gebhart/patrepeval huggingface dataset:
Poly(ethylene oxide) Grafted to Silicon Surfaces: Grafting Density and Protein Adsorption (1998)

Poly(ethylene oxide) (PEO) polymer, in linear and star form, was covalently grafted to silicon surfaces, and the surfaces were tested for their ability to adsorb proteins. Linear PEG of molecular weight 3400, 10 000, and 20 000 g/mol and star PEO molecules were coupled via their terminal hydroxyl groups activated by tresyl chloride to aminosilane-treated silicon wafers. The amount of PEO coupled to the surface was varied by changing the concentration of the tresyl-PEO solution. The dry PEO thickness on the surface was measured using X-ray photoelectron spectroscopy (XPS) and ellipsometry, from which the grafting density was calculated. The PEO surfaces were exposed to solutions of each of three proteins: cytochrome-c, albumin, and fibronectin. The degree of adsorption of each protein was determined by XPS and ellipsometry and recorded as a function of PEO grafting density. All three proteins were found to reach zero adsorption at the highest grafting densities on all three PEG surfaces, which for all three PEG surfaces was a PEO content of 100 +/- 10 ng/cm2. On both star PEO surfaces, albumin and fibronectin decreased to zero adsorption at intermediate values of grafting density, whereas cytochrome-c continued to adsorb at all grafting densities, although with a decreasing trend. A physical model of the surface helped explain these protein adsorption results in terms of the spacing and degree of overlap of grafted PEO chains.
Anti‐tumor effect of combination therapy with intratumoral controlled‐release paclitaxel (PACLIMER® microspheres) and radiation (2003)

A controlled-release formulation of paclitaxel can be very effective in the treatment of prostate cancer. Additionally, PACLIMER Microspheres may be effectively used as a radiosensitizer in genitourinary cancers.
Simultaneous Multi-Scale Diffusion Estimation and Tractography Guided by Entropy Spectrum Pathways (2015)

We have developed a method for the simultaneous estimation of local diffusion and the global fiber tracts based upon the information entropy flow that computes the maximum entropy trajectories between locations and depends upon the global structure of the multi-dimensional and multi-modal diffusion field. Computation of the entropy spectrum pathways requires only solving a simple eigenvector problem for the probability distribution for which efficient numerical routines exist, and a straight forward integration of the probability conservation through ray tracing of the convective modes guided by a global structure of the entropy spectrum coupled with a small scale local diffusion. The intervoxel diffusion is sampled by multi b-shell multi q-angle diffusion weighted imaging data expanded in spherical waves. This novel approach to fiber tracking incorporates global information about multiple fiber crossings in every individual voxel and ranks it in the most scientifically rigorous way. This method has potential significance for a wide range of applications, including studies of brain connectivity.
Positive contrast magnetic resonance imaging of cells labeled with magnetic nanoparticles (2005)

Contrast agents incorporating superparamagnetic iron-oxide nanoparticles have shown promise as a means to visualize labeled cells using MRI. Labeled cells cause significant signal dephasing due to the magnetic field inhomogeneity induced in water molecules near the cell. With the resulting signal void as the means for detection, the particles behave as a negative contrast agent, which can suffer from partial-volume effects. In this paper, a new method is described for imaging labeled cells with positive contrast. Spectrally selective RF pulses are used to excite and refocus the off-resonance water surrounding the labeled cells so that only the fluid and tissue immediately adjacent to the labeled cells are visible in the image. Phantom, in vitro, and in vivo experiments show the feasibility of the new method. A significant linear correlation (r = 0.87, P < 0.005) between the estimated number of cells and the signal was observed.
Sleep Disturbances and Inflammatory Bowel Disease (2014)

