gebhart/patrepeval huggingface dataset:
Minimally invasive cystectomy approaches in the treatment of bladder cancer (2012)

Bladder cancer is the most frequently occurring tumor of the urinary system, with over 10,000 new diagnoses each year in the UK. Approximately 70% of these are non-muscle-invasive and limited to the mucosa (Ta) or submucosa (T1). These tumors are generally managed with transurethral resection followed by adjuvant intravesical chemo- or immuno-therapy and regular cystoscopic surveillance. The principal end points in the management of these tumors are prevention of recurrence and progression. Muscle-invasive bladder cancer is a life-threatening disease with overall 5-year mortality of 50%. Neoadjuvant chemotherapy, where possible followed by radical surgery, is currently considered the best standard of care. Open radical cystectomy is the gold-standard treatment for muscle-invasive or high-risk non-muscle-invasive (multifocal or recurrence after intravesical therapy) bladder cancer. Historically, this procedure has carried significant morbidity, although mortality of open radical cystectomy has reduced to 1-2% owing to improvements in anesthesia and intensive care facilities. Over the last 15 years, minimally invasive techniques in radical cystectomy have evolved, with the aim of reducing morbidity. In this article, we review the development of laparoscopic radical cystectomy and robot-assisted radical cystectomy, along with current evidence on perioperative morbidity and medium-term oncological outcomes.
Gage control of film and sheet‐forming processes (1996)

Abstract A new methodology for gage control of sheet and film processes is presented. A linear process model is developed that is capable of describing many of the interesting features of the process, including a noisy and moving gage sensor, significant process noise, strong coupling between the gage in different lanes, constraints on the actuators, and significant time delay between the actuators and the sensor. An automatic control of this process given this model form is designed. Novel features of the controller are that it can contend with information from a moving sensor and handle hard constraints on the actuators. Control performance and robustness to noise are demonstrated favorably via simulations.
Comparison of Electrodeposited Copper-Zinc Alloys Prepared Individually and Combinatorially (2003)

Combinatorial methods provide a new paradigm for advancing scientific discovery. These methods have captured the attention of the materials industry with the promise of providing new discoveries "faster, better and cheaper." Thousands of similar, but unique, materials can be created in a single experiment and then tested for a desired property. Typical methods for creating these "libraries" of materials are complex, expensive, and slow. Here we describe a simple method for creating a composition-spread library of copper-zinc alloys, where composition varies as a function of position, via electrodeposition. Electrodeposition is a simple, inexpensive, and fast deposition method that is easily scaled to industrial proportions. Seven copper-zinc alloys with different compositions were prepared, in bulk, by one-at-a-time electrodeposition methods. The composition and structure of these alloys are compared to alloys prepared by combinatorial methods. It is shown that copper-zinc alloys prepared using combinatorial methods via electrodeposition are representative of bulk alloys prepared by one-at-a-time methods. Therefore, combinatorial methods via electrodeposition embodies, and even extends, the advantages of combinatorial methods: "faster, better, cheaper, simpler, and scalable." © 2003 The Electrochemical Society. All rights reserved.
Robust quantization of memoryless sources using dispersive FIR filters (1992)

An approach to quantizing discrete-time memoryless sources is presented. An important feature is that its performance is largely insensitive to errors in modeling the input PDF. The method involves changing the amplitude distribution of the source to be approximately Gaussian by all-pass filtering, then applying a Lloyd-Max quantizer designed for a Gaussian source. After quantization, the samples are passed through another all-pass filter, which is an approximate inverse of the first filter. The mean-square error (MSE) for the overall process is roughly equal to the quantization MSE for the intermediate Gaussian signal, independent of the source statistics. For some sources, this is actually an improvement over direct, correct-model Lloyd-Max quantization. The cost of this technique is some delay due to filtering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cycloaddition of Diphenylcyclopropenone with Carboximidate, Carboximidamide, and Carboximidothioate (1983)

