gebhart/patrepeval huggingface dataset:
Predictors of response to systemic therapy in breast cancer (2002)

The most appropriate systemic therapy for a population of patients with breast cancer is determined from clinical trial data. However, the heterogeneity of breast cancer is such that within a population individual patients derive variable benefit. There is therefore a need for predictive molecular factors in order that treatment can be individualised. This review describes the roles of HER-2, epidermal growth factor receptor (EGFR), oestrogen receptor (ER)/progesterone receptor (PgR), Ki67, Bcl-2, p53 and gene expression profiling in predicting responses to endocrine, cytotoxic and biological therapies. ER and PgR remain the only well-established predictive markers of responses to endocrine therapy, although HER-2/neu has an emerging role in this area and in choice of adjuvant chemotherapy. There are considerable methodological difficulties in identifying useful predictive factors but on the basis of current evidence other biomarkers add little additional information. The development of targeted therapies means that the molecular targets themselves may become useful predictive factors for directing use of these therapies. HER-2 already has an established role in this area, but the role of EGFR requires further elaboration. The use of DNA microarrays to assess gene expression profiles may revolutionise our ability to predict responses to therapy. [References: 110]
The AG1478 tyrosine kinase inhibitor is an effective suppressor of leiomyoma cell growth (2004)

The growth-arresting properties of AG1478, unaffected by ovarian steroidal hormones, identify it as a potential lead agent for the non-surgical management of uterine leiomyomas.
Involvement of Akt in synergistic effects of thermo-chemotherapy on human small cell lung cancer H446 cell apoptosis (2010)

Thermo-chemotherapy has a stronger inhibitory effect than chemotherapy alone in lung tumor cell growth, probably through induction of ROS production and subsequent inhibition of Akt pathway activation and Caspase pathway-induced cancer cell apoptosis.
The effect of desferrithiocin, an oral iron chelator, on T-cell function (1990)

Desferrithiocin is a new, potent, orally available iron chelator. To determine whether this drug might be useful not only for iron-overload but also for immunosuppression, we studied the in vitro effects of desferrithiocin on T-lymphocyte function. Like deferoxamine, desferrithiocin inhibited, in a dose-dependent fashion, mitogen- and lectin-induced proliferation of both human and murine T cells. It was active at a concentration of 10 micrograms/mL. The inhibition of proliferation was reversed by ferrous chloride, but not by other metal salts, recombinant IL-2, or conditioned medium. Desferrithiocin also inhibited proliferation of constitutively dividing, and factor- independent EBV-transformed B cell and leukemic T-cell lines. Although desferrithiocin inhibited the induction of cytotoxic T lymphocyte (CTL) activity, it did not inhibit CTL- or natural killer-induced cytotoxicity. The agent did not inhibit the expression of activation antigens such as the IL-2 receptor on T cells, nor early measures of T- cell activation such as the influx of intracellular calcium. Thus, desferrithiocin, like deferoxamine, is a potent and reversible inhibitor of T-cell proliferation. This anti-proliferative effect inhibits T-cell function. Bioavailability after oral administration is a unique property of desferrithiocin, and would make it an attractive alternative to deferoxamine. Its immunomodulating properties may therefore be exploited in vivo to inhibit graft rejection or autoreactive T cells.
Current Gastroenterology (2nd ed.) (1983)

Journal of Clinical Gastroenterology gathers the world's latest, most relevant clinical studies and reviews, case reports, and technical expertise in a single source. Regular features include cutting-edge, peer-reviewed articles and clinical reviews that put the latest research and development into the context of your practice. Also included are biographies, focused organ reviews, practice management, and therapeutic recommendations.
Control, wear testing & integration of stick-slip micropositioning (2004)

These Ecole polytechnique federale de Lausanne EPFL, n° 2843 (2003)Section de microtechniqueFaculte des sciences et techniques de l'ingenieurInstitut de production et robotiqueJury: Hannes Bleuler, Bradley Nelson, Philippe Renaud, Heinz Woern Public defense: 2003-10-3 Reference doi:10.5075/epfl-thesis-2843Print copy in library catalog Record created on 2005-03-16, modified on 2016-08-08
Energetics and mechanics of human running on surfaces of different stiffnesses (2002)

