gebhart/patrepeval huggingface dataset:
Enhanced apoptosis of ovarian cancer cells via nanocarrier-mediated codelivery of siRNA and doxorubicin (2012)

A folate conjugated ternary copolymer, FA-PEG-PEI-PCL, of poly(ethylene glycol) (PEG), poly(ethylene imine) (PEI), and poly(ɛ-caprolactone) (PCL) was synthesized. The copolymer self-assembled into cationic micelles capable of co-delivering siRNA and the anticancer drug doxorubicin (DOX). This dual functional nanocarrier demonstrated low cytotoxicity and high performance in drug/siRNA delivery. Upon the codelivery of siRNA, targeting the Bcl-2 gene, and DOX, using the folate-targeted nanocarrier, DOX-induced apoptosis in the skov-3 cells overexpressing folate receptor was significantly enhanced through a mechanism of downregulating the antiapoptotic protein Bcl-2, while simultaneously upregulating the proapoptotic protein Bax. This work suggested that the combination of Bcl-2 siRNA and DOX therapies is feasible, based on our dual functional nanocarrier, which set up a good basis for a future in vivo test.
d‐Glucose as a Regioselectively Addressable Scaffold for Combinatorial Chemistry on Solid Phase (2003)

d‐Glucose derivatives bearing an anomeric thiophenyl group and orthogonally protections on secondary hydroxyl groups were linked to solid supports (PS/DV polymer, tentagel resin) through an ester bond on C‐6. It was investigated the possibility to remove orthogonally protecting groups and functionalize selectively the free hydroxyls groups and the anomeric carbon of sugars in solid phase.
IMMUNIZATION OF INFANTS WITH FORMALINIZED POLIOMYELITIS VACCINE (SALK TYPE) (1960)

The antibody response of young infants after immunization with formalinized poliomyelitis vaccine was investigated. The infants were 1 to 6 months of age at the time of primary immunization. The effect of primary as well as booster immunization was studied by testing pre- and post-primary, and pre- and post-booster specimens of blood. Vaccine lots used for immunization were of high potency as judged from guinea pig antigenic extinction titers. Prior to these tests the status of maternal antibody was determined in 594 infants, 0 to 6 months of age. These tests showed that at birth, 87 to 94% of infants have antibody for the three types of poliomyelitis virus, about 50% at the age of 3 months, and 11 to 16% at the age of 5 and 6 months. For convenience of analysis of results, the infants were divided into three "age-groups": Group A consisted of infants 1 and 2 months of age, Group B, 3 and 4 months, and Group C, 5 and 6 months of age. To facilitate interpretation, the antibody response to primary immunization in Groups A and B was tested at the age of 6 months. Development of antibody after primary immunization was pronounced in all three groups. It was shown, however, that the greater the age at primary immunization, the better the response; the conversion rates and antibody titers in infants of Group C were higher than in Group B and these in turn higher than in Group A. With the vaccines employed, post-primary conversion rates in infants of Group C were 71, 98 and 53% for poliomyelitis virus types 1, 2 and 3, respectively, after a course of two inoculations, and 90, 100 and 85%, respectively, after three inoculations of vaccine. In all infants, the best response to the vaccines employed was to type 2 antigen, less to type 1 and poorest to type 3. Presence of maternal antibody seemed to interfere with active production of antibody. The booster response was excellent in all infants studied. It was shown to be independent of age at primary immunization and of presence or absence of maternal antibody at the time when primary immunization had been carried out. Adequate primary immunization of infants, i.e. with antigen of high potency and large amount, either produces demonstrable antibody or "sensitizes" in such a way that a booster inoculation will promptly show presence of antibody.
Recent Developments in Portfolio Insurance (2008)

The aim of this article is to describe how portfolio insurance works, the main strategies employed and how these have evolved over recent years, and the possible links between their use and financial market stability. The key benefit of portfolio insurance is that it enables financial risk to be distributed among those agents most willing to absorb it. The downside is that it can possibly create conditions for greater fragility in financial markets and leaves issuers of portfolio insurance exposed to potential unexpectedly high losses. It seems unlikely that portfolio insurance-elated investments contributed significantly to the financial market volatility that began in Summer 2007. Nonetheless, it is important to keep alert to situations when portfolio insurance could potentially work to amplify financial market instability.
Identification of an Additive NFIR System and its applications in generalized Hammerstein models (2006)