Abstract The reaction of diphenylcyclopropenone with R1N=C(R2)X (2) (R1, R2= alkyl, aryl, X=MeO, EtO, MeS, or Me2N) gave 2-pyrrolin-4-one (3) in good yield. The less reactive carboximidothioate (2, R1=4-MeC6H4, R2=Ph, X=MeS) yielded isomeric 3-pyrrolin-2-one together with 3.
Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions (2005)

A new ion source has been developed for rapid, noncontact analysis of materials at ambient pressure and at ground potential. The new source, termed DART (for "Direct Analysis in Real Time"), is based on the reactions of electronic or vibronic excited-state species with reagent molecules and polar or nonpolar analytes. DART has been installed on a high-resolution time-of-flight mass spectrometer (TOFMS) that provides improved selectivity and accurate elemental composition assignment through exact mass measurements. Although DART has been applied to the analysis of gases, liquids, and solids, a unique application is the direct detection of chemicals on surfaces without requiring sample preparation, such as wiping or solvent extraction. DART has demonstrated success in sampling hundreds of chemicals, including chemical agents and their signatures, pharmaceutics, metabolites, peptides and oligosaccharides, synthetic organics, organometallics, drugs of abuse, explosives, and toxic industrial chemicals. These species were detected on various surfaces, such as concrete, asphalt, human skin, currency, airline boarding passes, business cards, fruits, vegetables, spices, beverages, body fluids, horticultural leaves, cocktail glasses, and clothing. DART employs no radioactive components and is more versatile than devices using radioisotope-based ionization. Because its response is instantaneous, DART provides real-time information, a critical requirement for screening or high throughput.
A novel two‐component system controls the expression of Pseudomonas aeruginosa fimbrial cup genes (2004)

Biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa requires the expression of a number of surface adhesive components. The expression of surface organelles facilitating biofilm formation is controlled by environmental signals acting through transcriptional regulatory networks. We analysed the expression of a family of P. aeruginosa adhesins encoded by three distinct fimbrial gene clusters (cupA, cupB and cupC). Using transposon mutagenesis, we have identified several regulatory loci that upregulated cupB and cupC transcription. One such locus contains three components, RocS1, RocR and RocA1, which represent a variant of a classical two-component signal transduction pathway. RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity. Using a two-hybrid assay, we have shown that RocS1 interacts with receiver domains of both RocA1 and RocR. Expression of the Cup system in response to environmental stimuli is accomplished by a novel mechanism in which the sensor kinase activates its cognate response regulator through a phosphorelay pathway, while an additional repressor protein modulates this interaction.
Effect of non-swelling layers on the dissolution of reduced-charge montmorillonite in hydrochloric acid (1996)

Abstract A series of reduced-charge montmorillonites (RCM), prepared from the same parent Li-montmorillonite (Jelšový Potok, Slovakia) by heating at various temperatures (105–210°C) for 24 h, was treated with 6 m HCl at 95°C for periods up to 30 h. Reaction solutions obtained were analysed for Al, Fe, Mg and Li and the solid reaction products were investigated by FTIR spectroscopy. Both analyses provided evidence that the extent of dissolution decreased with increased amounts of Li fixed within the montmorillonite structure, i.e. with increased heating temperature. Differences in the acid dissolution process were reflected in the structural changes which occurred within the RCM samples, due presumably to different positions of fixed Li. The ethylene glycol monoethyl ether (EGME) surface areas, and XRD and HRTEM analyses of the RCM series revealed an increased amount of non-swelling layers in the samples prepared at higher temperatures, which caused a substantially slower decomposition of M7 and M8 in HCl. The calculated XRD patterns of M6 and M7 confirmed the presence of 20% and 45% pyrophyllite-like layers, respectively, in these samples. Mixed-layer pyrophyllite-like-smectite and pyrophyllite-like crystals, containing only non-swelling layers, were found in sample M8. The results confirmed that the amount of swelling layers in RCM significantly affects their dissolution rate in HCl.
Receptor- and heparin-binding domains of basic fibroblast growth factor. (1988)

