gebhart/patrepeval huggingface dataset:
Poloxamer surfactant preserves cell viability during photoacoustic delivery of molecules into cells (2014)

Efficient intracellular delivery of molecules is needed to modulate cellular behavior for laboratory and medical applications, but is often limited by trade-offs between achieving high intracellular delivery and maintaining high cell viability. Here, we studied photoacoustic delivery of molecules into cells by exposing DU145 human prostate carcinoma cells to nanosecond laser pulses in the presence of carbon black nanoparticles. Under strong laser exposure conditions, less than 30% of cells were viable and exhibited uptake. Addition of poloxamer surfactant at those laser exposure conditions increased cell viability to almost 90%, with intracellular uptake in >80% of cells. This remarkable increase in efficiency of intracellular delivery and cell viability may be attributed to enhanced cell membrane resealing by poloxamer surfactant after photoacoustic delivery. While F-68 poloxamer was effective, the larger, more-hydrophobic F-127 poloxamer provided the best results. There was no significant protective effect from addition of Ca(2+) , BAPTA-AM, ATP, fetal bovine serum or glycine betaine, which were expected to promote active cell membrane repair mechanisms and other active intracellular protective processes. We conclude that poloxamer surfactant preserves cell viability during photoacoustic delivery of molecules into cells, thereby enabling highly efficient intracellular delivery.
Harnessing the antigenic fingerprint of each individual cancer for immunotherapy of human cancer: genomics shows a new way and its challenges (2013)

The idea that individual tumors are antigenically unique has been around since the very dawn of our recognition of adaptive immune response to tumors. That idea has inspired a small number of attempts at individualized immunotherapy of human cancers. Such previous attempts for solid tumors have been hobbled by an inability to define the individually unique antigenic repertoire of tumors because of technological difficulties. The new availability of rapid and cheap high throughput DNA sequencing promises to overcome that hurdle. Using this new ability, coupled with bio-informatic tools, it is now possible to define the immunogenic repertoire of any tumor to a high degree of granularity within a practical time frame and an acceptable cost. The development of these ideas, and a small number of such studies that underscore this promise, is discussed. This new way--of characterizing the tumor immunome through characterization of the tumor genome--has distinct challenges, including selection of the appropriate peptides, choosing methods of immunizations that can incorporate tens of epitopes, and addressing issues of antigenic heterogeneity of tumors. However, tools for meeting these challenges exist and are emergent.
Zirconium Tetraisopropoxide (2001)

[2171-98-4] C12H28O4Zr (MW 327.62) (·i-PrOH)[50939-84-9] C15H36O5Zr (MW 387.73) (hydrogenation catalyst; Meerwein–Ponndorf–Verley reduction; Oppenauer oxidation; ester synthesis; diketopiperazine synthesis) Physical Data: Zr(O-i-Pr)4: bp 160 °C/0.1 mmHg; Zr(O-i-Pr)4·i-PrOH: mp 138–141 °C.1 Solubility: Zr(O-i-Pr)4 readily sol organic solvents; Zr(O-i-Pr)4·i-PrOH sparingly sol isopropanol. Form Supplied in: Zr(O-i-Pr)4·i-PrOH: white solid. Purification: Zr(O-i-Pr)4·i-PrOH: crystallization from isopropanol followed by drying at rt/0.5 mmHg. Zr(O-i-Pr)4: heating of Zr(O-i-Pr)4·i-PrOH at 90–120 °C/1 mmHg to remove isopropanol followed by distillation.1 Handling, Storage, and Precautions: moisture sensitive; irritating to eyes, respiratory system, and skin. Use in a fume hood.
Isolation and characterization of Staufen-containing ribonucleoprotein particles from rat brain (2003)