Identification of a nonlinear additive system is considered. An input signal is designed in such a way that the problem of identification of nonlinear additive systems is reduced to a problem of identification of static nonlinear functions. Then, three approaches are established to estimate the order of the system. The methods exploit the structure of the nonlinear additive model so that their implementations are easy.
Survey and analysis of multimodal sensor planning and integration for wide area surveillance (2009)

Although sensor planning in computer vision has been a subject of research for over two decades, a vast majority of the research seems to concentrate on two particular applications in a rather limited context of laboratory and industrial workbenches, namely 3D object reconstruction and robotic arm manipulation. Recently, increasing interest is engaged in research to come up with solutions that provide wide-area autonomous surveillance systems for object characterization and situation awareness, which involves portable, wireless, and/or Internet connected radar, digital video, and/or infrared sensors. The prominent research problems associated with multisensor integration for wide-area surveillance are modality selection, sensor planning, data fusion, and data exchange (communication) among multiple sensors. Thus, the requirements and constraints to be addressed include far-field view, wide coverage, high resolution, cooperative sensors, adaptive sensing modalities, dynamic objects, and uncontrolled environments. This article summarizes a new survey and analysis conducted in light of these challenging requirements and constraints. It involves techniques and strategies from work done in the areas of sensor fusion, sensor networks, smart sensing, Geographic Information Systems (GIS), photogrammetry, and other intelligent systems where finding optimal solutions to the placement and deployment of multimodal sensors covering a wide area is important. While techniques covered in this survey are applicable to many wide-area environments such as traffic monitoring, airport terminal surveillance, parking lot surveillance, etc., our examples will be drawn mainly from such applications as harbor security and long-range face recognition.
Molecular remedy of complex I defects: Rotenone-insensitive internal NADH-quinone oxidoreductase of Saccharomyces cerevisiae mitochondria restores the NADH oxidase activity of complex I-deficient mammalian cells (1998)

The NDI1 gene encoding rotenone-insensitive internal NADH-quinone oxidoreductase of Saccharomyces cerevisiae mitochondria was cotransfected into the complex I-deficient Chinese hamster CCL16-B2 cells. Stable NDI1-transfected cells were obtained by screening with antibiotic G418. The NDI1 gene was shown to be expressed in the transfected cells. The expressed Ndi1 enzyme was recognized to be localized to mitochondria by immunoblotting and confocal immunofluorescence microscopic analyses. Using digitonin-permeabilized cells, it was shown that the transfected cells, but not nontransfected control cells, exhibited the electron transfer activities with glutamate/malate as the respiratory substrate. The activities were inhibited by flavone, antimycin A, and KCN but not by rotenone. Added NADH did not serve as the substrate, suggesting that the expressed Ndi1 enzyme was located on the matrix side of the inner mitochondrial membranes. Furthermore, although nontransfected cells could not survive in a medium low in glucose (0.6 mM), which is a substrate of glycolysis, the NDI1-transfected cells were able to grow in the absence of added glucose. When glycolysis is slow, either at low glucose concentrations or in the presence of galactose, respiration is required for cells to survive. The mutant cells do not survive at low glucose or in galactose, but they can be rescued by Ndi1. These results indicated that the S. cerevisiae Ndi1 was expressed functionally in CCL16-B2 cells and catalyzed electron transfer from NADH in the matrix to ubiquinone-10 in the inner mitochondrial membranes. It is concluded that the NDI1 gene provides a potentially useful tool for gene therapy of mitochondrial diseases caused by complex I deficiency.
Cytotoxic Necrotizing Factor Type 2 Produced by Pathogenic Escherichia coli Deamidates a Gln Residue in the Conserved G-3 Domain of the Rho Family and Preferentially Inhibits the GTPase Activity of RhoA and Rac1 (1999)

