gebhart/patrepeval huggingface dataset:
Radiobiological Characterization of 53 Human Tumor Cell Lines (1989)

We investigated the in vitro radiobiological survival parameters of 53 human tumor cell lines studied in exponential growth. Epithelial cell lines derived from 24 patients with head and neck carcinoma, 15 patients with ovarian carcinoma, and mesenchymal tumor cell lines derived from 14 patients with bone and soft tissue sarcomas were studied. Survival data are analyzed using the multi-target and linear quadratic models. The head and neck and ovarian carcinoma tumor cell lines were more radioresistant as measured by D0, D, and alpha parameters, compared with the bone and soft-tissue sarcoma lines. The radiobiological parameters of tumor cell lines reported herein are similar to parameters of tumor cell lines derived from head and neck and soft tissue sarcoma patients presently being followed for clinical outcome following radiotherapy in our clinic.
Molecular linkage of the Ly-3 and Ly-2 genes. Requirement of Ly-2 for Ly-3 surface expression. (1988)

We have isolated the Ly-3 gene by chromosomal walking from the previously cloned Ly-2 gene. These genes are shown to be 36 kb apart and in the same transcriptional orientation. Transfection of the Ly-3 gene into mouse L cells results in cell surface expression of Ly-3 protein only in the presence of Ly-2 (or its human homolog, CD8), although Ly-2 surface expression is not similarly dependent on Ly-3. cDNA clones encoding Ly-3 have been isolated and sequenced and show little sequence similarity to Ly-2, whereas both Ly-2 and Ly-3 are homologous to Ig variable regions. One cDNA clone encodes a form of Ly-3 lacking a transmembrane region. Although two alleles of Ly-3 have been previously defined serologically, Northern blot analyses of Ly-3 mRNA from a series of inbred mouse strains show unusual polymorphisms in the lengths of Ly-3 mRNA species defining at least three allelic variants of this gene.
Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization (2017)

Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein's insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal's DNA-ratchet function.
Irreversible Electroporation (2010)

Relaxant general anesthesia is required for IRE of the liver, lung, and kidney. An electrocardiogram synchronizer should be used to minimize the risk of arrhythmias. Attention to the position of the arms is required to maximize CT scan quality but minimize brachial plexus strain. Simple postoperative analgesia is all that is required in most patients.
Enhancement of DNA Vaccine Potency by Coadministration of a Tumor Antigen Gene and DNA Encoding Serine Protease Inhibitor-6 (2004)

Serine protease inhibitor 6 (SPI-6), also called Serpinb9, inhibits granzyme B and thus may provide a method for delaying apoptotic cell death in dendritic cells. We have previously enhanced DNA vaccine potency by targeting antigen to MHC antigen presentation pathways, using proteins such as Mycobacterium tuberculosis heat shock protein 70, calreticulin, domain II of Pseudomonas aeruginosa exotoxin A, or the sorting signal of the lysosome-associated membrane protein type 1. In this study, we explored intradermal coadministration of DNA encoding SPI-6 with DNA constructs encoding human papillomavirus type 16 E7 linked to these intracellular targeting molecules for its ability to generate E7-specific CD8+ T-cell immune responses and E7-specific antitumor effects. This combination of strategies resulted in significantly increased E7-specific CD8+ T-cell and CD4+ Th1-cell responses, enhanced tumor treatment ability, and stronger tumor protection when compared with vaccination without SPI-6. Among these targeting strategies tested, mice vaccinated with Sig/E7/lysosome-associated membrane protein type 1 mixed with SPI-6 showed the greatest fold increase in E7-specific CD8+ T cells ( approximately 5-fold). Vaccination with a nonfunctional mutant of SPI-6 did not result in immune enhancement, indicating that enhancement was dependent on the antiapoptotic function of SPI-6. Our results suggest that DNA vaccines combining strategies that enhance MHC class I and II antigen processing with SPI-6 have potential clinical implications for control of viral infection and neoplasia.
Synthesis of a [1,4]dioxane-2,5-dione based-peptidomimetic scaffold (2005)

