gebhart/patrepeval huggingface dataset:
Potential tumor- or organ-imaging agents. 26. Polyiodinated 2-substituted triacylglycerols as hepatographic agents (1986)

A series of omega-(3-amino-2,4,6-triiodophenyl)alkanoic acids and the corresponding 1,3-dipalmitoylglycerol 2-[omega-(3-amino-2,4,6-triiodophenyl)alkanoates] were synthesized, radioiodinated with iodine-125, and evaluated for their ability to selectively localize in the liver for potential use as hepatographic imaging agents. Acid analogues 1d and 1e afforded relatively high levels of radioactivity in the liver (45 and 49% injected dose) 5 min after intravenous administration to rats. These acids displayed a marked propensity to become bound to plasma albumin. In contrast, triacylglycerol analogues 10a and 10c did not become immediately associated with plasma albumin but instead rapidly became associated with plasma lipoproteins and showed a different tissue distribution profile than free acids 1a and 1c. Although long-chain triacylglycerol analogues 10d and 10e exhibited some capacity to accumulate in the liver at 5 and 30 min, respectively, analysis of the plasma revealed significant in vivo ester hydrolysis. It would thus appear that liver radioactivity following administration of 10d and 10e was due to uptake of the free acid and not the intact triacylglycerol. Triacylglycerol analogues 10a and 10c, on the other hand, were taken up intact and showed liver accumulations of 25 and 35% of the administered dose at 30 min.
Ex vivo expansion of enriched peripheral blood CD34+ progenitor cells by stem cell factor, interleukin-1 beta (IL-1 beta), IL-6, IL-3, interferon-gamma, and erythropoietin (1993)

To provide sufficient numbers of peripheral blood progenitor cells (PBPCs) for repetitive use after high-dose chemotherapy, we investigated the ability of hematopoietic growth factor combinations to expand the number of clonogenic PBPCs ex vivo. Chemotherapy plus granulocyte colony-stimulating factor (G-CSF) mobilized CD34+ cells from 18 patients with metastatic solid tumors or refractory lymphomas were cultured for up to 28 days in a liquid culture system. The effects of interleukin-1 beta (IL-1), IL-3, IL-6, granulocyte-macrophage-CSF (GM-CSF), G-CSF, macrophage-CSF (M-CSF), stem cell factor (SCF), erythropoietin (EPO), leukemia inhibitory factor (LIF), and interferon-gamma, as well as 36 combinations of these factors were tested. A combination of five hematopoietic growth factors, including SCF, EPO, IL-1, IL-3, and IL-6, was identified as the optimal combination of growth factors for both the expansion of total nucleated cells as well as the expansion of clonogenic progenitor cells. Proliferation peaked at days 12 to 14, with a median 190-fold increase (range, 46- to 930-fold) of total clonogenic progenitor cells. Expanded progenitor cells generated myeloid (colony-forming unit-granulocyte-macrophage), erythroid (burst-forming unit-erythroid), as well as multilineage (colony-forming unit-granulocyte, erythrocyte, monocyte, megakaryocyte) colony-forming units. The number of multilineage colonies increased 250-fold (range, 33- to 589-fold) as compared with pre-expansion values. Moreover, the absolute number of early hematopoietic progenitor cells (CD34+/HLA-DR-; CD34+/CD38-), as well as the number of 4-HC-resistant progenitors within expanded cells increased significantly. Interferon-gamma was shown to synergize with the 5-factor combination, whereas the addition of GM-CSF significantly decreased the number of total clonogenic progenitor cells. Large-scale expansion of PB CD34+ cells (starting cell number, 1.5 x 10(6) CD34+ cells) in autologous plasma supplemented with the same 5-factor combination resulted in an equivalent expansion of progenitor cells as compared with the microculture system. In summary, our data indicate that chemotherapy plus G-CSF-mobilized PBPCs from cancer patients can be effectively expanded ex vivo. Moreover, our data suggest the feasibility of large-scale expansion of PBPCs, starting from small numbers of PB CD34+ cells. The number of cells expanded ex vivo might be sufficient for repetitive use after high-dose chemotherapy and might be candidate cells for therapeutic gene transfer.
Capillary zone electrophoretic detection of biological thiols and their S-nitrosated derivatives (1992)