Mammals use the elastic components in their legs (principally tendons, ligaments, and muscles) to run economically, while maintaining consistent support mechanics across various surfaces. To examine how leg stiffness and metabolic cost are affected by changes in substrate stiffness, we built experimental platforms with adjustable stiffness to fit on a force-plate-fitted treadmill. Eight male subjects [mean body mass: 74.4 +/- 7.1 (SD) kg; leg length: 0.96 +/- 0.05 m] ran at 3.7 m/s over five different surface stiffnesses (75.4, 97.5, 216.8, 454.2, and 945.7 kN/m). Metabolic, ground-reaction force, and kinematic data were collected. The 12.5-fold decrease in surface stiffness resulted in a 12% decrease in the runner's metabolic rate and a 29% increase in their leg stiffness. The runner's support mechanics remained essentially unchanged. These results indicate that surface stiffness affects running economy without affecting running support mechanics. We postulate that an increased energy rebound from the compliant surfaces studied contributes to the enhanced running economy.
Cellular Fibronectin Binds to Lysyl Oxidase with High Affinity and Is Critical for Its Proteolytic Activation (2005)

Lysyl oxidase (LOX) is a copper-containing amine oxidase known to catalyze the covalent cross-linking of fibrillar collagens and elastin at peptidyl lysine residues. In addition, its involvement in cancer, wound healing, cell motility, chemotaxis, and differentiation reflect a remarkable functional diversity of LOX. To investigate novel mechanisms of LOX regulation and function, we performed a yeast two-hybrid screen to identify LOX-interacting proteins. Three overlapping positive clones were identified as C-terminal fragments of fibronectin (FN). Glutathione S-transferase pull-downs and solid phase binding assays confirmed this interaction. LOX binds to the cellular form of FN (cFN) with a dissociation constant (K(d)) of 2.5 nm. This was comparable with our measured K(d) of LOX binding to tropoelastin (1.9 nm) and type I collagen (5.2 nm), but LOX demonstrated a much lower binding affinity for the plasma form of FN (pFN). Immunofluorescent microscopy revealed co-localization of FN and LOX in normal human tissues, where these proteins may interact in vivo. LOX enzymatic activity assays showed that cFN does not seem to be a substrate of LOX. However, cFN can act as a scaffold for enzymatically active 30-kDa LOX. Furthermore, in FN-null mouse embryonic fibroblasts, we observed dramatically decreased proteolytic processing of the 45-kDa LOX proenzyme to the 30-kDa active form, with a corresponding decrease in LOX enzyme activity. Our results suggest that the FN matrix may provide specific microenvironments to regulate LOX catalytic activity.
A critical view on conservative mutations (2001)

By analysing the surface composition of a set of protein 3D structures, complemented with predicted surface compositional information for homologous proteins, we have found significant evidence for a layer composition of protein structures. In the innermost and outermost parts of proteins there is a net negative charge, while the middle has a net positive charge. In addition, our findings indicate that the concept of conservative mutation needs substantial revision, e.g. very different spatial preferences were found for glutamic acid and aspartic acid. The alanine screening often used in protein engineering projects involves the substitution of residues to alanine, based on the assumption that alanine is a "neutral" residue. However, alanine has a high negative correlation with all but the non-polar residues. We therefore propose the use of, for example, serine as a substitute for the residues that are negatively correlated with alanine.
Automated electrical measurements of registration errors in step-and-repeat optical lithography systems (1980)

An automated electrical measurement technique for evaluating registration errors in step-and-repeat optical lithography systems is discussed, with emphasis on the ability of such equipment to meet the manufacturing requirements of very-large-scale integration (VLSI). Sources of registration error are outlined, and the relative contributions of these errors for a group of wafers stepped on a commercial 10:1 reduction system are reported. The components of registration error obtained from specially designed resistor structures are displayed using computer-drawn vector displacement maps and frequency plots. The data are analyzed using a six-parameter model which determines the extent to which level-to-level translation, rotation, and linear dimensional changes are present. Estimates of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</tex> stage-stepping precision are made by determining the residual errors in both the registration data and the data obtained from specially designed control structures.
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks (2014)

Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ∼85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.
RoBo-1, a Novel Member of the Urokinase Plasminogen Activator Receptor/CD59/Ly-6/Snake Toxin Family Selectively Expressed in Rat Bone and Growth Plate Cartilage (1998)

Using differential display polymerase chain reaction, we cloned a novel cDNA named RoBo-1 from rat tibia. RoBo-1 is abundantly expressed in bone, including the hypertrophic chondrocytes of the growth plate where cartilage is remodeled into bone. RoBo-1 mRNA expression increased in response to two modulators of bone metabolism, estradiol and intermittent mechanical loading, suggesting a role in bone homeostasis. The 1.6-kilobase cDNA encodes a 240-amino acid protein with a cysteine spacing pattern, suggesting that RoBo-1 is a novel member of the urokinase plasminogen activator receptor/CD59/Ly-6/snake toxin family. Furthermore, the C-terminal contains a glycosyl-phosphatidylinositol attachment site, suggesting that it is a cell surface protein similar to other mammalian members of this family. The strongest homology of RoBo-1 is to the snake serum-derived phospholipase A2 inhibitors, which uniquely contain two of the cysteine domains but are secreted proteins. Interestingly, RoBo-1 is likely the first membrane-anchored member of this family containing two cysteine domains. Thus, the tissue specificity, responsiveness to bone protective mediators, along with its relationship to the multifunctional urokinase plasminogen activator receptor/CD59/Ly-6/snake toxin family suggests that RoBo-1 may play a novel role in the growth or remodeling of bone.
Synthetic Triterpenoids Prolong Survival in a Transgenic Mouse Model of Pancreatic Cancer (2010)

Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States and is nearly always fatal. Whereas early detection offers the most promising approach for reducing the mortality of this disease, there is still a need to develop effective drugs for the prevention and treatment of pancreatic cancer. We tested two promising classes of noncytotoxic drugs, synthetic oleanane triterpenoids and rexinoids, for the prevention of carcinogenesis in the highly relevant LSL-Kras(G12D/+);LSL-Trp53(R127H/+);Pdx-1-Cre (KPC) mouse model of pancreatic cancer. KPC transgenic mice closely recapitulate the genetic mutations, clinical symptoms, and histopathology found in human pancreatic cancer. Beginning at 4 weeks of age, mice were fed powdered control diet or a diet containing the triterpenoids CDDO-methyl ester (CDDO-Me) or CDDO-ethyl amide, the rexinoid LG100268 (LG268), or the combination, until the mice displayed overt symptoms of pancreatic cancer. CDDO-Me, LG268, the combination of CDDO-Me and LG268, and the combination of CDDO-ethyl amide and LG268, all significantly (P < 0.05) increased survival in the KPC mice by 3 to 4 weeks. Recent studies have shown that gemcitabine, the current standard of care for human pancreatic cancer, does not extend survival in KPC mice. In cell lines developed from the KPC mice, the triterpenoids directly interact with both signal transducer and activator of transcription 3 and IκB kinase (IKK) to decrease constitutive interleukin-6 secretion, inhibit constitutive signal transducer and activator of transcription 3 phosphorylation, and block the degradation of IκBα when challenged with tumor necrosis factor α. These results suggest that oleanane triterpenoids and rexinoids have the potential to prevent pancreatic cancer.
Layered networks as a tool for software development (1981)

Most software systems use simple text files to represent the current state of an evolving design. We propose that layered networks provide a much better medium to represent the design of a software system and its documentation. PIE is an experimental personal information environment which provides users with descriptive structures for documents and programs. In PIE, alternative designs for programs and documents can be examined and manipulated within the systems context structured database. This data base also facilitates cooperative design among several people.
Disruption of either the Nfkb1 or the Bcl3 gene inhibits skeletal muscle atrophy (2004)

The intracellular signals that mediate skeletal muscle protein loss and functional deficits due to muscular disuse are just beginning to be elucidated. Previously we showed that the activity of an NF-B-dependent reporter gene was markedly increased in unloaded muscles, and p50 and Bcl-3 proteins were implicated in this induction. In the present study, mice with a knockout of the p105/p50 (Nfkb1) gene are shown to be resistant to the decrease in soleus fiber cross-sectional area that results from 10 days of hindlimb unloading. Furthermore, the marked unloading-induced activation of the NF-B reporter gene in soleus muscles from WT mice was completely abolished in soleus muscles from Nfkb1 knockout mice. Knockout of the B cell lymphoma 3 (Bcl3) gene also showed an inhibition of fiber atrophy and an abolition of NF-B reporter activity. With unloading, fast fibers from WT mice atrophied to a greater extent than slow fibers. Resistance to atrophy in both strains of knockout mice was demonstrated clearly in fast fibers, while slow fibers from only the Bcl3 -/-mice showed atrophy inhibition. The slow-to-fast shift in myosin isoform expression due to unloading was also abolished in both Nfkb1 and Bcl3 knockout mice. Like the soleus muscles, plantaris muscles from Nfkb1 -/-and Bcl3 -/-mice also showed inhibition of atrophy with unloading. Thus both the Nfkb1 and the Bcl3 genes are necessary for unloading-induced atrophy and the associated phenotype transition.
Coupling of Microwave Resonators to Feed Lines (2009)

Superconducting transmission line resonators can be used to read out different sensors, e.g. flux qubit, transition edge sensor, or as detection element in kinetic inductance detectors. For both applications, high loaded quality factors of the microwave resonators are required, so that it is possible to detect small deviations in their resonance frequency. Thus high loaded quality factors lead to a high sensitive readout.
Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers (2023)

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.
Updating the sequence-based classification of glycosyl hydrolases (1996)

