gebhart/patrepeval huggingface dataset:
Musical query-by-description as a multiclass learning problem (2004)

We present the query-by-description (QBD) component of "Kandem", a time-aware music retrieval system. The QBD system we describe learns a relation between descriptive text concerning a musical artist and their actual acoustic output, making such queries as "Play me something loud with an electronic beat" possible by merely analyzing the audio content of a database. We show a novel machine learning technique based on regularized least-squares classification (RLSC) that can quickly and efficiently learn the non-linear relation between descriptive language and audio features by treating the problem as a large number of possible output classes linked to the same set or input features. We show how the RLSC training can easily eliminate irrelevant labels.
Receptor tyrosine kinases expressed in metastatic colon cancer (1995)

Using a PCR-based cloning technique, we have isolated a series of DNA fragments coding for tyrosine kinases that are expressed in a metastatic human colon tumor, and have subsequently analyzed their expression pattern at the protein level in human tumors. We identified both the alpha and the beta forms of the platelet-derived growth factor receptor (PDGFR), axl and 8 other genes, including 3 cytoplasmic tyrosine kinases. To study their expression in human colon cancer, we performed Western blots of matched sets of normal tissues and of carcinomas from the same patient. These revealed that the alpha-PDGFR migrates predominantly as a 200-kDa band in 8/8 normal tissues, and as a 170-kDa band in 17/17 malignant tissues, as well as in colonic polyps, suggesting that expression of an isoform of this receptor may be a marker for the progression of colon cancer. Additional studies showed that the Axl receptor tyrosine kinase was expressed at 10-fold higher levels in a peritoneal metastatic nodule than in other normal and malignant tissues. Immunohistochemistry revealed Axl over-expression specifically in the malignant cells of the tumor. This indicates that over-expression and possibly a differential processing event of tyrosine kinase receptors may be involved in colon cancer, and that they are potential markers for the progression of this disease.
Use of Retroviral Vectors for Mapping of Splice Sites in Cottontail Rabbit Papillomavirus (1988)

Cottontail rabbit papillomavirus (CRPV) genomic sequences coding for virus early functions were introduced into a retroviral vector in order to produce cDNAs of the viral early region. Two constructs differing in the length of control sequences preceding the E6 open reading frame were transfected into Psi-2 cells and the released retroviral stock was used to infect NIH3T3 cells. The proviral sequences were rescued from antibiotic G418-resistant virus-infected cells after fusion with Cos cells, amplified as plasmids in Escherichia coli and analysed. Nucleotide sequencing showed that the splicing signals used in the construct containing only the early coding region are the same as in CRPV-expressing tumours, linking the beginning of E1 to the middle of E2. On the other hand, in a construct including most of the long control region a splice donor site located in the 5' end of this region, at position 7810, was very efficiently used, totally excluding the use of the donor site at position 1371. None of the constructs containing CRPV sequences transcribed from Moloney murine leukaemia virus promoter was able to transform mouse fibroblasts after DNA transfection.
Prognostic Value of a Combined Estrogen Receptor, Progesterone Receptor, Ki-67, and Human Epidermal Growth Factor Receptor 2 Immunohistochemical Score and Comparison With the Genomic Health Recurrence Score in Early Breast Cancer (2011)

This study suggests that the amount of prognostic information contained in four widely performed IHC assays is similar to that in the GHI-RS. Additional studies are needed to determine the general applicability of the IHC4 score.
Calcium electroporation and electrochemotherapy for cancer treatment: Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy (2019)

Abstract Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy.
Effect of Second-Sphere Coordination. 4.1Factors Influencing the Electrochemical Behavior of Ruthenium−Ammine Complexes Caused by Second-Sphere Coordination of Crown Ethers (1996)

Second-sphere coordination was investigated spectrophotometrically and electrochemically with various ruthenium−ammine complexes with crown ethers in acetonitrile solution. Spectrophotometric results revealed that the acidity of the ammine ligands of the complex, which depends on the valence of the metal center, predominantly affects the second-sphere coordination of the crown ether to the ruthenium−ammine complexes. This fact explains the difference in the stoichiometry between the adducts of ruthenium(II) and ruthenium(III) complexes with 18-crown-6 ether. It was found that the number of ammine ligands, the π-electron acceptability of ancillary ligands of the complex, and the flexibility of the crown ether ring affected the change in the redox potential of the complexes caused by second-sphere coordination of crown ethers.
Drug resistance and gene amplification potential regulated by transforming growth factor beta 1 gene expression. (1995)

