11b. In summary, the present study demonstrates the expression of molecular markers that are distinctive for the osteoblastic phenotype in MBA-15 marrow stroma cells and have crucial role in cell-matrix interaction, in establishing the cellular osteogenic phenotype and their survival.
Higher-order clique reduction in binary graph cut (2009)

We introduce a new technique that can reduce any higher-order Markov random field with binary labels into a first-order one that has the same minima as the original. Moreover, we combine the reduction with the fusion-move and QPBO algorithms to optimize higher-order multi-label problems. While many vision problems today are formulated as energy minimization problems, they have mostly been limited to using first-order energies, which consist of unary and pairwise clique potentials, with a few exceptions that consider triples. This is because of the lack of efficient algorithms to optimize energies with higher-order interactions. Our algorithm challenges this restriction that limits the representational power of the models, so that higher-order energies can be used to capture the rich statistics of natural scenes. To demonstrate the algorithm, we minimize a third-order energy, which allows clique potentials with up to four pixels, in an image restoration problem. The problem uses the fields of experts model, a learned spatial prior of natural images that has been used to test two belief propagation algorithms capable of optimizing higher-order energies. The results show that the algorithm exceeds the BP algorithms in both optimization performance and speed.
Object recognition from local scale-invariant features (1999)

An object recognition system has been developed that uses a new class of local image features. The features are invariant to image scaling, translation, and rotation, and partially invariant to illumination changes and affine or 3D projection. These features share similar properties with neurons in inferior temporal cortex that are used for object recognition in primate vision. Features are efficiently detected through a staged filtering approach that identifies stable points in scale space. Image keys are created that allow for local geometric deformations by representing blurred image gradients in multiple orientation planes and at multiple scales. The keys are used as input to a nearest neighbor indexing method that identifies candidate object matches. Final verification of each match is achieved by finding a low residual least squares solution for the unknown model parameters. Experimental results show that robust object recognition can be achieved in cluttered partially occluded images with a computation time of under 2 seconds.
Emerging antibody combinations in oncology (2011)

The use of monoclonal antibodies (mAbs) has become a general approach for specifically targeting and treating human disease. In oncology, the therapeutic utility of mAbs is usually evaluated in the context of treatment with standard of care, as well as other small molecule targeted therapies. Many anti-cancer antibody modalities have achieved validation, including the targeting of growth factor and angiogenesis pathways, the induction of tumor cell killing or apoptosis, and the blocking of immune inhibitory mechanisms to stimulate anti-tumor responses. But, as with other targeted therapies, few antibodies are curative because of biological complexities that underlie tumor formation and redundancies in molecular pathways that enable tumors to adapt and show resistance to treatment. This review discusses the combinations of antibody therapeutics that are emerging to improve efficacy and durability within a specific biological mechanism (e.g., immunomodulation or the inhibition of angiogenesis) and across multiple biological pathways (e.g., inhibition of tumor growth and induction of tumor cell apoptosis).
Human bronchial epithelial cells modulate collagen gel contraction by fibroblasts (1998)

Connective tissue contraction is an important aspect of both normal wound healing and fibrosis. This process may contribute to small airway narrowing associated with certain airway diseases. Fibroblast-mediated contraction of a three-dimensional collagen gel has been considered a model of tissue contraction. In this study, the ability of primary cultured human bronchial epithelial cells (HBEC) obtained by bronchial brushings to modulate fibroblast gel contraction was evaluated. Human lung fibroblasts (HFL1) were cast into type I collagen gels. The gels were floated both in dishes containing a monolayer of HBEC or in dishes without HBEC. Contraction assessed by measuring the area of gels was increased at all time points from 24 h up to 96 h of coculture. At 48 h, coculture of HBEC with fibroblasts resulted in significantly more contraction than fibroblasts alone (36.6 +/- 1.2 vs. 20.4 +/- 1.7%, P < 0.05). Lipopolysaccharide (LPS, 10 micrograms/ml) stimulation of the HBEC augmented the contraction (44.9 +/- 1.0%, P < 0.05 vs. HBEC). In the presence of indomethacin, the augmentation by LPS was increased further (52.2 +/- 4.3%, P < 0.05 vs. HBEC with LPS), suggesting that prostaglandins (PGs) are present and may inhibit contraction. Consistent with this, PGE was present in HBEC-conditioned medium. Bronchial epithelial cell conditioned medium had an effect similar to coculturing. SG-150 column chromatography revealed augmentive activity between 20 and 30 kDa and inhibitory activity between 10 and 20 kDa. Measurement by enzyme-linked immunosorbent assay confirmed the presence of the active form of transforming growth factor (TGF)-beta 2. The stimulatory activity of conditioned medium was blocked by adding anti-TGF-beta antibody. These data demonstrate that, through the release of factors including TGF-beta 2 which can augment and PGE which can inhibit, HBEC can modulate fibroblast-mediated collagen gel contraction. In this manner, HBEC may modulate fibroblast activities that determine the architecture of bronchial tissue.
Functional characterization of human pluripotent stem cell-derived arterial endothelial cells (2017)

Here, we report the derivation of arterial endothelial cells from human pluripotent stem cells that exhibit arterial-specific functions in vitro and in vivo. We combine single-cell RNA sequencing of embryonic mouse endothelial cells with an <i>EFNB2-tdTomato/EPHB4-EGFP</i> dual reporter human embryonic stem cell line to identify factors that regulate arterial endothelial cell specification. The resulting xeno-free protocol produces cells with gene expression profiles, oxygen consumption rates, nitric oxide production levels, shear stress responses, and TNFα-induced leukocyte adhesion rates characteristic of arterial endothelial cells. Arterial endothelial cells were robustly generated from multiple human embryonic and induced pluripotent stem cell lines and have potential applications for both disease modeling and regenerative medicine.