Reduced thiols (RSH) react with certain oxides of nitrogen to yield S-nitroso thiols (RSNO) possessing smooth muscle relaxant and platelet inhibitory properties. Nitrosated derivatives of the biological thiols--glutathione, cysteine, and homocysteine--have therefore been considered as bioactive intermediates in the metabolism of organic nitrates and the endothelium-derived relaxing factor with properties of nitric oxide. As yet, however, there is no established chemical method for identifying the biological S-nitroso thiols and, consequently, little is known of their distinguishing chemical characteristics or biochemistry. In this study, we demonstrate for the first time a simple, rapid, and reproducible method for separating these thiols from their S-nitrosated derivatives using capillary zone electrophoresis. Cysteine, homocysteine, and glutathione were separated from one another and from their corresponding disulfides in 0.01 M phosphate buffer, pH 2.5, by capillary zone electrophoresis and absorbance detection at 200 nm with measured elution times of 5.92-16.15 min; corresponding S-nitroso thiols were selectively detected at 320 nm and eluted at 2.50-18.20 min. These data support the specificity and reproducibility of this technique for separation and identification of thiols, disulfides, and S-nitroso thiol derivatives.
Targeted detection of prostate cancer proteins in serum using heavy‐isotope‐labeled‐peptide standards and MALDI‐TOF/TOF (2009)

Abstract Proteins released from cancer tissues to patient sera can potentially be used to achieve sensitive, specific, and early detection of cancer by means of blood tests. In this study, we used a platform that combines glycopeptide capture, heavy‐isotope‐labeled‐peptide standards, and liquid chromatography coupled to tandem mass spectrometry to determine which glycoproteins from prostate cancer can be detected in sera from patients with early‐stage prostate cancer. The detection limit for prostate‐specific antigen in serum was 3.44 ng/mL; thus, direct identification of low abundance, cancer‐specific proteins was achieved using our platform. We showed that prostatic acid phosphatase and membrane metallo‐endopeptidase that were detected in sera were preferentially expressed in prostate cancer tissues. Levels of these two proteins were elevated in biopsy‐positive patients but not biopsy‐negative groups. Therefore, these two proteins are candidate biomarkers for analysis of patient samples with levels of prostate‐specific antigen in the diagnostic gray zone.
Object instance recognition using triplets of feature symbols (2007)

Known object recognition is the task of recognizing specific objects, such as cereal boxes or soda cans. Millions of such objects exist, and finding a computationally feasible method for recognition can be difficult. Ideally, the computational costs should scale with the complexity of the testing image, and not the size of the object database. To accomplish this goal we propose a method for detection and recognition based on triplets of feature descriptors. Each feature is given a label based on a modified K-means clustering algorithm. Object matching is then done by inverse lookup within a table of possible triplets. The ambiguity of the matches is further reduced by having each triplet vote on its proposed object center. For planar objects, the proposed object centers should cluster at a single point. In general, assuming orthographic projection, the proposed centers will lie along a line. If enough triplets are in agreement on a specific object’s center, the object is labeled as detected. Our algorithm has been evaluated on a new database with 118 training objects and various testing scenarios.
COOH-terminal sequence of the cellular prion protein directs subcellular trafficking and controls conversion into the scrapie isoform (1997)

Efficient formation of scrapie isoform of prion protein (PrP(Sc)) requires targeting PrP(Sc) by glycophosphatidyl inositol (GPI) anchors to caveolae-like domains (CLDs). Redirecting the cellular isoform of prion protein (PrP(C)) to clathrin-coated pits by creating chimeric PrP molecules with four different COOH-terminal transmembrane domains prevented the formation of PrP(Sc). To determine if these COOH-terminal transmembrane segments prevented PrP(C) from refolding into PrP(Sc) by altering the structure of the polypeptide, we fused the 28-aa COOH termini from the Qa protein. Two COOH-terminal Qa segments differing by a single residue direct the transmembrane protein to clathrin-coated pits or the GPI form to CLDs; PrP(Sc) was formed from GPI-anchored PrP(C) but not from transmembrane PrP(C). Our findings argue that PrP(Sc) formation is restricted to a specific subcellular compartment and as such, it is likely to involve auxiliary macromolecules found within CLDs.
Expression of endogenous granzyme B in a subset of human primary breast carcinomas (2003)