With an estimated 70 million Americans suffering, sleep disorders have become a global issue, and discovering their causes and consequences are the focus of many clinical research studies. Sleep is now also considered to be an important environmental and behavioral factor associated with the process of inflammation and the immune system. Increased sleepiness is considered part of the acute phase of response to tissue injury, and sleep loss activates inflammatory cytokines such as interleukin (IL)-1 and tumor necrosis factor (TNF)-α. Clinical studies in many immune-mediated diseases, such as systemic lupus erythematosus, rheumatoid arthritis, and ankylosing spondylitis, have revealed an association of sleep disturbances with disease activity. Recent research suggests that individuals with sleep abnormalities are also at greater risk of serious adverse health, economic consequences, and most importantly increased all-cause mortality. The importance of sleep in inflammatory bowel disease has recently gained attention with some published studies demonstrating the association of sleep disturbances with disease activity, subclinical inflammation, and risk of disease relapse. A comprehensive review of sleep physiology and its association with the immune system is provided here. Experimental and clinical studies exploring this relationship in inflammatory bowel disease are reviewed, and the clinical implications of this relationship and future directions for research are also discussed.
Characteristics of Electrodeposited Single-Walled Carbon Nanotube Films (2006)

Thin films of chemically-functionalized single walled carbon nanotubes (SWNTs) were fabricated by using a direct current (DC) electrodeposition method. SWNTs were shortened and then functionalized with acid chloride group to combine with amine group-terminated gold substrate. The electrodeposited SWNT films were characterized by using Raman spectroscopy, attenuated total reflectance infrared (ATR/IR) spectrometry and atomic force microscopy. We demonstrated that the SWNT film was well distributed on an electrode with robust adhesion.
Site‐directed mutagenesis but not γ‐carboxylation of Glu‐35 in factor VIIa affects the association with tissue factor (1996)

Factor VIIa is a vitamin K-dependent enzyme whose gamma-carboxyglutamic acid (Gla)-containing domain is important for calcium ion-dependent binding to the cofactor tissue factor and membrane surfaces. This domain contains 10 Gla residues, the individual roles and importance of which are not known. Comparisons with the homologous protein C, factor IX and prothrombin may provide functional information on the first nine Gla residues, whereas no data can be extrapolated to Gla-35 in factor VIIa. Therefore, the effects of posttranslational gamma-carboxylation and site-directed mutagenesis of Glu-35 were investigated. Mutations to Asp, Gln or Val all lead to a lower affinity for tissue factor by decreasing the rate of association, in the case of the Val mutant by a factor of 200, as measured by surface plasmon resonance. In contrast, Glu or Gla side chains at position 35 appear to fulfil the functional roles equally well.
Ep-CAM LEVELS IN PROSTATIC ADENOCARCINOMA AND PROSTATIC INTRAEPITHELIAL NEOPLASIA (1999)

These findings suggest that increased levels of Ep-CAM represent an early event in the development of prostatic adenocarcinoma.
Imatinib mesylate for the treatment of gastrointestinal stromal tumours: best monitored with FDG PET (2004)

FDG PET is a valuable tool in patients with gastrointestinal stromal tumours treated with imatinib mesylate. It improves staging, accurately separates responders from non-responders in an early phase, and is helpful during follow-up.
Stereoselective carbonyl reductases from rat skin and leukocyte microsomes converting 12‐ketoeicosatetraenoic acid to 12(S)‐HETE (1990)

Cell-free preparations from rat polymorphonuclear leukocytes and skin were found to catalyze the reduction of 12-keto-5,8,10,14-eicosatetraenoic acid (12-KETE) to 12-hydroxyeicosatetraenoic acid (12-HETE). The reductase activity was associated with the microsomal fraction and showed a marked preference for NADH over NADPH as reducing cofactor. Characterization of the reaction product by chiral phase HPLC of the methyl ester derivative indicated that 12-KETE reduction generated almost exclusively 12(S)-HETE. The results demonstrate that rat skin and leukocyte microsomes possess an NADH-dependent 12-KETE reductase activity that forms 12(S)-HETE as a major product. The identification of stereoselective 12-KETE reductases provides a basis for further defining the role these enzymes may play in the regulation of 12-KETE levels and in the protection against degradation of 12-KETE to the pro-inflammatory 12(R)-HETE by selectively generating 12-HETE of the S configuration.
[Changes in the immune status of peptic ulcer patients after combined treatment including deep massage]. (1999)

Unsatisfactory results of ulcer drug medication necessitate introduction of new approaches to treatment of this disease. We tried massage and therapeutic exercise as alternative methods of ulcer treatment as they provide biologically validated ways to mobilization of the body defenses. The results of our studies showed that deep reflex muscular massage and exercises for extension of the skeletal muscles are not inferior in effectiveness in ulcer than routine drug therapy. Therefore, the massage and the exercises are advisable adjuvant modalities in sparing drug medication improving immune status and treatment outcomes in patients with ulcer in exacerbation.
Plant hormones : physiology, biochemistry and molecular biology (1995)