Localized mRNAs are thought to be transported in defined particles to their final destination. These particles represent large protein complexes that may be involved in recognizing, transporting, and anchoring localized messages. Few components of these ribonucleoparticles, however, have been identified yet. We chose the strategy to biochemically enrich native RNA-protein complexes involved in RNA transport to identify the associated RNAs and proteins. Because Staufen proteins were implicated in intracellular RNA transport, we chose mammalian Staufen proteins as markers for the purification of RNA transport particles. Here, we present evidence that Staufen proteins exist in two different complexes: (i) distinct large, ribosome- and endoplasmic reticulum-containing granules preferentially found in the membrane pellets during differential centrifugation and (ii) smaller particles in the S100 from rat brain homogenates. On gel filtration of the S100, we identified soluble 670-kDa Staufen1-containing and 440-kDa Staufen2-containing particles. They do not cofractionate with ribosomes and endoplasmic reticulum but rather coenrich with kinesin heavy chain. Furthermore, the fractions containing the Staufen1 particles show a 15-fold enrichment of mRNAs compared with control fractions. Most importantly, these fractions are highly enriched in BC1, and, to a lesser extent, in the alpha-subunit of the Ca(2+)/calmodulin-dependent kinase II, two dendritically localized RNAs. Finally, both RNAs colocalize with Staufen1-hemagglutinin in particles in dendrites of transfected hippocampal neurons. We therefore propose that these Staufen1-containing particles may represent RNA transport intermediates that are in transit to their final destination within neurons.
Adenosine modulates Toll-like receptor function: basic mechanisms and translational opportunities (2011)

Adenosine is an endogenous purine metabolite whose concentration in human blood plasma rises from nanomolar to micromolar concentrations during the inflammatory process. Leukocytes express seven-transmembrane adenosine receptors whose engagement modulates Toll-like receptor-mediated cytokine responses, in part via modulation of intracellular cyclic adenosine monophosphate. Adenosine analogs are used clinically to treat arrhythmias and apnea of prematurity. Herein, we consider the potential of adenosine analogs as innate immune response modifiers to prevent and/or treat infection.
Effect of Metal Dopant on the Performance of Ni@CeMeO2 Embedded Catalysts (Me = Gd, Sm and Zr) for Dry Reforming of Methane (2022)

Biogas upgrading by a catalytic process has been studied in order to obtain syngas using renewable source of methane. This work evaluates the influence of metal dopant (Gd, Sm, and Zr) on the CeO2 structure for the dry reforming of methane over Ni nanoparticle embedded catalysts. The doping with Zr improved the thermal stability of the catalyst, leading to the formation of small Ni nanoparticles, while Ni metal sintering was observed for Ni@CeO2, Ni@CeGdO2, and Ni@SmO2, according to in situ XRD under reduction conditions. The ceria reducibility was affected by the dopant nature, for which the addition of Zr caused distortions in the ceria lattice, promoting the diffusion of oxygen bulk to surface. The doping with Gd and Sm created oxygen vacancies by charge compensation, and the saturation of oxygen vacancies in the fresh samples decreased the degree of Ce reduction, according to TPR results. The larger Ni particles and poor redox behavior for Ni@CeGdO2 and Ni@CeSmO2 were responsible for the high carbon formation on these catalysts during the DRM reaction. The Ni@CeZrO2 catalyst did not present coke formation because of smaller Ni crystallite size and higher ceria reducibility. Therefore, the control of Ni particle size and the high oxygen mobility in the Ni@CeZrO2 catalyst inhibits carbon deposition and enhances the mechanism of carbon removal, promoting the catalyst stability.
Family With Dominantly Inherited Ataxia, Amyotrophy, and Peripheral Sensory Loss (1990)

A family of German extraction with progressive ataxia, eye movement abnormalities, peripheral sensory loss, and spinal muscular atrophy of adult onset is described. Three members came to autopsy, and neuropathologically, the major changes included varying degrees of atrophy of the basis pontis and degeneration of the spinocerebellar tracts, Clarke's columns, anterior horn neurons, and fasciculus gracilis. The dentate nucleus was spared, and there was slight neuron loss from the substantia nigra in one patient. Clinically and neuropathologically, our family resembles that reported by Boller and Segarra as having spinopontine atrophy. However, several kindreds with similar findings have recently been described as having Azorean or Machado-Joseph disease in non-Portuguese families. Comparison of clinical and neuropathological features in spinopontine atrophy and Machado-Joseph disease, both in Portuguese and non-Portuguese families, reveals clinical and pathological similarities and differences between the two. The major differences in our patients include only minor extraocular movement abnormality and absence of protuberant eyes, and muscular rigidity clinically, and the sparing of the substantia nigra and the dentate nucleus neuropathologically. These differences suggest that spinopontine atrophy, as manifested in our family, is distinct from Machado-Joseph disease. Our family showed no linkage to the HLA locus on chromosome 6.
NO and hepatocellular cancer (2019)