Two functional domains in the primary structure of basic fibroblast growth factor (FGF) have been identified on the basis of their ability to interact with the FGF receptor, bind radiolabeled heparin, and modulate the cellular response to FGF. Peptides derived from these two functional domains can act as partial agonists and antagonists in biological assays of FGF activity. Peptides related to the sequences of FGF-(24-68)-NH2 and FGF-(106-115)-NH2 inhibit thymidine incorporation into 3T3 fibroblasts when they are stimulated by FGF but have no effect when the cells are treated with either platelet-derived growth factor or epidermal growth factor. They also possess partial agonist activity and can stimulate DNA synthesis when tested in the absence of exogenous FGF. The active peptides have no effect on the binding of epidermal growth factor to its receptor on A431 cells and they can modulate the effects of FGF, but not fibronectin, on endothelial cell adhesion. The results suggest the possibility of designing specific analogs of FGF that are capable of inhibiting the biological effects of FGF.
An insulin response element in the glyceraldehyde-3-phosphate dehydrogenase gene binds a nuclear protein induced by insulin in cultured cells and by nutritional manipulations in vivo. (1990)

Two independent cis-acting insulin response elements (IREs) in the gene encoding glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12], designated IRE-A and IRE-B, are sufficient to direct insulin-inducible gene expression. Using the electrophoretic mobility shift assay, a 4-fold increase in the amount of IRE-A DNA bound to nuclear proteins was detected when extracts isolated from insulin-stimulated differentiated 3T3-L1 cells or from the liver of rats refed a high-carbohydrate/low-fat diet after a 72-hr fast were compared to control nuclear extracts. The points of contact between protein and IRE-A DNA may represent a sequence recognized by at least one class of insulin-sensitive transcription factor(s).
Dasatinib (BMS-354825) inhibits KITD816V, an imatinib-resistant activating mutation that triggers neoplastic growth in most patients with systemic mastocytosis (2006)

Mastocytosis is associated with an activating mutation in the KIT oncoprotein (KITD816V) that results in autophosphorylation of the KIT receptor in a ligand-independent manner. This mutation is inherently resistant to imatinib and, to date, there remains no effective curative therapy for systemic mastocytosis associated with KITD816V. Dasatinib (BMS-354825) is a novel orally bioavailable SRC/ABL inhibitor that has activity against multiple imatinib-resistant BCR-ABL isoforms in vitro that is presently showing considerable promise in early-phase clinical trials of chronic myeloid leukemia (CML). Pharmacokinetic analysis suggests that high nanomolar concentrations of dasatinib can be achieved safely in humans. In this study, we demonstrate significant inhibitory activity of dasatinib against both wild-type KIT and the KITD816V mutation in the nanomolar range in in vitro and cell-based kinase assays. Additionally, dasatinib leads to growth inhibition of a KITD816V-harboring human masto-cytosis cell line. Significantly, dasatinib selectively kills primary neoplastic bone marrow mast cells from patients with systemic mastocytosis while sparing other hematopoietic cells. Computer modeling suggests that the KITD816V mutation destabilizes the inactive conformation of the KIT activation loop to which imatinib binds, but it is not predicted to impair binding of KIT by dasatinib. Based upon our results, further evaluation of dasatinib for the treatment of systemic masto-cytosis in clinical trials is warranted. Moreover, dasatinib may be of clinical utility in other disease settings driven by activating KIT mutations.
Immunocytochemistry in the differential diagnosis of serous effusions (2001)

Immunohistochemical studies performed on Papanicolaou stained cytologic smears proved to be useful in the differentiation between metastatic AC and mesothelial proliferation. HBME-1, thrombomodulin, MOC-31, Ber-EP4, and CD-15 were the most useful. In selected cases, it appeared that double immunostaining aided the differential diagnosis. Cancer (Cancer Cytopathol)
Solution Structure of a DNA Dodecamer Containing the Anti-Neoplastic Agent Arabinosylcytosine: Combined Use of NMR, Restrained Molecular Dynamics, and Full Relaxation Matrix Refinement (1994)