Research Article| June 01 1996 Updating the sequence-based classification of glycosyl hydrolases Bernard HENRISSAT; Bernard HENRISSAT ‡ *Centre de Recherches sur les Macromolécules Végétales, France§C.N.R.S., BP 53, 38041 Grenoble Cédex, France ‡To whom correspondence should be addressed. Search for other works by this author on: This Site PubMed Google Scholar Amos BAIROCH Amos BAIROCH †Medical Biochemistry Department, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland§C.N.R.S., BP 53, 38041 Grenoble Cédex, France Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1996) 316 (2): 695–696. https://doi.org/10.1042/bj3160695 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Bernard HENRISSAT, Amos BAIROCH; Updating the sequence-based classification of glycosyl hydrolases. Biochem J 1 June 1996; 316 (2): 695–696. doi: https://doi.org/10.1042/bj3160695 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. The Biochemical Society, London © 19961996 Article PDF first page preview Close Modal You do not currently have access to this content.
Atomic radiative and radiationless yields for K and L shells (1979)

The available body of information on (a) fluorescence, Auger, and Coster-Kronig yields, (b) radiative and radiationless transition rates, (c) level widths, (d) x-ray and Auger line widths, (e) x-ray and Auger spectra, and (f) Coster-Kronig energies has been used to generate an internally consistent set of values of atomic radiative and radiationless yields for the K shell (5 ?Z?110) and the L subshells (12 ?Z?110). Values of fluorescence yields ωk, ω1, ω2, ω3, Coster-Kronig yields ℱ1, ℱ1.2, ℱ1.3, ℱ1.3, ℱ2.3. Auger yields ak, a1, a2, a3, and effective fluorescence yields ν1 and ν2 are presented in tables and graphs. Estimates of uncertainties are given. Updated and expanded graphs of partial and total widths of K, L1, L2, and L3 levels are presented as well as a reference list of papers published since about 1972.
Modeling Epidemics on a Regular Tree Graph (2016)

We will first provide a brief introduction to models of disease transmission on so-called contact networks, which can be represented by various structures from the mathematical field of graph theory. These models allow for exploration of stochastic effects and incorporation of more biological detail than the classical compartment-based ordinary differential equation models, which usually assume both homogeneity in the population and uniform mixing. In particular, we use an agent-based modelling platform to compare theoretical predictions from mathematical epidemiology to results obtained from simulations of disease transmission on a regular tree graph. We also demonstrate how this graph reveals connections between network structure and the spread of infectious diseases. Specifically, we discuss results for how certain properties of the tree graph, such as network diameter and density, alter the duration of an outbreak.
Ivermectin treatment for massive orbital myiasis in an empty socket with concomitant scalp pediculosis (2012)

We report a rare case of massive orbital myiasis following recent lid injury, occurring in the empty socket of an elderly lady, who had concurrent scalp pediculosis. The orbital myiasis was effectively treated with the broad-spectrum antiparasitic agent, ivermectin, thus precluding the need for an exploratory surgery. Ivermectin was also effective in managing the concurrent scalp pediculosis.
Regioselective Synthesis of 1,3,5-Substituted Pyrazoles from Acetylenic Ketones and Hydrazines (2003)

The synthesis of diversely substituted 1,3,5-substituted pyrazoles from the reaction of acetylenic ketones with substituted hydrazines is reported. The reactions were shown to be highly regio­selective regardless of the nature of the substituents in the substrates and afforded essentially single pyrazole isomers in excellent yields.
Hoechst staining and exposure to UV laser during flow cytometric sorting does not affect the frequency of detected endogenous DNA nicks in abnormal and normal human spermatozoa (1997)

Controlling the sex of offspring by the separation of X and Y chromosome-bearing spermatozoa using flow cytometry has been reported as a clinical technique aiding prevention of X-linked diseases. Although this technique has resulted in several hundred normal births in animals and at least one human birth, there is still concern over its genetic safety due to the involvement of two potentially mutagenic agents: UV light and the fluorochrome dye, Hoechst 33342 (H33342). Human spermatozoa, particularly those considered abnormal, may be more likely to suffer DNA damage following exposure to mutagenic agents, compared with other mammalian species. The stability of normal fresh and decondensed human spermatozoa were examined after exposure to a range of levels of UV and H33342 staining, using an assay that detects endogenous nicks in the DNA of spermatozoa. The stability of abnormal and normal, fresh and frozen-thawed human spermatozoa was examined following UV laser, H33342 staining and flow cytometry treatments utilizing the same assay. There was an increase in the presence of endogenous nicks when spermatozoa were decondensed compared with fresh spermatozoa. There was no increase in the incidence of nicks in any group of spermatozoa after UV and fluorochrome exposure compared with controls without exposure.