NO has broad and sometimes dichotomous roles in cancer. The effects of NO in tumours depend on the type and localization of NOS isoforms, concentration and duration of NO exposure, and cellular sensitivity to NO. Hepatocellular carcinoma (HCC) is a common and lethal disease for which no effective therapy other than surgical resection exists. Over two decades of research has yielded evidence that NO generated by the inducible NOS (iNOS or NOS2) contributes to HCC progression in at least a subset of patients with HCC. The co-expression of iNOS with COX-2 may portend a particularly aggressive cancer phenotype in HCC and at the same time reveal an opportunity for pharmacological intervention. In this review, we focus on what is known about the influence of NO in HCC neoplastic transformation, proliferation and apoptosis, angiogenesis, invasion, and metastasis, cancer stem cells, and the host immune response against the tumour. We discuss the implications of recent findings for targeting the NO pathways in HCC.
Improving Transaxle Performance at Low Temperature with Reduced-Viscosity Automatic Transmission Fluids (1987)

The effects of automatic transmission fluid viscosity on the low-temperature performance of a front-wheel-drive transaxle were determined in a cold room maintained at a temperature of -20/sup 0/F (-28.9/sup 0/C), using both a cranking apparatus and a vehicle. Cranking and vehicle tests were conducted to determine the effects of fluid viscosity on the power required to crack a transaxle and on transaxle performance under low-temperature transient operation, respectively. Four automatic transmission fluids were tested, ranging in viscosity from 2 600 to 16 000 cP at - 20/sup 0/F. All test fluids contained the same additive package and were blended using the same types of base oils.
DevoFlow (2011)

OpenFlow is a great concept, but its original design imposes excessive overheads. It can simplify network and traffic management in enterprise and data center environments, because it enables flow-level control over Ethernet switching and provides global visibility of the flows in the network. However, such fine-grained control and visibility comes with costs: the switch-implementation costs of involving the switch's control-plane too often and the distributed-system costs of involving the OpenFlow controller too frequently, both on flow setups and especially for statistics-gathering. In this paper, we analyze these overheads, and show that OpenFlow's current design cannot meet the needs of high-performance networks. We design and evaluate DevoFlow, a modification of the OpenFlow model which gently breaks the coupling between control and global visibility, in a way that maintains a useful amount of visibility without imposing unnecessary costs. We evaluate DevoFlow through simulations, and find that it can load-balance data center traffic as well as fine-grained solutions, without as much overhead: DevoFlow uses 10--53 times fewer flow table entries at an average switch, and uses 10--42 times fewer control messages.
Suppression of Programmed Cell Death 4 (PDCD4) Protein Expression by BCR-ABL-regulated Engagement of the mTOR/p70 S6 Kinase Pathway (2008)

There is accumulating evidence that mammalian target of rapamycin (mTOR)-activated pathways play important roles in cell growth and survival of BCR-ABL-transformed cells. We have previously shown that the mTOR/p70 S6 kinase (p70 S6K) pathway is constitutively activated in BCR-ABL transformed cells and that inhibition of BCR-ABL kinase activity by imatinib mesylate abrogates such activation. We now provide evidence for the existence of a novel regulatory mechanism by which BCR-ABL promotes cell proliferation, involving p70 S6K-mediated suppression of expression of programmed cell death 4 (PDCD4), a tumor suppressor protein that acts as an inhibitor of cap-dependent translation by blocking the translation initiation factor eIF4A. Our data also establish that second generation BCR-ABL kinase inhibitors block activation of p70 S6K and downstream engagement of the S6 ribosomal protein in BCR-ABL transformed cells. Moreover, PDCD4 protein expression is up-regulated by inhibition of the BCR-ABL kinase in K562 cells and BaF3/BCR-ABL transfectants, suggesting a mechanism for the generation of the proapoptotic effects of such inhibitors. Knockdown of PDCD4 expression results in reversal of the suppressive effects of nilotinib and imatinib mesylate on leukemic progenitor colony formation, suggesting an important role for this protein in the generation of antileukemic responses. Altogether, our studies identify a novel mechanism by which BCR-ABL may promote leukemic cell growth, involving sequential engagement of the mTOR/p70 S6K pathway and downstream suppression of PDCD4 expression.
Light chain cardiomyopathy. Structural analysis of the light chain tissue deposits. (1996)

