gebhart/patrepeval huggingface dataset:
Cold Atmospheric Plasma for Selectively Ablating Metastatic Breast Cancer Cells (2013)

Traditional breast cancer treatments such as surgery and radiotherapy contain many inherent limitations with regards to incomplete and nonselective tumor ablation. Cold atmospheric plasma (CAP) is an ionized gas where the ion temperature is close to room temperature. It contains electrons, charged particles, radicals, various excited molecules, UV photons and transient electric fields. These various compositional elements have the potential to either enhance and promote cellular activity, or disrupt and destroy them. In particular, based on this unique composition, CAP could offer a minimally-invasive surgical approach allowing for specific cancer cell or tumor tissue removal without influencing healthy cells. Thus, the objective of this research is to investigate a novel CAP-based therapy for selectively bone metastatic breast cancer treatment. For this purpose, human metastatic breast cancer (BrCa) cells and bone marrow derived human mesenchymal stem cells (MSCs) were separately treated with CAP, and behavioral changes were evaluated after 1, 3, and 5 days of culture. With different treatment times, different BrCa and MSC cell responses were observed. Our results showed that BrCa cells were more sensitive to these CAP treatments than MSCs under plasma dose conditions tested. It demonstrated that CAP can selectively ablate metastatic BrCa cells in vitro without damaging healthy MSCs at the metastatic bone site. In addition, our study showed that CAP treatment can significantly inhibit the migration and invasion of BrCa cells. The results suggest the great potential of CAP for breast cancer therapy.
Mechanisms of monoclonal antibody‐facilitated tolerance induction: a possible role for the CD4 (L3T4) and CD11a (LFA‐1) molecules in self‐non‐self discrimination (1988)

In vivo therapy with a CD4 (L3T4) monoclonal antibody is able to provide a tolerogenic milieu for a limited number of protein antigens. In this study we have analyzed the mechanisms of such tolerance to human gamma globulin, and show that tolerance is induced in adult T helper cells without a need for cellular depletion, and that it is probably not maintained by suppressor mechanisms nor by regulatory cellular circuits involving CD8+ (Ly-2+) cells. Tolerance induction is not a property peculiar to the CD4 molecule, as similar effects can be elicited with a monoclonal antibody directed to the CD11a (LFA-1) molecule. We suggest that tolerance is maintained by the functional deletion of mature T helper cells and that adhesion molecules, such as CD4, CD8 and CD11a, may play a critical role in T cell discernment of self from nonself.
The use of alefacept in the treatment of psoriasis. (2003)

Alefacept (AMEVIVE or LFA#TIP, Biogen) is the newest effective systemic therapy for chronic plaque psoriasis and was approved by the US FDA in January 2003. Clinical studies have shown that alefacept, given via weekly IM or IV injections for 12 weeks, was well tolerated, with no reported serious adverse events. Most significantly, it was found that alefacept provides a long-lasting remittive effect. These findings support the use of alefacept as a viable treatment of psoriasis, without the toxicities associated with some of the current systemic treatments available.
Site-directed mutagenesis of active site cysteines in human thioredoxin produces competitive inhibitors of human thioredoxin reductase and elimination of mitogenic properties of thioredoxin. (1994)

Thioredoxin and thioredoxin reductase comprise a redox system ubiquitous in all organisms. To better understand the thiol chemistry of the mammalian thioredoxin-thioredoxin reductase redox system, mutants of human thioredoxin were produced by site-directed mutagenesis in which the two active site cysteines were replaced by serine residues, individually (C32S and C35S) and in combination (C32S/C35S). C35S and C32S/C35S were found to be competitive inhibitors of the reduction of human thioredoxin by human thioredoxin reductase with Ki values of 1.8 and 6.7 microM, respectively. C32S did not inhibit thioredoxin reductase, apparently due to aggregation of the oxidized C32S species. Examination of the three mutant forms of thioredoxin by circular dichroism spectroscopy indicated that there were significant differences in the secondary structures when compared with thioredoxin. There were detectable changes in the circular dichroism spectra when thioredoxin, C35S, and C32S/C35S were bound to thioredoxin reductase, whereas C32S with thioredoxin reductase underwent only a small spectral change. Recombinant human thioredoxin stimulated DNA synthesis and the proliferation of murine fibroblasts. The ability of thioredoxin to stimulate cell proliferation could not be duplicated by either dithiothreitol or glutathione. C32S, C35S, and C32S/C35S failed to stimulate cell proliferation, showing that the redox active form of thioredoxin is necessary for eliciting growth stimulation.
In vitro production of IgE by human peripheral blood lymphocytes: effect of cholera toxin and beta adrenergic stimulation. (1976)