Cytotoxic necrotizing factor types 1 and 2 (CNF1 and -2) produced by pathogenic Escherichia coli strains have 90% conserved residues over 1,014-amino-acid sequences. Both CNFs are able to provoke a remarkable increase in F-actin structures in cultured cells and covalently modify the RhoA small GTPases. In this study, we demonstrated that CNF2 reduced RhoA GTPase activity in the presence and absence of P122(RhoGAP). Subsequently, peptide mapping and amino acid sequencing of CNF2-modified FLAG-RhoA produced in E. coli revealed that CNF2 deamidates Q63 of RhoA-like CNF1. In vitro incubation of the C-terminal domain of CNF2 with FLAG-RhoA resulted also in deamidation of the FLAG-RhoA, suggesting that this region contains the enzymatic domain of CNF2. An oligopeptide antibody (anti-E63) which specifically recognized the altered G-3 domain of the Rho family reacted with glutathione S-transferase (GST)-RhoA and GST-Rac1 but not with GST-Cdc42 when coexpressed with CNF2. In addition, CNF2 selectively induced accumulation of GTP form of FLAG-RhoA and FLAG-Rac1 but not of FLAG-Cdc42 in Cos-7 cells. Taken together, these results indicate that CNF2 preferentially deamidates RhoA Q63 and Rac1 Q61 and constitutively activates these small GTPases in cultured cells. In contrast, anti-E63 reacted with GST-RhoA and GST-Cdc42 but not with GST-Rac1 when coexpressed with CNF1. These results indicate that CNF2 and CNF1 share the same catalytic activity but have distinct substrate specificities, which may reflect their differences in toxic activity in vivo.
Pillow lavas and the Leidenfrost effect (1984)

Field observations of the formation of pillows by hot, de-gassed lava entering the sea have proved that their generation involves the underwater exposure and movement of incandescent material. This is made possible by the Leidenfrost effect, the phenomenon whereby film boiling replaces the usual nucleated boiling above a certain temperature, thereby forming an insulating sheath of vapour around any sufficiently hot body immersed in a liquid. Only on cooling below a certain temperature (defined here as the Nukiyama temperature) will rapid heat exchange occur between water and hot, gas-free lava. Near the surface, this could produce phreatic explosions and extensive clouds of steam.
Echocardiogram view classification using edge filtered scale-invariant motion features (2009)

In an 2D echocardiogram exam, an ultrasound probe samples the heart with 2D slices. Changing the orientation and position on the probe changes the slice viewpoint, altering the cardiac anatomy being imaged. The determination of the probe viewpoint forms an essential step in automatic cardiac echo image analysis. In this paper we present a system for automatic view classification that exploits cues from both cardiac structure and motion in echocardiogram videos. In our framework, each image from the echocardiogram video is represented by a set of novel salient features. We locate these features at scale invariant points in the edge-filtered motion magnitude images and encode them using local spatial, textural and kinetic information. Training in our system involves learning a hierarchical feature dictionary and parameters of a pyramid matching kernel based support vector machine. While testing, each image, classified independently, casts a votes towards parent video classification and the viewpoint with maximum votes wins. Through experiments on a large database of echocardiograms obtained from both diseased and control subjects, we show that our technique consistently outperforms state-of-the-art methods in the popular four-view classification test. We also present results for eight-view classification to demonstrate the scalability of our framework.
Narrowing Down the Targets： Towards Successful Genetic Engineering of Drought-Tolerant Crops (2010)

干旱是影响世界范围的农业的最重要的环境压力。利用收益潜力并且坚持说在水有限环境的庄稼的收益稳定性是必须被承担以便为增加的世界人口保证食物供应的迫切任务。巨大的努力被奉献给通过使用的基因、分子、生物化学的研究在植物干旱反应识别关键管理者，在大多数情况中，模型种类 Arabidopsis thaliana。然而，仅仅这些管理者的小部分在干旱忍耐的改进为他们的申请作为潜在的候选人基因被探索了在庄稼。基于生物功能，这些基因能被分类进下列三个范畴：(1 ) 压力应答的 transcriptional 规定(例如 DREB1， AREB， NF-YB ) ；(2 ) post-transcriptional RNA 或蛋白质修正象 phosphorylation/dephosphorylation 那样(例如 SnRK2， ABI1 ) 并且 farnesylation (例如 ERA1 ) ；并且(3 ) osomoprotectant 新陈代谢或分子的女伴(例如 CspB ) 。当在路径下面继续到新目标基因的发现时，严肃的努力也集中于在特定的时间、空间的模式为压力忍耐调整已知的候选人基因的表达式在植物生长和开发避免否定效果。这些努力开始由在许多水剥夺条件下面在几庄稼显示出收益改进正在忍受水果。当最如此的评估在控制生长环境下面被执行了，差距在这块地里在实验室和这些技术的申请在早成功之间尚待到主食庄稼的精英栽培变种。不过，重要进步在为干旱忍耐表明小径和主人管理者的鉴定被取得了。获得的知识将在关键庄稼便于单个或多重的目标和量的特点 loci 的遗传工程在最佳、非最优的条件下面与 high-yielding 潜力创造商业等级的栽培变种。
Identification of shared antigenic determinants of the putative human T lymphocyte antigen receptor. (1984)