Cardiomyopathy due to monoclonal light chain deposits is a complication of plasma cell disorders. The deposits may be either fibrillar as in light chain amyloid or nonfibrillar as in light chain deposition disease. The reasons for these structural differences are still unknown. We characterized the myocardial deposits by immunohistochemical examination of sections and extraction and biochemical analysis of the tissue deposits in a patient (MCM) who died of myeloma and systemic light chain deposition disease. Amino acid sequence analysis of the extracted nonfibrillar MCM kappa-light chain reveals that it belongs to the L12a germline subset of the kappa(I) protein and contains five distinctive amino acid substitutions (three in the framework region III and two in the complementarity-determining region III) that have not been reported previously in the same positions in other kappa(I) light chains. The theoretically determined isoelectric point (pI 8.21) of the MCM light chain is high compared with the low isoelectric point of other Bence Jones proteins from subjects without light chain deposition disease. The diffuse binding to basement membranes and the high isoelectric point of the MCM kappa-light chain suggest electrostatic interaction as a possible mechanism of tissue deposition. The spatial locations of the five distinctive residues and a sixth rare substitution of the MCM protein modeled on the backbone structure of REI, a kappa(I)-soluble Bence Jones light chain of known three-dimensional structure, may be responsible for protein destabilization, partial unfolding, and aggregation leading to tissue deposition.
Integrin α v β 3 as a Promising Target to Image Neoangiogenesis Using In-House Generator-Produced Positron Emitter 68 Ga-Labeled DOTA-Arginine-Glycine-Aspartic Acid (RGD) Ligand (2015)

For the growth and spread of a tumor beyond 2 mm, angiogenesis plays a crucial role, and association of various integrins with angiogenesis is evidential. The aim of the study was radiolabeling of DOTA-chelated RGD (arginine-glycine-aspartic acid) peptide with (68)Ga for PET imaging in locally advanced breast carcinoma. DOTA-RGD was incubated with (68)GaCl3, eluted in 0.05 m HCl. Elution volume, peptide amount, and reaction pH were studied. Radio-ITLC, gas chromatography, endotoxin, and sterility testing were performed. Serial (n=3) and whole-body (n=2) PET/CT imaging was done on patients post i.v. injection of 111-185 MBq of (68)Ga-DOTA-RGD. Maximum radiolabeling yield was achieved with 3 mL elution volume of 15-20 μg peptide at pH 3.5-4.0 with 10 minutes of incubation at 95°C. Product samples were sterile having 99.5% radiochemical purity with residual ethanol content and endotoxins in injectable limits. Intense radiotracer uptake was noticed in the tumor with SUVmax 15.3 at 45 minutes in serial images. Physiological radiotracer uptake was seen in the liver, spleen, ventricles, and thyroid with excretion through the kidneys. The authors concluded that (68)Ga-DOTA-RGD has the potential for imaging α,vβ3 integrin-expressing tumors.
A NEW METHOD TO ESTIMATE LOCAL PITCH ANGLES IN SPIRAL GALAXIES: APPLICATION TO SPIRAL ARMS AND FEATHERS IN M81 AND M51 (2014)