Peripheral blood lymphocytes from two human donors with elevated serum IgE concentrations were maintained in short term tissue culture preparations. Repeated culture preparations demonstrated that IgE was produced in vitro in amounts that could be measured by the double antibody radioimmunoassay technique. The amount of IgE produced by replicate cultures of cells from a single bleeding of the donor was similar when the cultures were simultaneously prepared. In contrast, IgE production by the same donor's lymphocytes varied when the culture preparations were initiated from separate bleedings. The results of simultaneous cultures of a single bleeding were sufficiently consistent to provide a means of testing the effect of pharmacologic agents on the in vitro production of IgE. Cholera toxin effected a marked reduction in production of IgE by lymphocytes of both cell donors. Isoproterenol showed marked inhibition of IgE production at 10(-3) M but cell viability studies suggested that this may have been due to decreased cell viability. At lower, nontoxic concentrations of isoproterenol (10(-4) M-10(-6) M) slight but definite inhibition of in vitro IgE production was evident. This inhibition was more pronounced subsequent to the first 24 hr of exposure of the cells to isoproterenol.
Cellular Assays with a Molecular Endpoint Measured by SAMDI Mass Spectrometry (2016)

Cell-based, high-throughput screening (HTS) assays are increasingly important tools used in drug discovery, but frequently rely on readouts of gene expression or phenotypic changes and require development of specialized, labeled reporters. Here a cell-based, label-free assay compatible with HTS is introduced that can report quantitatively on enzyme activities by measuring mass changes of substrates with matrix-assisted laser desorption/ionization mass spectrometry. The assay uses self-assembled monolayers to culture cells on arrays presenting substrates, which serve as reporters for a desired enzyme activity. Each spot of cells is treated with a compound, cultured and lysed, enabling endogenous enzymes to act on the immobilized peptide substrate. It is demonstrated that the assay can measure protein tyrosine phosphatase (PTP) activity from as few as five cells and a screen is described that identifies a compound that reduces PTP activity in cell lysates. This approach offers a valuable addition to the methods available for cell-based screening.
The video explorer (2010)

We propose a video browsing tool supporting new efficient navigation means and content-based search within a single video, allowing for interactive exploration and playback of video content. The user interface provides flexible navigation indices by visualizing low-level features and frame surrogates along one or more timelines, called interactive navigation summaries. By applying simple and fast content analysis, navigation summary computation becomes feasible during browsing, enabling addition, removal, and update of navigation summaries at runtime. Semantically similar video segments will be visualized by similar patterns in certain navigation summaries, which enables users to quickly recognize and navigate to potential similar segments. Moreover, free-shape regions of video frames or video segments within navigation summaries can be selected by the user to launch a fast content-based search to find frames with similar regions or segments with similar navigation summaries.
New approach to the production of concentrated and purified inactivated polio and rabies tissue culture vaccines. (1978)

The preparation of inactivated polio and rabies vaccine in tissue culture has been developed into a "Unit Process" at our laboratory during recent years. The process comprises trypsinization of animal kidney cells by the perfusion method, cell/virus cultivation in microcarrier culture and concentration and purification of the virus suspension followed by inactivation. Also, the control tests on the virus suspensions and vaccines are performed, to the greatest possible extent, according to the same procedures. In the meantime, both vaccines thus prepared have been tested in man. High antibody titres have been obtained and no adverse reactions have been observed. The results of a field trial with inactivated poliovaccine, administered at different concentrations, will be presented by Dr Salk. Preliminary concepts for further development of the production and control of these inactivated virus vaccines are discussed.
Brain Lesions: To Biopsy or Not To Biopsy. A Single Institution Experience (2016)

Objectives: Patients presenting with intracranial lesions represent a diagnostic dilemma. Imaging and laboratory tests lack the specificity needed for decision-making. We aimed to detect what intervention and findings made the study patients eligible for brain biopsy, for observation or for treatment. Methods: From January 2010 to December 2012, electronic medical records of 312 adult patients were selected from the hospital database using key words aimed to identify brain lesions, in two-affiliated tertiary-care, county-based hospitals in Houston, Texas.Decision to biopsy, to observe or to treat brain lesions was the main outcome variable. Clinical, laboratory and imaging information were correlated with the main variable to determine which factors made the need for biopsy more likely. Results:Forty biopsied patients and 272 non-biopsied patients were included. Motor deficit, confusion or coma, single brain lesion, larger than 3 cm, with midline shift and complete ring enhancement made brain biopsy more likely, whereas bilateral brain or cerebellar lesion, presence of subcortical lesions with homogeneous enhancement, and history of cancer with potential for brain metastases made the biopsy less likely. Laboratory tests evaluated were inadequate surrogates of brain histology, whereas abnormalities on chest X ray or CT of the chest, abdomen or pelvis made the probability of brain biopsy lower. The above predictors for biopsy were not present among our HIV positive patients. Conclusions: The path from lesion finding to the decision to observe, to treat or to biopsy was heterogeneous. Prospective validation and generalization to other institutions are needed to strengthen our observations.
Pro-apoptotic Bid induces membrane perturbation by inserting selected lysolipids into the bilayer (2005)