Granzyme B (GrB) is the prototypic member of a serine protease family primarily used by cytotoxic lymphocytes to kill target cells. We report here that, by immunohistochemical staining of paraffin-embedded tumour sections, GrB protein was unexpectedly detected in malignant cells of a subset of breast cancers and their adjacent reactive endothelial and mesenchymal cells in which endogenous retinoblastoma protein (pRB) is overexpressed. The identity of the endogenous GrB was further confirmed experimentally in RB-deficient breast carcinoma cell culture upon overexpression of ectopic pRB. Our finding extends the recent paradigm-shifting trend for a more diverse biological role of granzyme B, and might provide a rational basis for exploring its potential prognostic value in a variety of human cancers.
Identification of Nitroxoline and Halogenated Quinoline Analogues with Antibacterial Activities against Plant Pathogens (2017)

Abstract Bacterial pathogens that infect and kill plants are responsible for major crop damage (e.g. citrus canker). As is the case with human pathogens, bacterial species which are invasive to plants acquire resistance to common crop‐bactericidal agents. Herein we report the identification of nitroxoline and simple halogenated quinoline (HQ) antibacterial agents that demonstrate antibacterial activities against a panel of plant pathogens, including Xanthomonas citri and Burkholderia andropogonis . A subset of active analogues was identified from an in‐house library of 36 nitrogen‐containing heterocycles which our group previously evaluated against multiple human pathogenic bacteria (e.g., Staphylococcus aureus ). In this report, we also demonstrate that the phytochemical gallic acid (GA) potentiates the antibacterial activity of select halogenated quinolines against multiple Xanthomonas strains, including Xcc 306. We also show that nitroxoline and HQ 1 alone and in combination with GA inhibit Xcc 306 infection in a plant model, demonstrating the potential these compounds have as crop‐bactericidal agents.
10 Gb/s all-optical AND gate by using semiconductor optical amplifiers (2003)

By using gain saturation of semiconductor optical amplifiers (SOA), an all-optical AND gate has been successfully demonstrated. Firstly, inversion of signal B is obtained using the first SOA with signal B and clock injection. Then, the all-optical AND gate is achieved using the second SOA.
Skin thermal response to sapphire contact and cryogen spray cooling: a comparative study based on measurements in a skin phantom (2000)

Non-specific thermal injury to the epidermis may occur as a result of laser treatment of cutaneous hypervascular malformations (e.g. port wine stains) and other dermatoses. Methods to protect the epidermis from thermal injury include sapphire contact cooling (SCC) and cryogen spray cooling (CSC). Evaluation of the skin thermal response to either cooling method and better understanding of the heat transfer process at the skin surface are essential for further optimization of cooling technique during laser therapy. We present internal temperature measurements in an epoxy resin phantom in response to both SCC and CSC, and use the results in conjunction with a mathematical model to predict the temperature distributions within human skin. Based on our results, a conductive heat transfer process at the skin interface appears to be the primary mechanism for both SCC and CSC. In the case of CSC, 'film cooling' rather than 'evaporative cooling' seems to be the dominant mode during the spurt duration. Currently, due to the lower temperature of the cryogen film and its shorter time of application, CSC produces larger temperature reductions at the skin surface and smaller temperature reductions at depths greater than 200 micrometer (i.e., higher spatial selectivity) when compared to SCC. However, SCC can potentially induce temperature reductions comparable to those produced by CSC if a sapphire temperature similar to that for a cryogen could be achieved in practice.
PIXSAR (2008)

XML is one of the primary encoding schemes for data and knowledge. We investigate incremental physical data clustering in systems that store XML documents using a native format. We formulate the XML clustering problem as an augmented (with sibling edges) tree partitioning problem and propose the PIXSAR (Practical Incremental XML Sibling Augmented Reclustering) algorithm for incrementally clustering XML documents. We show the fundamental importance of workload-driven dynamically rearranging storage.
Computationally efficient methods for analysis and synthesis of real signals using FFT and IFFT (1999)