A: Introduction. 1. The plant hormones: Their nature, occurrence, and functions P.J. Davies. 2. The plant hormone concept: Concentration, and sensitivity and transport P.J. Davies. B: Hormone Synthesis and Metabolism. 1. Auxin biosynthesis and metabolism R.S. Bandurski, J.D. Cohen, J. Slovin, D.M. Reinecke. 2. Gibberellin biosynthesis and metabolism V.M. Sponsel. 3.Cytokinin biosynthesis and metabolism B.A. McGaw. 4. Biosynthesis and metabolism of ethylene T.A. McKeon, J.C. Fernandez-Maculet, S.F. Yang. 5. Abscisic acid biosynthesis and metabolism D.C. Walton. C: Other Hormonal Compounds. 1. Polyamines as endogenous growth regulators A.W. Galston, R. Kaur-Sawhney. 2. Jasmonates, salicylic acid and brassinosteroids P.E. Staswick, I. Raskin, R.N. Arteca. D: How Hormones Work. 1. Auxin and cell elongation R.E. Cleland. 2. The control of gene expression by auxin G. Hagen. 3. Gibberellin action in germinating cereal grains J.V. Jacobsen, F. Gubler, P.M. Chanderl. 4. Hormone binding and signal transduction K.R. Libbenga, A.M. Mennes. 5. Calcium and plant hormone action P.C. Bethke, S. Gilroy, R.L. Jones. E: Molecular Aspects of Hormone Synthesis and Action. 1. Genes specifying auxin and cytokinin biosynthesis in prokaryotes R.O. Morris. 2. Transgenic plants in hormone biology H.J. Klee, M.B. Lanahan. 3. Biochemical and genetic approaches to study the mechanism of action of auxins J. Schell, K. Palme, R. Walden. 4. Ethylene genes and fruit ripening S. Picton, J.E. Gray, D. Grierson. 5. The role of hormones in gene activation in response to wounding H. Pena-Cortes, L. Willmitzer. F: Hormone Analysis. 1.Instrumental methods of plant hormone analysis R. Horgan. 2. Immunoassay methods of plant hormone analysis J.L. Caruso, V.C. Pence, L.A. Leverone. G: The Functioning of Hormones in Plant Growth and Development. 1. Hormone mutants and plant development J.B. Reid, S.H. Howell. 2. Ethylene in plant growth, development, and senescence M.S. Reid. 3. Auxin transport T.L. Lomax, G.K. Muday, P.H. Rubery. 4. The induction of vcascular tissues by auxin R. Aloni. 5. Hormones and the orientation of growth P.B. Kaufman, L-L. Wu, T.G. Brock, D. Kim. 6. Hormonal regulation of apical dominance I.A. Tamas. 7. Hormones as regulators of water balance T.A. Mansfield, M.R. McAinsh. 8. Hormones and reproductive development J.D. Metzger. 9. The role of hormones in photosynthate partitioning and seed filling M.L. Brenner, N. Cheikh. 10. The role of hormones during seed development C.D. Rock, R.S. Quatrano. 11. The role of hormones in potato (Solanum tuberosum L.) tuberization E.E. Ewing. 12. Postharvest hormone changes in vegetables and fruit P.M. Ludford. 13. Hormones in tissue culture and micropropagation A.D. Krikorian. 14. Natural and synthetic growth regulators and their use in horticultural and agronomic crops T.J. Gianfagna.
Mechanics of Catalyst Motion during Metal Assisted Chemical Etching of Silicon (2013)

Metal assisted chemical etching (MACE) of Si has been used to fabricate both simple and complex Si nanostructures, through the relatively straightforward process of noble metal deposition and patterning followed by immersion in a suitable etching solution. Under appropriate conditions, etching is catalyzed by the metal and occurs only at the metal–silicon interface. MACE therefore requires that a force be present that keeps the metal and silicon in close proximity during etching. The geometrical characteristics of the etched nanostructures therefore depend not only on the solution chemistry, but also on the mechanical properties and constraints of the noble metal catalysts. Here we report experimental studies of etching with nanoscale Au catalyst strips that are mechanically constrained at both ends. The mechanical constraint of these strips leads to termination of etching when a mechanical force balance is achieved. Through experimental characterization of the etching end-state and through modeling, we determine the force between the catalyst and the silicon during etching, and determine how this force depends on the chemistry of the solution.
A novel cladding structure for semiconductor quantum-well lasers with small beam divergence and low threshold current (1996)