2S,3S)-3-[N-Cbz-L-Leucinyl]amino-2-hydroxy-4-phenylbutanoic acid 5 dimerised on treatment with EDCI and HOBT to give the symmetrical [1,4]dioxane-2,5-dione-based peptidomimetic 6.
Fully integrated planar magnetics for primary-parallel isolated boost converter (2011)

A high efficient planar integrated magnetics (PIM) design approach for primary parallel isolated boost converters is presented. All magnetic components in the converter including two input inductors and two transformers with primary-parallel and secondary-series windings are integrated into an E-I-E core geometry. Due to a low reluctance path provided by the shared I-core, the two transformers as well as the two input inductors can be integrated independently, reducing the total ferrite volume and core loss. AC losses in the windings and the leakage inductance of the transformer are kept low by interleaving the primary and secondary turns of the transformers. To verify the validity of the design approach, a 1-kW prototype converter with two primary power stages is implemented for a fuel cell fed battery charger application with 20-40 V input and 170-230 V output. An efficiency of 96% can be achieved during nominal operating conditions. Also experimental comparisons between the PIM module and two separate cases have been done in order to illustrate the advantages of the proposed method.
p-Hydroxyphenylacetaldehyde Is the Major Product of L-Tyrosine Oxidation by Activated Human Phagocytes (1996)

Reactive aldehydes generated during lipid peroxidation have been implicated in the pathogenesis of atherosclerosis as well as other inflammatory diseases. A potential catalyst for such reactions is myeloperoxidase, a hemeprotein secreted by activated phagocytes. We now report that activated neutrophils utilize the myeloperoxidase-H2O2-chloride system to convert L-tyrosine to p-hydroxyphenylacetaldehyde. Production of p-hydroxyphenylacetaldehyde was nearly quantitative at physiological concentrations of L-tyrosine and chloride. Aldehyde generation required myeloperoxidase, H2O2, L-tyrosine, and chloride ion; it was inhibited by the H2O2 scavenger catalase and by the heme poisons azide and cyanide. Phorbol ester- and calcium ionophore-stimulated human neutrophils likewise generated p-hydroxyphenylacetaldehyde from L-tyrosine by a pathway inhibited by azide, cyanide, and catalase. Aldehyde production accounted for 75% of H2O2 generated by optimally stimulated neutrophils at plasma concentrations of L-tyrosine and chloride. Collectively, these results indicate that activated phagocytes, under physiological conditions, utilize myeloperoxidase to execute the chloride-dependent conversion of L-tyrosine to the lipid-soluble aldehyde, p-hydroxyphenylacetaldehyde, in near quantitative yield. Moreover, like aldehydes derived from lipid peroxidation, amino acid-derived aldehydes may exert potent biological effects in vascular lesions and other sites of inflammation.
The methodology and an application to fight against Unicode attacks (2006)

Unicode is becoming a dominant character representation format for information processing. This presents a very dangerous usability and security problem for many applications. The problem arises because many characters in the UCS (Universal Character Set) are visually and/or semantically similar to each other. This presents a mechanism for malicious people to carry out Unicode Attacks, which include spam attacks, phishing attacks, and web identity attacks. In this paper, we address the potential attacks, and propose a methodology for countering them. To evaluate the feasibility of our methodology, we construct a Unicode Character Similarity List (UC-SimList). We then implement a visual and semantic based edit distance (VSED), as well as a visual and semantic based Knuth-Morris-Pratt algorithm (VSKMP), to detect Unicode attacks. We develop a prototype Unicode attack detection tool, IDN-SecuChecker, which detects phishing weblinks and fake user name (account) attacks. We also introduce the possible practical use of Unicode attack detectors.
Seamless Mosaicing of Image-Based Texture Maps (2007)