A mouse antiserum, anti-gp40,49 was obtained by immunizing BALB/c mice with the putative T cell antigen receptor isolated from HPB-MLT cells. This antiserum reacted with peripheral blood lymphocyte (PBL) and a panel of immunocompetent T cell lines and clones in each case precipitating from lysates of cells labeled by surface iodination, a disulfide-linked dimer consisting of an alpha subunit Mr (46,000-49,000) and a beta subunit Mr (40,000-45,000). Variability in Mr of the two subunits, particularly of the beta (light) subunit, was observed when the receptors of immunocompetent T cell lines with different antigen specificities were compared. Anti-gp40,49 serum reacted selectively with the alpha subunit after reduction and alkylation of the protein complex. These results confirm the relationship between the gp40,49 protein complex of HPB-MLT cells and the putative T cell antigen receptor on normal immunocompetent T cells and indicate that the alpha subunit of the human receptor expressed shared determinant(s) that are immunogenic in the mouse. Some features of the T cell antigen receptor appear to be unusual in that even with a xenoantiserum against the purified molecule, only antibodies against clonotypic determinants could be detected at the cell surface by quantitative immunofluorescence analysis.
Protracted low-dose effects on human endothelial cell proliferation and survival in vitro reveal a selective antiangiogenic window for various chemotherapeutic drugs. (2002)

Recent preclinical studies have shown that frequent administration in vivo of low doses of chemotherapeutic drugs ("metronomic" dosing) can affect tumor endothelium and inhibit tumor angiogenesis, reducing significant side effects (e.g., myelosuppression) involving other tissues, even after chronic treatment. This suggests that activated endothelial cells may be more sensitive, or even selectively sensitive, to protracted ("high-time") low-dose chemotherapy compared with other types of normal cells, thus creating a potential therapeutic window. To examine this hypothesis, we assessed the effects of several different chemotherapeutic drugs--namely paclitaxel, 4-hydroperoxycyclophosphamide, BMS-275183 (an oral taxane), doxorubicin, epothilone B (EpoB) and its analogue 5-methylpyridine EpoB--on human microvascular or macrovascular endothelial cells, fibroblasts, and drug-sensitive or multidrug-resistant breast cancer cell lines in cell culture, using both short-term (24 h) versus long-term (144 h), continuous exposures, where drug-containing medium was replaced every 24 h. Whereas little differential and only weak effects were observed using the short-term exposure, a striking trend of comparative vascular endothelial cell hypersensitivity was induced using the continuous long-term exposure protocol. Potent differential growth inhibition effects as well as induction of apoptosis were observed with IC(50) values in the range of 25-143 pM for paclitaxel, BMS-275183, EpoB, and 5-methylpyridine-EpoB. In contrast, the IC(50) values for tumor cells and fibroblasts tested were in the range of 500 pM to >1 nM for these drugs. Similar differential IC(50) values were noted using 4-hydroperoxycyclophosphamide. The results are consistent with the possibility that continuous low-dose therapy with various chemotherapeutic drugs may have a highly selective effect against cycling vascular endothelial cells, and may be relevant to the use of continuous or frequent administration of low doses of certain types of drugs as an optimal way of delivering antiangiogenic therapy.
O-GlcNAc Integrates the Proteasome and Transcriptome To Regulate Nuclear Hormone Receptors (2006)