Transforming growth factor beta 1 (TGF-beta 1) regulates a multitude of diverse biological functions in mammalian cells, and there is good evidence that aberrant expression of this growth factor can play an important role in mechanisms of malignant progression. We show that a TGF-beta 1-overexpressing mouse 10T1/2 cell line transfected with a TGF-beta 1 sequence that allows the synthesis of bioactive growth factor exhibits reduced sensitivity to the cytotoxic effects of the drug N-(phosphonacetyl)-L-aspartate (PALA) in colony-forming experiments. Furthermore, six independent 10T1/2 TGF-beta 1-transfected cell lines containing TGF-beta 1 gene expression under the control of a zinc sulfate-responsive metallothionein promoter were selected. In all cases, sensitivity to PALA cytotoxic effects was significantly reduced when cells were cultured under conditions that led to elevated levels of TGF-beta 1 gene expression when compared to cells containing basal levels of this growth factor. Fluctuation analysis to determine the rate of PALA resistance was performed with several TGF-beta 1-transfected cell lines in which growth factor expression was regulated by the metallothionein promoter. We observed significantly higher rates of PALA resistance/cell/generation in cell populations expressing high levels of TGF-beta 1 than in the same cells expressing relatively low levels of this growth factor. The only mechanism known for PALA resistance in mouse cells involves the amplification of the gene coding for the protein target of PALA, CAD, a multifunctional polypeptide containing carbamyl phosphate synthetase, aspartate transcarbamylase, and dihydroorotase. Southern blot analysis of colonies that survived normally cytotoxic concentrations of PALA exhibited CAD gene amplification. In total, these observations indicate that aberrant expression of TGF-beta 1 gene expression decreases the genetic stability of 10T1/2 cells, leading to increased rates of drug resistance and elevated gene amplification potential. The results of this study indicate a new malignancy related function for TGF-beta 1 alterations and suggest a novel role for aberrant expression of this growth factor in mechanisms of drug resistance and tumor progression.
In-Plane Optical Absorption and Free Carrier Absorption in Graphene-on-Silicon Waveguides (2013)

We experimentally study the in-plane optical absorption and free carrier absorption (FCA) in graphene-on-silicon waveguides using a pump-probe measurement over microsecond timescales. The silicon waveguide is fabricated using complementary metal-oxide-semiconductor compatible processes, and directly covered by a graphene layer. Saturable absorption in the graphene is observed at the beginning of the pump pulse followed by an increase in absorption. The increase in absorption builds up over several microseconds, and is experimental evidence that free carriers generated by the pump absorption in graphene can transfer into silicon waveguides. The FCA in silicon waveguides eventually dominates the optical loss, which reaches ~9 dB, after several microseconds. All-optical modulations of the probe light are thus demonstrated. There is also a large thermally induced change in waveguide effective refractive index because of the optical absorption in the graphene.
Apolipoprotein E Receptors Mediate Neurite Outgrowth through Activation of p44/42 Mitogen-activated Protein Kinase in Primary Neurons (2004)

Several ligands of the endocytic low density lipoprotein receptor-related protein (LRP), such as apoE-containing lipoproteins and activated alpha2-macroglobulin (alpha2M*), promote neurite outgrowth, suggesting that LRP may have signaling functions. In this study, we found that the treatment of neurons with alpha2M* significantly increased the individual length (by 71%) and numbers (by 139%) of neurites of primary mouse cortical neurons. These effects were blocked by the LRP antagonist, the receptor-associated protein. We found similar neurite outgrowth with purified apoE3 and a tandem apoE peptide containing only the receptor-binding domain. To investigate the intracellular pathway of the LRP signaling involved in neurite outgrowth, we tested the effects of alpha2M* on the phosphorylation of the mitogen-activated protein (MAP) extracellular signal-regulated kinases 1 and 2 (ERK1/2). We found that 1) phospho-MAP kinase levels were altered within 30 min after treatment with alpha2M*, 2) the MAP kinase inhibitor, PD98059, specifically blocked the alpha2M*-induced neurite outgrowth, 3) manipulating intracellular calcium by BayK or BAPTA altered the neurite outgrowth and associated changes in the phospho-MAP kinase levels, which were blunted by alpha2M*, 4) alpha2M* promoted the phosphorylation of the transcription factor CREB through MAP kinase, and 5) LRP-specific antibodies increased levels of phosphorylated MAP kinase and phosphorylated CREB. The effects of alpha2M*, apoE3, and apoE peptides increased LRP levels in the cortical neurons, whereas LRP receptor-associated protein reduced dendritic LRP expression. These results demonstrate that p44/42 MAP kinase plays an important role in LRP-mediated neurite outgrowth with activation involving the effects on calcium homeostasis and downstream effects involving the activation of gene transcription through CREB.
Relaxometric and Magnetic Characterization of Ultrasmall Iron Oxide Nanoparticles with High Magnetization. Evaluation as Potential T1 Magnetic Resonance Imaging Contrast Agents for Molecular Imaging (2007)