We examine $8\mu$m IRAC images of the grand design two-arm spiral galaxies M81 and M51 using a new method whereby pitch angles are locally determined as a function of scale and position, in contrast to traditional Fourier transform spectral analyses which fit to average pitch angles for whole galaxies. The new analysis is based on a correlation between pieces of a galaxy in circular windows of $(\ln R, \theta)$ space and logarithmic spirals with various pitch angles. The diameter of the windows is varied to study different scales. The result is a best-fit pitch angle to the spiral structure as a function of position and scale, or a distribution function of pitch angles as a function of scale for a given galactic region or area. We apply the method to determine the distribution of pitch angles in the arm and interarm regions of these two galaxies. In the arms, the method reproduces the known pitch angles for the main spirals on a large scale, but also shows higher pitch angles on smaller scales resulting from dust feathers. For the interarms, there is a broad distribution of pitch angles representing the continuation and evolution of the spiral arm feathers as the flow moves into the interarm regions. Our method shows a multiplicity of spiral structures on different scales, as expected from gas flow processes in a gravitating, turbulent and shearing interstellar medium. We also present results for M81 using classical 1D and 2D Fourier transforms, together with a new correlation method, which shows good agreement with conventional 2D Fourier transforms.
Radiomics of pulmonary nodules and lung cancer (2017)

The large number of indeterminate pulmonary nodules encountered incidentally or during CT-based lung screening provides considerable diagnostic and management challenges. Conventional nodule evaluation relies on visually identifiable discriminators such as size and speculation. These visible nodule features are however small in number and subject to considerable interpretation variability. With the development of novel targeted therapies for lung cancer the diagnosis and characterization of early stage lung tumours has never been more important. Radiomics is a developing field aimed at deriving automated quantitative imaging features from medical images that can predict nodule and tumour behavior non-invasively. In contrast to conventional visual image features radiomics can extract substantially greater numbers of nodule features with much better reproducibility. This paper summarizes the basic process of radiomics and outlines why radiomic feature analysis may be particularly well suited to the evaluation of lung nodules. We review the current evidence for its clinical application with regards to pulmonary nodule management, considering promising applications such as predicting malignancy, histological subtyping, gene expression and post-treatment prognosis. Radiomics has the potential to transform the management of pulmonary nodules offering early diagnosis and personalized medicine using a method that is in cost-effective and non-invasive.
Transforming Growth Factor- β Expression in Mucosal Biopsies in Asthma and Chronic Bronchitis (1997)

We assessed whether transforming growth factor-beta (TGF-beta), a fibrogenic growth factor, may be involved in remodeling of asthma and chronic bronchitis; its expression was compared with that of epidermal growth factor (EGF) and granulocyte macrophage colony-stimulating factor (GM-CSF) in bronchial mucosal biopsies from 13 normal subjects, 24 asthmatics, and 19 patients with chronic bronchitis. TGF-beta immunoreactivity was highly increased in epithelium and submucosa of those with bronchitis and to a lesser extent in asthmatics. By comparison, with normal subjects, EGF immunoreactivity was significantly increased in the epithelium of bronchitic subjects and submucosa of asthmatics, and, GM-CSF immunoreactivity was increased in both epithelial and submucosal cells of asthmatics and to a lesser extent in submucosa of bronchitics. A significant correlation was found between the number of epithelial or submucosal cells expressing TGF-beta in both asthma and chronic bronchitis and basement membrane thickness and fibroblast number. No such correlation was found for EGF or GM-CSF. in situ hybridization for TGF-beta 1 mRNA confirmed the results obtained by immunohistochemistry. By combining in situ hybridization and immunohistochemistry, it was found that eosinophils and fibroblasts were synthetizing TGF-beta in asthma and bronchitis. These data suggest that TGF-beta, but not EGF or GM-CSF, is involved in airways remodeling in asthma and chronic bronchitis.
Discovering rare behaviours in stochastic differential equations using decision procedures: applications to a minimal cell cycle model (2014)

Stochastic Differential Equation (SDE) models are used to describe the dynamics of complex systems with inherent randomness. The primary purpose of these models is to study rare but interesting or important behaviours, such as the formation of a tumour. Stochastic simulations are the most common means for estimating (or bounding) the probability of rare behaviours, but the cost of simulations increases with the rarity of events. To address this problem, we introduce a new algorithm specifically designed to quantify the likelihood of rare behaviours in SDE models. Our approach relies on temporal logics for specifying rare behaviours of interest, and on the ability of bit-vector decision procedures to reason exhaustively about fixed-precision arithmetic. We apply our algorithm to a minimal parameterised model of the cell cycle, and take Brownian noise into account while investigating the likelihood of irregularities in cell size and time between cell divisions.