Bid is a BH3-only member of the Bcl-2 family that regulates cell death at the level of mitochondrial membranes. Bid appears to link the mitochondrial pathway with the death receptor-mediated pathway of cell death. It is generally assumed that the f.l. (full-length) protein becomes activated after proteolytic cleavage, especially by apical caspases like caspase 8. The cleaved protein then relocates to mitochondria and promotes membrane permeabilization, presumably by interaction with mitochondrial lipids and other Bcl-2 proteins that facilitate the release of apoptogenic proteins like cytochrome c. Although the major action may reside in the C-terminus part, tBid (cleaved Bid), un-cleaved Bid also has pro-apoptotic potential when ectopically expressed in cells or in vitro. This pro-apoptotic action of f.l. Bid has remained unexplained, especially at the biochemical level. In the present study, we show that f.l. (full-length) Bid can insert specific lysolipids into the membrane surface, thereby priming mitochondria for the release of apoptogenic factors. This is most effective for lysophosphatidylcholine species that we report to accumulate in mitochondria during apoptosis induction. A Bid mutant that is not pro-apoptotic in vivo is defective in lysophosphatidylcholine-mediated membrane perturbation in vitro. Our results thus provide a biochemical explanation for the pro-apoptotic action of f.l. Bid.
Discovering object instances from scenes of Daily Living (2011)

We propose an approach to identify and segment objects from scenes that a person (or robot) encounters in Activities of Daily Living (ADL). Images collected in those cluttered scenes contain multiple objects. Each image provides only a partial, possibly very different view of each object. An object instance discovery program must be able to link pieces of visual information from multiple images and extract the consistent patterns.
Predicting the News of Tomorrow Using Patterns in Web Search Queries (2008)

The novel task we aim at in this work is to predict top terms that will prominently appear in the future news. This is a difficult task that nobody attempted before, as far as we know. We present a novel methodology for using patterns of user queries to predict future events. Query history is obtained from Web resources such as Google trends. In order to predict whether a term will appear in tomorrow's news, we examine if the terms in today's queries indicated this term in the past. We provide empirical support for the effectiveness of our method by showing its prediction power on news archives.
Plant triacylglycerols as feedstocks for the production of biofuels (2008)

Triacylglycerols produced by plants are one of the most energy-rich and abundant forms of reduced carbon available from nature. Given their chemical similarities, plant oils represent a logical substitute for conventional diesel, a non-renewable energy source. However, as plant oils are too viscous for use in modern diesel engines, they are converted to fatty acid esters. The resulting fuel is commonly referred to as biodiesel, and offers many advantages over conventional diesel. Chief among these is that biodiesel is derived from renewable sources. In addition, the production and subsequent consumption of biodiesel results in less greenhouse gas emission compared to conventional diesel. However, the widespread adoption of biodiesel faces a number of challenges. The biggest of these is a limited supply of biodiesel feedstocks. Thus, plant oil production needs to be greatly increased for biodiesel to replace a major proportion of the current and future fuel needs of the world. An increased understanding of how plants synthesize fatty acids and triacylglycerols will ultimately allow the development of novel energy crops. For example, knowledge of the regulation of oil synthesis has suggested ways to produce triacylglycerols in abundant non-seed tissues. Additionally, biodiesel has poor cold-temperature performance and low oxidative stability. Improving the fuel characteristics of biodiesel can be achieved by altering the fatty acid composition. In this regard, the generation of transgenic soybean lines with high oleic acid content represents one way in which plant biotechnology has already contributed to the improvement of biodiesel.
Metalloorganic Polymerization Catalysis as a Tool To Probe Crystallization Properties of Polymers: The Case of Isotactic Poly(1‐butene) (2009)

Age shall not weary them: Stereodefective isotactic polybutene samples, synthesized with single-center metallocene catalysts, crystallize from the melt into the stable form I (see picture) and do not undergo phase transformation upon aging at room temperature. Hence, the corresponding physical and mechanical properties of molded objects are not altered by aging. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Dynamic channel allocation based on a Hopfield neural network and requirements for autonomous operation in a distributed environment (1999)