The discrete Fourier transform (DFT) and the inverse discrete Fourier transform (IDFT) are used in a wide variety of signal processing applications. Even with the increased speed of modern processors, there is an ongoing need to further develop more efficient methods for computing DFT and IDFT, with a particular effort to reduce the number of complex multiplications. The properties of certain complex sequences are extraordinarily useful in the sense that they lead to data manipulation schemes that result in the sequences to which traditional but much shorter fast Fourier transform (FFT) algorithms may be applied. This is achieved by exploiting a certain regularity in the complex data. The index-reversed complex conjugate sequence and the mirror symmetric complex conjugate sequence were defined. A significant reduction in the number of complex computations is achieved if a sequence in either domain exhibits such symmetry.
Targeting Type III Secretion in <i>Yersinia pestis</i> (2008)

Yersinia pestis, the causative agent of plague, utilizes a plasmid-encoded type III secretion system (T3SS) to aid it with its resistance to host defenses. This system injects a set of effector proteins known as Yops (Yersinia outer proteins) into the cytosol of host cells that come into contact with the bacteria. T3SS is absolutely required for the virulence of Y. pestis, making it a potential target for new therapeutics. Using a novel and simple high-throughput screening method, we examined a diverse collection of chemical libraries for small molecules that inhibit type III secretion in Y. pestis. The primary screening of 70,966 compounds and mixtures yielded 421 presumptive inhibitors. We selected eight of these for further analysis in secondary assays. Four of the eight compounds effectively inhibited Yop secretion at micromolar concentrations. Interestingly, we observed differential inhibition among Yop species with some compounds. The compounds did not inhibit bacterial growth at the concentrations used in the inhibition assays. Three compounds protected HeLa cells from type III secretion-dependent cytotoxicity. Of the eight compounds examined in secondary assays, four show good promise as leads for structure-activity relationship studies. They are a diverse group, with each having a chemical scaffold not only distinct from each other but also distinct from previously described candidate type III secretion inhibitors.
Gas metal arc process sensing and control (1986)

Welding automation is normally concerned with directly controlling such factors as current, arc voltage, travel speed, and filler wire speed. There are at least two levels of control beyond present technology which may be identified. The first would involve direct control of weld heat input, cooling rate, and bead geometry (bead width, penetration, and reinforcement). The second would involve direct control of weld defects, microstructure, and properties. Although this second level of control is clearly in the distant future, the first will be achieved in the near future. This work describes the evaluation of a relatively simple steady state model of the gas metal arc (GMA) welding process which considers wire melting and heat input to the base metal, allowing independent control of the heat and mass input to the base metal. This allows direct, independent control of the weld bead reinforcement area and cooling rate to be achieved. 6 refs., 4 figs., 2 tabs.
Ocelot's Knapsack Calculations for Modeling Power Amplifier and Walsh Code Limits (2007)

We give a model for the performance impact on wireless systems of the limitations of certain resources, namely, the base-station power amplifier and the available OVSF codes. These limitations are readily modeled in the loss model formulation as a stochastic knapsack. A simple and well-known recurrence of Kaufman and Roberts allows the predictions of the model to be efficiently calculated. We discuss the assumptions and approximations we have made that allow the use of the model. We have included the model in Ocelot, an Alcatel-Lucent tool for modeling and optimizing cellular phone systems. The model is fast to compute, differentiable with respect to the relevant parameters, and able to model broad ranges of capacity and resource use. These conditions are critical to our application of optimization.
The role of the reticulocyte-binding-like protein homologues of<i>Plasmodium</i>in erythrocyte sensing and invasion (2012)

Malaria remains a serious public health problem with significant morbidity and mortality accounting for nearly 20% of all childhood deaths in Africa. The cyclical invasion, cytoadherence and destruction of the host's erythrocyte by the parasite are responsible for the observed disease pathology. The invasive form of the parasite, the merozoite, uses a complex set of interactions between parasite ligands and erythrocyte receptors that leads to the formation of a tight junction and ultimately successful erythrocyte invasion. Understanding the molecular mechanism underlying host cell recognition and invasion is crucial for the development of a targeted intervention strategy. Two parasite protein families termed reticulocyte-binding-like protein homologues (RBL) and the erythrocyte-binding-like (EBL) protein family are conserved in all Plasmodium species and have been shown to play an important role in host cell recognition and invasion. Over the last few years significant new insights have been gained in understanding the function of the RBL family and this review attempts to provide an update with a specific focus on the role of RBL in signal transduction pathways during invasion.
WE‐G‐BRB‐04: BEST IN PHYSICS (THERAPY) ‐ A Novel Multi‐Point Plastic Scintillation Detector for in Vivo Dosimetry and Quality Assurance in Radiation Therapy (2012)