Mechanisms controlling nuclear hormone receptors are a central question to mammalian developmental and disease processes. Herein, we show that a subtle increase in O-GlcNAc levels inhibits activation of nuclear hormone receptors. In vivo, increased levels of O-GlcNAc impair estrogen receptor activation and cause a decrease in mammary ductal side-branching morphogenesis associated with loss of progesterone receptors. Increased O-GlcNAc levels suppress transcriptional expression of coactivators and of the nuclear hormone receptors themselves. Surprisingly, increased O-GlcNAc levels are also associated with increased transcription of genes encoding corepressor proteins NCoR and SMRT. The association of the enzyme O-GlcNAc transferase with these corepressors contributes to specific regulation of nuclear hormone receptors by O-GlcNAc. Overall, transcriptional inhibition is related to the integrated effect of O-GlcNAc by direct modification of critical elements of the transcriptome and indirectly through O-GlcNAc modification of the proteasome.
PI3K isoforms as drug targets in inflammatory diseases: lessons from pharmacological and genetic strategies. (2009)

Inflammation protects the body against infection and injury, but it is a process that can become dysregulated with deleterious consequences, including the development of rheumatoid arthritis, inflammatory bowel disease, psoriasis and multiple sclerosis. In recent years, inflammation has also been demonstrated to play a key role in other widely prevalent diseases not previously considered to have inflammatory etiologies, such as Alzheimer's disease, cardiovascular diseases and cancer. The current anti-inflammatory therapies such as steroids, NSAIDs and antihistamines are mainly based on inhibiting the synthesis or action of inflammatory mediators. The more recently developed biopharmaceuticals (eg, TNFalpha-neutralizing therapies, and anti-IgE and anti-CD20 antibodies) follow a similar therapeutic strategy. However, both the established anti-inflammatory therapies and the more recent biopharmaceutical innovations have shortcomings and there remains a need for the identification and validation of new anti-inflammatory drug targets. This review focuses on the description of the data indicating that PI3K isoforms control inflammation at many levels, from the generation of inflammatory cells to the migration and function of these cells. More specifically, the contribution of the gamma and delta isoforms of PI3K to the immune processes that underpin inflammatory responses, as well as their potential as therapeutic targets, are evaluated.
The Destruction of Cyanobacterial Toxins by Titanium Dioxide (1999)

Cyanobacterial (blue-green algal) toxins are extremely toxic naturally occurring substances which display hepato- and neurotoxic behaviour (1, 2). In this paper we report the application of titanium dioxide photocatalysis for the destruction of two of these compounds, microcystin-LR and anatoxin-a. The destruction of microcystin appears to follow Langmuir-Hinshelwood kinetics although a discrepancy was observed between adsorption constants determined for the photocatalytic process with those obtained from dark isotherms. A square root dependence between illumination intensity and rate of microcystin destruction was noted. When the destruction was performed in the presence of the naturally occurring pigment it appeared that the pigment also contributes to the destruction of the toxin. Toxicity studies on the photocatalysed toxin solutions indicates that the toxicity is substantially reduced within 30 min photolysis.
Measuring the activity of BioBrick promoters using an in vivo reference standard (2008)

Abstract Background The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it difficult to predict the extent to which such efforts will succeed. As a first practical example, the Registry of Standard Biological Parts started at MIT now maintains and distributes thousands of BioBrick™ standard biological parts. However, BioBrick parts are only standardized in terms of how individual parts are physically assembled into multi-component systems, and most parts remain uncharacterized. Standardized tools, techniques, and units of measurement are needed to facilitate the characterization and reuse of parts by independent researchers across many laboratories. Results We found that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments. We choose one promoter (BBa_J23101) to serve as an in vivo reference standard for promoter activity. We demonstrated that, by measuring the activity of promoters relative to BBa_J23101, we could reduce variation in reported promoter activity due to differences in test conditions and measurement instruments by ~50%. We defined a Relative Promoter Unit (RPU) in order to report promoter characterization data in compatible units and developed a measurement kit so that researchers might more easily adopt RPU as a standard unit for reporting promoter activity. We distributed a set of test promoters to multiple labs and found good agreement in the reported relative activities of promoters so measured. We also characterized the relative activities of a reference collection of BioBrick promoters in order to further support adoption of RPU-based measurement standards. Conclusion Relative activity measurements based on an in vivo<it/>reference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These improvements are sufficient to begin to support the measurement of promoter activities across many laboratories. Additional in vivo reference standards for other types of biological functions would seem likely to have similar utility, and could thus improve research on the design, production, and reuse of standard biological parts.