Image-based object modeling has emerged as an important computer vision application. Typically, the process starts with the acquisition of the image views of an object. These views are registered within the global coordinate system using structure-and-motion techniques, while on the next step the geometric shape of an object is recovered using stereo and/or silhouette cues. This paper considers the final step, which creates the texture map for the recovered geometry model. The approach proposed in the paper naturally starts by backprojecting original views onto the obtained surface. A texture is then mosaiced from these back projections, whereas the quality of the mosaic is maximized within the process of Markov random field energy optimization. Finally, the residual seams between the mosaic components are removed via seam levelling procedure, which is similar to gradient-domain stitching techniques recently proposed for image editing. Unlike previous approaches to the same problem, intensity blending as well as image resampling are avoided on all stages of the process, which ensures that the resolution of the produced texture is essentially the same as that of the original views. Importantly, due to restriction to non-greedy energy optimization techniques, good results are produced even in the presence of significant errors on image registration and geometric estimation steps.
Relationships between caveolae and eNOS: everything in proximity and the proximity of everything (2002)

Caveolae, flask-shaped invaginations of the plasma membrane occupying up to 30% of cell surface in capillaries, represent a predominant location of endothelial nitric oxide synthase (eNOS) in endothelial cells. The caveolar coat protein caveolin forms high-molecular-weight, Triton-insoluble complexes through oligomerization mediated by interactions between NH2-terminal residues 61-101. eNOS is targeted to caveolae by cotranslational N-myristoylation and posttranslational palmitoylation. Caveolin-1 coimmunoprecipitates with eNOS; interaction with eNOS occurs via the caveolin-1 scaffolding domain and appears to result in the inhibition of NOS activity. The inhibitory conformation of eNOS is reversed by the addition of excess Ca2+/calmodulin and by Akt-induced phosphorylation of eNOS. Here, we shall dissect the system using the classic paradigm of a reflex loop: 1) the action of afferent elements, such as fluid shear stress and its putative caveolar sensor, on caveolae; 2) the ways in which afferent signals may affect the central element, the activation of the eNOS-nitric oxide system; and 3) several resultant well-established and novel physiologically important effector mechanisms, i.e., vasorelaxation, angiogenesis, membrane fluidity, endothelial permeability, deterrance of inflammatory cells, and prevention of platelet aggregation.
Comparative thrombolytic properties of single-chain forms of urokinase- type plasminogen activator (1987)

The specific thrombolytic properties of urokinase and three molecular forms of single-chain urokinase-type plasminogen activator (scu-PA) were compared in a human plasma milieu in vitro and in an experimental thrombosis model in rabbits. These scu-PA molecules included Mr 54,000 scu-PA from human urine (urinary scu-PA), scu-PA from conditioned media of a human lung adenocarcinoma cell line (CALU-3,ATCC,HTB-55) (cellular scu-PA) and an Mr 32,000 proteolytic derivative of cellular scu-PA (scu- PA-32k). All four molecular forms induced significant lysis of a 125I- labeled human plasma clot immersed in citrated human plasma at concentrations between 50 and 200 IU/mL. None of the four showed absolute fibrin-specificity, but at equivalent lytic dose the three single-chain forms appeared to cause less fibrinogen degradation and alpha 2-antiplasmin consumption than two-chain urokinase. In addition, the fibrinolytic potential of the three single-chain forms was largely maintained during pre-incubation in plasma for up to 48 hours whereas that of urokinase was completely inhibited. Intravenous (IV) infusion of cellular scu-PA or scu-PA-32k into rabbits with a 125I-labeled thrombus in the jugular vein caused significant dose-dependent lysis at concentrations ranging from 8,700 to 35,000 and from 9,000 to 36,000 IU/kg respectively. Clot lysis was accompanied by minor alpha 2- antiplasmin consumption or fibrinogen breakdown. In contrast, urokinase induced lysis at doses between 20,000 and 200,000 IU/kg, but at higher doses was associated with significant systemic activation of the fibrinolytic system. It is concluded that scu-PA obtained from CALU-3 cell cultures has identical thrombolytic properties to that obtained from urine. In addition, the scu-PA-32k proteolytic derivative has the same fibrin-specific thrombolytic properties as the intact molecule. Cellular scu-PA and scu-PA-32k may therefore constitute more readily available alternatives for clot-selective thrombolytic therapy in man.
ISOLATION, GENETIC MAPPING AND SOME CHARACTERIZATION OF A MUTATION IN ESCHERICHIA COLI THAT AFFECTS THE PROCESSING OF RIBONUCLEIC ACID (1978)