A novel cladding structure is proposed and analyzed for semiconductor quantum-well lasers to achieve a small vertical-beam divergence and a low threshold current density simultaneously. This cladding structure is designed to guide a wide optical mode but with a high peak intensity in quantum wells. The wide expansion of the optical mode results in a small beam divergence. In addition, the high optical Intensity in quantum wells causes a low threshold current density. This novel cladding structure is optimized. The result shows that this type of cladding structures can achieve a beam divergence as small as 14.6/spl deg/ while the threshold current density remains small.
A surface enhanced resonance Raman study of cobalt phthalocyanine on rough Ag films: Theory and experiment (1987)

We present a combined experimental/theoretical study of the coverage and frequency dependence of surface (enhanced) resonance Raman scattering [S(E)RRS] of cobalt phthalocyanine (CoPc) on CaF2 roughened silver films. The experimental spectra indicate a rather strong coverage dependence at very low coverage for excitation at or close to the molecular resonance frequency, with a peak at 0.07 monolayer (ML) followed by a rapid decrease above that. This coverage dependence differs strongly with observations on smooth films, where a much weaker dependence is observed. At very low coverage on the rough Ag films S(E)RRS enhancements comparable to SERS are observed. To model this coverage dependence, we consider the electromagnetic interactions between the adsorbate and substrate, with the substrate modeled as a metal spheroid and the adsorbate as a layer with variable coverage. Two models for this layer are considered, an effective medium model in which the layer is taken to have a coverage dependent dielectric constant, and a coupled dipole model in which both the molecules and metal are taken to be polarizable dipoles. The dependence of field enhancement and S(E)RRS intensity is studied for these two models as a function of frequency, coverage, and Stokes shift. It is found that although there are differences between the two models, the coverage dependence is similar in both, with peak intensities at about 0.1 ML for reasonably prolate spheroids. These models also demonstrate that the drop in intensity above 0.1 ML arises from damping of the plasmon resonance by the adsorbed layer. Interadsorbate interactions are found to play a role in determining the coverage dependence of the S(E)RRS intensity that is secondary to this damping. The large enhancements seen below 0.1 ML suggest that excited state quenching by the surface is not important for this nonfluorescent molecule.
Albumin-conjugated C34 Peptide HIV-1 Fusion Inhibitor (2008)

Entry inhibitors of human immunodeficiency virus, type 1 (HIV-1) have been the focus of much recent research. C34, a potent fusion inhibitor derived from the HR2 region of gp41, was engineered into a 1:1 human serum albumin conjugate through stable covalent attachment of a maleimido-C34 analog onto cysteine 34 of albumin. This bioconjugate, PC-1505, was designed to require less frequent dosing and less peptide than T-20 and was assessed for its antifusogenic activity both in vitro and in vivo in the SCID-hu Thy/Liv mouse model. PC-1505 was essentially equipotent to the original C34 peptide and to T-20 in vitro. In HIV-1-infected SCID-hu Thy/Liv mice, T-20 lost activity with infrequent dosing, whereas the antiviral potency of PC-1505 was sustained, and PC-1505 was active against T-20-resistant ("DIV") virus with a G36D substitution in gp41. The in vivo results are the direct result of a significantly improved pharmacokinetic profile for the C34 peptide following albumin conjugation. Contrary to previous reports that the gp41 NHR trimer is poorly accessible to C34 fused to protein cargoes of increasing size (Hamburger, A. E., Kim, S., Welch, B. D., and Kay, M. S. (2005) J. Biol. Chem. 280, 12567-12572), these results are the first demonstration of the capacity for a large, endogenous serum protein to gain unobstructed access to the transient gp41 intermediates that exist during the HIV fusion process, and it supports further development of albumin conjugation as a promising approach to inhibit HIV-1 entry.
Multifunctional receptor-targeted nanocomplexes for the delivery of therapeutic nucleic acids to the Brain (2013)