This paper presents a distributed architecture that provides a platform for performance study of cellular radio dynamic channel allocation (DCA) schemes based on a Hopfield neural network (HNN). HNN-based DCA schemes have been studied over the recent years but these techniques are invariably centralised. Operation in a distributed environment necessitates certain system level requirements for accessing system-wide channel allocation information used by the algorithm. Distributed operation also suggests that the HNN-based DCA schemes operate autonomously and it would be of interest to evaluate how such schemes compare with the centralised schemes. The paper describes a suitable network architecture for a distributed HNN and highlights some of its key benefits through simulation.
Co-expression of RAGE and HMGB1 is associated with cancer progression and poor patient outcome of prostate cancer. (2014)

Receptor for advanced glycation end products (RAGE), along with its ligand high mobility group box 1 (HMGB1), is believed to play an important role in prostate cancer. The aim of this retrospective study was to investigate the expression of RAGE and HMGB1 and their clinical impact on prostate cancer progression and prognosis. The expression of RAGE and HMGB1 was assessed by immunohistochemistry in cancer lesions from 85 confirmed prostate cancer cases. We determined the potential association between the expression level of these two proteins and the clinicopathological features and overall patient survival. RAGE and HMGB1 were expressed in 78.8% (67/85) and 68.2% (58/85) cases of prostate cancer, respectively, and in the majority (54/85) of cases, these two proteins were co-expressed. There was a strong correlation between RAGE and HMGB1 expressions (P<0.001). The expression of RAGE, HMGB1 and their co-expression were all associated with advanced tumor clinical stage (P<0.05 for all). RAGE expression was also associated with the prostate specific antigen (PSA) level (P=0.014). However, neither the individual expression of those genes nor their co-expression was significantly related with age or Gleason score. The co-expression of RAGE and HMGB1 was associated with poor overall survival in patients with stage III and IV prostate cancer (P=0.047). These results suggest that the expression of RAGE and HMGB1 is associated with the progression and poor prognosis of prostate cancer. RAGE and HMGB1 could be new prognostic biomarkers for prostate cancer as well as molecular target for novel forms of therapies.
An in vitro model for the in vivo mobilization of cadmium by chelating agents using cadmium-113-NMR spectroscopy (1992)

An in vitro method, based on 113Cd-NMR spectroscopy, that provides an alternative to the use of animals for an initial screening of cadmium antagonists is presented. The relative values of the effective stability constants of potential chelating antagonists for cadmium are estimated by using 113Cd-NMR spectroscopy to determine the concentrations of the cadmium species involved in appropriate competitive equilibria. This is accomplished via an examination of the competition between the proposed antagonist and EDTA (ethylenediaminetetraacetic acid) for cadmium-113; previously, EDTA has been shown to be capable of removing cadmium from such in vivo binding sites as metallothionein. The reactions proceed via the stepwise addition of three dithiocarbamate groups to the cadmium accompanied by the concurrent stepwise release of donor groups from the EDTA. The resulting 113Cd-NMR data allow for the determination of the overall stability constant for the complex formed between cadmium and N-methyl-D-glucamine dithiocarbamate, iminodiacetic acid dithiocarbamate, proline dithiocarbamate, sarcosine dithiocarbamate. The use of 113Cd-NMR spectroscopy has the potential for providing direct evidence on the effectiveness of chelate antagonists to compete with endogenous ligands for other toxic metal ions. This technique could prove very useful for other compounds that are not stable enough toward acid and/or base to be examined by standard titrimetric methods.
Hepatitis B virus HBx protein deregulates cell cycle checkpoint controls. (1995)

The human hepatitis B virus (HBV) HBx protein is a small transcriptional activator that is essential for virus infection. HBx is thought to be involved in viral hepatocarcinogenesis because it promotes tumorigenesis in transgenic mice. HBx activates the RAS-RAF-mitogen-activated protein (MAP) kinase signaling cascade, through which it activates transcription factors AP-1 and NF-kappa B, and stimulates cell DNA synthesis. We show that HBx stimulates cell cycle progression, shortening the emergence of cells from quiescence (G0) and entry into S phase by at least 12 h, and accelerating transit through checkpoint controls at G0/G1 and G2/M. Compared with serum stimulation, HBx was found to strongly increase the rate and level of activation of the cyclin-dependent kinases CDK2 and CDC2, and their respective active association with cyclins E and A or cyclin B. HBx is also shown to override or greatly reduce serum dependence for cell cycle activation. Both HBx and serum were found to require activation of RAS to stimulate cell cycling, but only HBx could shorten checkpoint intervals. HBx therefore stimulates cell proliferation by activating RAS and a second unknown effector, which may be related to its reported ability to induce prolonged activation of JUN or to interact with cellular p53 protein. These data suggest a molecular mechanism by which HBx likely contributes to viral carcinogenesis. By deregulating checkpoint controls, HBx could participate in the selection of cells that are genetically unstable, some of which would accumulate unrepaired transforming mutations.