Temperature-sensitive mutants were isolated from an rnc (RNase III-) strain of Escherichia coli, and their rRNA metabolism was analyzed on 3% polyacrylamide gels. One of these mutants was unable to produce 23S and 5S rRNAs at the nonpermissive temperature. When an rnc+ allele was introduced to this strain, it remained temperature sensitive. At the nonpermissive temperature, this strain could then produce 23S rRNA but was unable to make normal levels of 5S rRNA. In matings and transduction experiments, the defect in rRNA metabolism and temperature sensitivity behaved as a syndrome caused by a single point mutation, which was mapped at min 23.5 on the E. coli chromosome. This mutation probably affects an enzyme, ribonuclease E (RNase E), which introduces a cut in the nascent rRNA transcript between the 23S and the 5S rRNA cistrons. The mutation rne is recessive with respect to temperature sensitivity and the pattern of rRNA. Revertants able to grow at 43 degrees and with normal metabolism of rRNA were isolated; genetic analysis showed that they do not contain the original rne mutation, suggesting that they were true revertants. By combining the rne mutation with an rnc mutation, double rnc rne strains were synthesized, which behaved very similarly to the original rnc strain from which the rne mutation was isolated. Such strains have RNA metabolism that is similar to that of rnc strains at permissive temperatures, but at the nonpermissive temperature they fail to synthesize p23, m23, and 5S rRNAs. Thus, the experiments reported here, together with previous studies, suggest the existence of a new processing ribonuclease activity in Escherichia coli, which is called ribonuclease E.
Characterization of the Dunning R3327H prostatic adenocarcinoma: an appropriate animal model for prostatic cancer. (1977)

Oocyte vitrification causes a temporary disassembly of the metaphase plate and spindle, which needs time to recover after warming. As a consequence, early post-fertilization events-such as timing of second polar body extrusion-might be altered, with unknown effects on preimplantation development, timing to pronuclear breakdown, and timing of cleavages. The aim of this study was to evaluate if differences exist among these events when comparing embryos obtained from fresh-donated versus vitrified/warmed oocytes from young women. We performed a prospective study with 201 embryos from 100 fresh and 101 vitrified/warmed oocytes that were subsequently fertilized by intracytoplasmic sperm injection. Kaplan-Meier curves of each time period were generated, in which we observed that median developmental times did not differ between embryos from fresh versus vitrified/warmed oocytes among all the metrics assessed. Thus, for young women without fertility problems, no differences exist between the timing of early developmental milestones in embryos derived from fresh or vitrified oocytes, and vitrification does not affect the preimplantation development of the resulting embryos. Mol. Reprod. Dev. 83: 624-629, 2016. © 2016 Wiley Periodicals, Inc.
ADP can induce aggregation of human platelets via both P2Y1 and P2T receptors (2000)

1. In the present study we have investigated the roles of P2Y(1) and P(2T) receptor subtypes in adenosine 5'-diphosphate (ADP)-induced aggregation of human platelets in heparinized platelet rich plasma. 2. The response to ADP can be characterized as the initial rate or the maximum or final extent of aggregation. The response profile is determined by the concentration of ADP used, being transient at lower and sustained at higher concentrations. 3. The P2Y(1) receptor antagonist, adenosine-3'-phosphate-5'-phosphate (A3P5P) competitively antagonized the initial rate of aggregation (pK(B) 5. 47) and transformed the response profile to a slowly developing but sustained response. Both maximum and final extents were also inhibited by A3P5P although not in a competitive manner (Schild slope <1). 4. The P(2T) receptor antagonist, AR-C67085, competitively antagonized the final extent of aggregation (pK(B) 8.54), transforming the response profile to one of rapid, transient aggregation. Its effect on maximum extent (the most widely used index of aggregation) was complex, and further supported the involvement of both receptor subtypes in the aggregation response. 5. ADP-induced aggregation is a complex phenomenon, the nature of which is determined by the relative occupancy of the two receptor subtypes. While P2Y(1) receptor activation causes a rapid and transient aggregation, the extent of sustained aggregation is determined by the level of P(2T) receptor occupancy. Hence, detailed analysis of the aggregation response is essential to correctly define the purinergic pharmacology of the platelet and interpretation of results is critically dependent on the response index chosen.
RAGE-Abeta interactions in the pathophysiology of Alzheimer's disease. (1998)