Convection enhanced delivery (CED) is a method of direct injection to the brain that can achieve widespread dispersal of therapeutics, including gene therapies, from a single dose. Non-viral, nanocomplexes are of interest as vectors for gene therapy in the brain, but it is essential that administration should achieve maximal dispersal to minimise the number of injections required. We hypothesised that anionic nanocomplexes administered by CED should disperse more widely in rat brains than cationics of similar size, which bind electrostatically to cell-surface anionic moieties such as proteoglycans, limiting their spread. Anionic, receptor-targeted nanocomplexes (RTN) containing a neurotensin-targeting peptide were prepared with plasmid DNA and compared with cationic RTNs for dispersal and transfection efficiency. Both RTNs were labelled with gadolinium for localisation in the brain by MRI and in brain sections by LA-ICP-MS, as well as with rhodamine fluorophore for detection by fluorescence microscopy. MRI distribution studies confirmed that the anionic RTNs dispersed more widely than cationic RTNs, particularly in the corpus callosum. Gene expression levels from anionic formulations were similar to those of cationic RTNs. Thus, anionic RTN formulations can achieve both widespread dispersal and effective gene expression in brains after administration of a single dose by CED.
New developments in acute lymphoblastic leukemia. (2014)

Acute lymphoblastic leukemia (ALL) occurs in both children and adults. Significant improvements in survival outcomes have been realized over the last decade for all age groups with de novo ALL. Frontline treatment incorporates a tailored approach, based on factors such as the patient’s age and the disease subtype. Children, adolescents, and young adults are likely to receive intensifying or deintensifying chemotherapy regimens using standard chemotherapeutics (eg, anthracyclines, vincristine, asparaginase) based on risk stratification. Older adults appear to benefit from reduced-intensity chemotherapy regimens, which incorporate targeted therapy (eg, monoclonal antibodies). New data suggest that a more intensive pediatric protocol might be feasible in adult patients. More than half of ALL patients relapse, and their limited survival has led to the development of novel approaches. Recently approved chemotherapeutic agents include clofarabine, nelarabine, asparaginase Erwinia chrysanthemi, and vincristine sulfate liposome injection, a novel formulation that permits administration of a higher dosage of vincristine than that used in standard regimens. Approaches under investigation include cell therapy using autologous T-cell technologies, antibody-drug conjugates, and agents targeting common gene mutations. Many novel agents are undergoing evaluation in both the frontline and relapsed settings.
The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein (1994)

Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of Salmonella typhimurium (OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.
ETV5 transcription factor is overexpressed in ovarian cancer and regulates cell adhesion in ovarian cancer cells (2011)

Epithelial ovarian cancer is the most lethal gynecological malignancy and the fifth leading cause of cancer deaths in women in the Western world. ETS transcription factors are known to act as positive or negative regulators of the expression of genes that are involved in various biological processes, including those that control cellular proliferation, differentiation, apoptosis, tissue remodeling, angiogenesis and transformation. ETV5 belongs to the PEA3 subfamily. PEA3 subfamily members are able to activate the transcription of proteases, matrix metalloproteinases and tissue inhibitor of metalloproteases, which is central to both tumor invasion and angiogenesis. Here, we examined the role of the ETV5 transcription factor in epithelial ovarian cancer and we found ETV5 was upregulated in ovarian tumor samples compared to ovarian tissue controls. The in vitro inhibition of ETV5 decreased cell proliferation in serum-deprived conditions, induced EMT and cell migration and decreased cell adhesion to extracellular matrix components. ETV5 inhibition also decreased cell-cell adhesion and induced apoptosis in anchorage-independent conditions. Accordingly, upregulation of ETV5 induced the expression of cell adhesion molecules and enhanced cell survival in a spheroid model. Our findings suggest that the overexpression of ETV5 detected in ovarian cancer cells may contribute to ovarian tumor progression through the ability of ETV5 to enhance proliferation of ovarian cancer cells. In addition, upregulation of ETV5 would play a role in ovarian cancer cell dissemination and metastasis into the peritoneal cavity by protecting ovarian cancer cells from apoptosis and by increasing the adhesion of ovarian cancer cells to the peritoneal wall through the regulation of cell adhesion molecules.