The feasibility and accuracy of mPSDs using a single transmission line was demonstrated. In addition to well-documented advantages of single-point PSDs, the multi-point capability of this single-fiber detector makes mPSDs a very promising new technique for quality assurance and on-line in vivo dosimetry.
Collective ion acceleration in a converging waveguide (1975)

An ion acceleration mechanism is proposed in which ions are trapped and accelerated by a negative energy space charge wave. Under certain conditions, an electron beam propagating down a slowly converging metal guide can be accelerated. A low phase velocity space charge wave initiated at the large radius end of the guide, because it is supported by the beam, will also accelerate. By trapping ions in the potential wells of a low phase velocity negative energy wave, ion acceleration down the converging drift tube, can be achieved. The ion acceleration leads to the growth in amplitude of the negative energy space charged wave, thus maintaining the trapping.
Clinical assessment of the backscatter coefficient in osteoporosis (2002)

Current commercial ultrasound "bone densitometers" process only the through-transmitted signals while failing to extract additional information contained in the scattered signals. This work was conducted to investigate the clinical interest of a backscatter ultrasound technique for bone characterization in 24 healthy premenopausal (group N), 24 postmenopausal (group PM), and 13 osteoporotic patients with fractures (group O). Pulse-echo measurements of the backscatter power were performed at the calcaneus (heel bone) using an ultrasound bone imaging scanner. The pulse-echo waveforms backscattered by the internal trabecular micro-architecture were recorded to compute the integrated backscatter coefficient (BUB, dB) in the frequency range 200-600 kHz. BUB was compared to the slope of the frequency-dependent attenuation (BUA, dB/MHz) derived from signals transmitted through the bone and to bone mineral density. Measurements were averaged in an operator-independent automatic ROI. The short-term reproducibility was 1.4%, and 3.5% for BUA, and BUB respectively. Femoral bone mass density (BMD) was measured in all subjects and calcaneal BMD was measured in a subset of 30 patients. The correlation between ultrasound and calcaneal BMD was moderate for BUB (r=0.55, p<10/sup -3/) and strong for BUA (r=0.82, p<10/sup -4/). Significant differences were found in ultrasound parameters and BMD between fracture and non-fracture groups. There was a significant difference in BMD and ultrasound parameters between young normal controls and healthy post-menopausal women. In summary, reflection ultrasound appears to be promising in osteoporosis and larger studies are clearly warranted.
Segmentation enhances material analysis in multi-energy CT: A simulation study (2013)

A segmentation algorithm that assists material analysis in multi-energy computed tomography is presented. Segmentation is typically used in conjunction with quantitative material analysis algorithms (known as material decomposition) to increase the total number of materials which can be discriminated and quantified. The algorithm illustrated here identifies voxels (in the image domain) with one of three material classes: air, soft tissues and dense tissue or contrast pharmaceuticals. Two soft tissue materials are chosen (the most and the least attenuating soft tissues) to define the boundaries between the different material classes. The intensity (calculated from the multi-energy representation using the Euclidean norm) of each voxel is compared to the two boundary materials to determine which material class it belongs to. Unlike other intensity based segmentation methods this algorithm checks, using multi-variate confidence intervals (ellipsoids), whether each voxel is statistically distinguishable from the two boundary materials. If the voxels are not distinguishable then they are defaulted to the soft tissue class. An advantage of this segmentation method is that noise which passes through to the binary representations of each material class typically resemble salt and pepper noise, which is easily removed with a median filter. Simulations demonstrate that the algorithm can correctly allocate a variety of medically relevant soft tissue and non soft tissue materials to their correct material classes and that segmentation using multi-energy information can handle noisier data than when using single-energy information. The proposed algorithm is also successfully applied to a multi-energy CT scan taken using the MARS (Medipix All Resolution System) scanner.