RAGE is a cell surface molecule primarily identified for its capacity to bind advanced glycation end-products and amphoterin. Immunocytochemical studies demonstrated that in Alzheimer's Disease (AD) the expression of RAGE is elevated in neurons close to neuritic plaque beta-amyloid (Abeta) deposits and in the cells of Abeta containing vessels. Cross-linking of surface bound Abeta 1-40 to endothelial cells, yielded a band of 50 kDa identified as RAGE. Using the soluble extracellular domain of recombinant human RAGE, we found that Abeta binds to RAGE with a Kd = 57 +/- 14 nM, a value close to those found for mouse brain endothelial cells and rat cortical neurons. The interaction of Abeta with RAGE in neuronal, endothelial, and RAGE-transfected COS-1 cells induced oxidative stress, as assessed by the TBARS and MTT assays. ELISA demonstrated a 2.5 times increase of RAGE in AD over control brains. Activated microglia also showed elevated expression of RAGE. In the BV-2 microglial cell line, RAGE bound Abeta in dose dependent manner with a Kd of 25 +/- 9 nM. Soluble Abeta induced the migration of microglia along a concentration gradient, while immobilized Abeta arrested this migration. Abeta-RAGE interaction also activated NF-kappaB, resulting in neuronal up-regulation of macrophage-colony stimulating factor (M-CSF) which also induced microglial migration. Taken together, our data suggest that RAGE-Abeta interactions play an important role in the pathophysiology of Alzheimer's Disease.
A scanning line source for simultaneous emission and transmission measurements in SPECT. (1993)

A scanning collimated line source for simultaneously acquiring emission and transmission data from a gamma camera has been developed. The line source is microprocessor-controlled and incorporates hardware to electronically window the spatial gamma camera signals in order to separate the emission signals of the subject from transmission signals from the line source. The device improves upon the previously described emission-transmission scanning technique using a flood source in three ways: (1) it overcomes the limitation that the transmission radionuclide must have a lower energy than the emission radionuclide; (2) it provides narrow-beam (scatter free) attenuation measurements of the subject being examined; and (3) it reduces the radiation exposure to staff. Attenuation coefficients for an elliptocal water-filled phantom were measured to be mu = 0.15 +/- 0.01 cm-1. The technique has been validated in phantom and human studies using a range of radionuclide combinations and imaging geometries and gives equivalent results using separate and simultaneous acquisitions.
Modification of low density lipoprotein by endothelial cells involves lipid peroxidation and degradation of low density lipoprotein phospholipids. (1984)

Low density lipoprotein (LDL) incubated with cultured endothelial cells from rabbit aorta or human umbilical vein is altered in several ways (EC-modified): (i) It is degraded by macrophages much faster than LDL similarly incubated in the absence of cells or incubated with fibroblasts. (ii) Its electrophoretic mobility is increased. (iii) Its density is increased. We report here that antioxidants completely prevent these changes. We also report that these changes do not take place if transition metals in the medium are chelated with EDTA. During EC-modification as much as 40% of the LDL phosphatidylcholine is degraded to lysophosphatidylcholine by a phospholipase A2-like activity. When incubation conditions in the absence of cells were selected to favor oxidation--for example, by extending the time of incubation of LDL at low concentrations, or by increasing the Cu2+ concentration--LDL underwent changes very similar to those occurring in the presence of cells, including degradation of phosphatidylcholine. Hence, some phospholipase activity appears to be associated with the isolated LDL used in these studies. The results suggest a complex process in which endothelial cells modify LDL by mechanisms involving generation of free radicals and action of phospholipase (s).