The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT) (araC)d(GCG)]2 was examined by comparing its nuclear magnetic resonance (NMR)-determined solution structure with that of the control duplex d[(CGCGAATTCGCG)]2. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H NMR and a 3-D 31P-1H heteroTOCSY-NOESY experiment. Proton-proton distances (determined from NOESY data) and sugar dihedral angles (from NOESY and COSY data) were used in restrained molecular dynamics simulations starting from canonical A- or B-form DNA models. Both the control and araC sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures which were in excellent agreement (R1/6 < 0.05) with the observed NOE intensities. A detailed comparison of the final control and araC structures revealed a global similarity (overall RMSD approximately 1.3 A), with significant differences localized at the araC site and neighboring bases. These included changes in sugar pucker, backbone torsion angles, base stacking, and other helical parameters. These findings are in general agreement with the previously published X-ray structure of a decamer duplex containing araC. One intriguing feature of the NMR solution structure not found in the crystal structure is the presence of an intramolecular hydrogen bond between the 2' hydroxyl on the araC sugar and the 3' phosphate group.
Live, Attenuated Mumps-Virus Vaccine (1967)

MUMPS is a common childhood disease that may be severely and even permanently crippling when it involves the brain, testis, ovary, auditory nerves or pancreas. Adult males may be permanently sterilized by mumps. The personal discomfort and time loss from productive effort resulting from ordinary mumps and the serious or even fatal aspect of the extraordinary case appear to justify development and application of a safe and effective live-virus vaccine.A first report in the present series describes the development by Buynak and Hilleman1 of a live, attenuated mumps-virus vaccine referred to as the Jeryl Lynn strain, level B. Early . . .
Molecular origins of fluorocarbon hydrophobicity (2010)

We have undertaken atomistic molecular simulations to systematically determine the structural contributions to the hydrophobicity of fluorinated solutes and surfaces compared to the corresponding hydrocarbon, yielding a unified explanation for these phenomena. We have transformed a short chain alkane, n-octane, to n-perfluorooctane in stages. The free-energy changes and the entropic components calculated for each transformation stage yield considerable insight into the relevant physics. To evaluate the effect of a surface, we have also conducted contact-angle simulations of water on self-assembled monolayers of hydrocarbon and fluorocarbon thiols. Our results, which are consistent with experimental observations, indicate that the hydrophobicity of the fluorocarbon, whether the interaction with water is as solute or as surface, is due to its "fatness." In solution, the extra work of cavity formation to accommodate a fluorocarbon, compared to a hydrocarbon, is not offset by enhanced energetic interactions with water. The enhanced hydrophobicity of fluorinated surfaces arises because fluorocarbons pack less densely on surfaces leading to poorer van der Waals interactions with water. We find that interaction of water with a hydrophobic solute/surface is primarily a function of van der Waals interactions and is substantially independent of electrostatic interactions. This independence is primarily due to the strong tendency of water at room temperature to maintain its hydrogen bonding network structure at an interface lacking hydrophilic sites.
State Regulation in Indian Country: The Supreme Court's Marketing Exemptions Concept, A Judicial Sword through the Heart of Tribal Self-Determination (1989)

State Regulation in Indian Country: The Supreme Court's Marketing Exemptions Concept, A Judicial Sword Through the Heart of Tribal Self-Determination
Protein synthesis rate is the predominant regulator of protein expression during differentiation (2013)

External perturbations, by forcing cells to adapt to a new environment, often elicit large-scale changes in gene expression resulting in an altered proteome that improves the cell's fitness in the new conditions. Steady-state levels of a proteome depend on transcription, the levels of transcripts, translation and protein degradation but system-level contribution that each of these processes make to the final protein expression change has yet to be explored. We therefore applied a systems biology approach to characterize the regulation of protein expression during cellular differentiation using quantitative proteomics. As a general rule, it seems that protein expression during cellular differentiation is largely controlled by changes in the relative synthesis rate, whereas the relative degradation rate of the majority of proteins stays constant. In these data, we also observe that the proteins in defined sub-structures of larger protein complexes tend to have highly correlated synthesis and degradation rates but that this does not necessarily extend to the holo-complex. Finally, we provide strong evidence that the generally poor correlation observed between transcript and protein levels can fully be explained once the protein synthesis and degradation rates are taken into account.
Proinflammatory Role of Glucocorticoid-Induced TNF Receptor-Related Gene in Acute Lung Inflammation (2006)

Glucocorticoid-induced TNFR-related gene (GITR) participates in the immune/inflammatory response. Because GITR expression has been described in cells other than T lymphocytes, we investigated whether it also modulates acute inflammatory response. Using GITR-deficient (GITR(-/-)) mice, we analyzed the role of GITR in the development of carrageenan-induced lung inflammation (pleurisy) by studying several proinflammatory markers 2-8 h after carrageenan injection. When compared with GITR(+/+), GITR(-/-) mice exhibited decreased production of turbid exudate containing a lower number of leukocytes. This was correlated with the reduction of inflammatory markers (including TNF-alpha, IL-1beta, myeloperoxidase, inducible NO synthase, and cyclooxygenase 2) in the pleural exudate and/or in the lung. Moreover, endothelial cells expressed lower levels of adhesion molecules. In lungs of GITR(+/+) mice, GITR ligand expression was not modulated during pleurisy, while that of GITR increased, as a consequence of increased infiltration by GITR-expressing cells and of GITR up-regulation in macrophages and endothelial cells. Finally, cotreatment of GITR(+/+) mice with carrageenan and Fc-GITR fusion protein decreased the number of inflammatory cells (pleural macrophages and lung neutrophils) as compared with carrageenan treatment alone, confirming that GITR plays a role in the modulation of pleurisy.
[Analysis of reporter gene expression at different segments of the vaccinia virus genome]. (1993)

Two reporter genes: the firefly Photinus pyralis luciferase gene and the Escherichia coli beta-galactosidase gene were used for construction and characterization of the five unique recombinant vaccinia strain LIVP viruses expressing these genes in three nonessential regions of the virus genome. We give comparative characteristics of beta-galactosidase and luciferase activities in experiments of transient expression and expression dynamics of reporter genes by different stable recombinant viruses. Both genes are expressed with high efficiency independent on the sites of virus genome localization. It is shown that the TK-, HA- and N-regions of vaccinia virus DNA may be used for inserting foreign genes.
Possible role of cytomegalovirus in atherogenesis (1990)

ATHEROSCLEROTIC plaques consist of complex accumulations produced by arterial smooth muscle cells, which proliferate excessively at the site of plaque formation. To explain the onset of this abnormal cellular proliferation, it has been suggested that injury to the endothelial lining of the artery results in exposure of underlying smooth muscle cells to hormones, low-density lipoproteins, and various growth-promoting factors associated with serum and platelets. It has also been suggested that a transforming event causes arterial smooth muscle cells to begin dividing and form a focus of proliferating cells. The possibility of viral infection playing a role in the pathogenesis of atherosclerosis is compatible with the hypotheses described above, since viruses may cause cell destruction, alter cellular metabolism, or induce transformation of infected cells. Recent work in this area has been stimulated by the finding that atherosclerotic lesions, strikingly similar to those in human disease, were reproducibly induced in chickens by
MARROW TRANSPLANTATION FROM HLA-MATCHED UNRELATED DONORS FOR TREATMENT OF HEMATOLOGIC MALIGNANCIES (1991)

Less than 40% of the patients who could benefit from marrow transplantation have an HLA-matched relative who can serve as a donor. For this reason, several centers have explored marrow transplantation from other categories of donors. This retrospective study analyzes the results of marrow transplantation for 52 patients receiving grafts from HLA-A,B,DR,Dw-phenotypically matched, MLC-compatible, unrelated volunteer donors compared to a disease, disease-stage, and age-matched cohort of 104 patients transplanted from HLA-genotypically identical sibling donors. The patients transplanted from unrelated donors had an increased incidence of grade II-IV acute graft-versus-host disease compared to patients transplanted from related donors (79% vs. 36%, P much less than 0.001). However, the probability of relapse-free survival appears similar in the two groups (P = 0.39 over all, with estimates of 41% vs. 46% at 1 year). We conclude from this preliminary data that marrow transplantation from HLA-matched unrelated donors should be considered in most, if not all, circumstances where transplantation from an HLA-matched sibling would be indicated if such a donor were available.