Here we report on the synthesis of ultrasmall gamma-Fe2O3 nanoparticles (5 nm) presenting a very narrow particle size distribution and an exceptionally high saturation magnetization. The synthesis has been carried out by decomposition of an iron organometallic precursor in an organic medium. The particles were subsequently stabilized in an aqueous solution at physiological pH, and the colloidal dispersions have been thoroughly characterized by complementary techniques. Particular attention has been given to the assessment of the mean particle size by transmission electron microscopy, X-ray diffraction, dynamic light scattering, magnetic, and relaxometric measurements. The good agreement found between the different techniques points to a very narrow particle size distribution. Regarding the magnetic properties, the particles are superparamagnetic at room temperature and present an unusually high saturation magnetization value. In addition, we describe the potential of these particles as specific positive contrast agents for magnetic resonance molecular imaging.
Angiogenesis Induced by Degradation Products of Hyaluronic Acid (1985)

Partial degradation products of sodium hyaluronate produced by the action of testicular hyaluronidase induced an angiogenic response (formation of new blood vessels) on the chick chorioallantoic membrane. Neither macromolecular hyaluronate nor exhaustively digested material had any angiogenic potential. Fractionation of the digestion products established that the activity was restricted to hyaluronate fragments between 4 and 25 disaccharides in length.
Design and Evaluation of Processes for Fuel Fabrication: Year 1 Final Report (2002)

The project objective is the design and evaluation of manufacturing processes for transmuter fuel fabrication. The large-scale deployment of remote fabrication and refabrication processes will be required for all transmutation scenarios. Current program emphasis is on a five-year effort to determine the feasibility of transmutation as a technology to limit the need for repository storage of spent commercial fuel. The evaluation of the fabrication processes will create a decision support data base to document design, operations, and costs. Fabrication processes required for different fuel types differ in terms of equipment types, throughput, and cost. The year 1 project was focused on collecting information on existing technologies, equipment costs, and material throughput. Another aspect during year 1 has been the assessment of robotic technology and robot supervision and control, and the simulation of material handling operations using 3D simulation tools with view towards the development of a fully automated and reliable, autonomous manufacturing process. Preliminary estimates of differential cost implications of various fuel choices have been developed.
Discrepancy between ELISPOT IFN-γ secretion and binding of A2/peptide multimers to TCR reveals interclonal dissociation of CTL effector function from TCR-peptide/MHC complexes half-life (2001)

Activation of CD8(+) cytolytic T lymphocytes (CTLs) by antigen is triggered by the interaction of clonotypic alphabeta T cell receptors (TCRs) with antigenic peptides bound to MHC class I molecules (pMHC complexes). Fluorescent multimeric pMHC complexes have been shown to specifically stain antigen-specific CTLs by directly binding the TCR. In tumor-infiltrating lymphocytes from a melanoma patient we found a high frequency of tyrosinase(368-376) peptide-specific cells as detected by IFN-gamma ELISPOT, without detectable staining with the corresponding A2/peptide multimers. Surprisingly, these T cells were able to lyse tyrosinase(368-376) peptide-pulsed target cells as efficiently as other specific T cells that were stained by multimers. Analysis of the staining patterns under different conditions of incubation time and temperature revealed that these results were explained by major differences in TCR-multimeric ligand interaction kinetics among the clones. Whereas no direct quantitative correlation between antigenic peptide concentration required for CTL effector functions and equilibrium multimer binding was observed interclonally, the latter was profoundly affected by the kinetics of TCR-ligand interaction. More importantly, our data indicate that similar levels of T cell activation can be achieved by independent CD8(+) T cell clonotypes displaying different TCR/pMHC complex dissociation rates.
Inhibition of CDK activity and PCNA-dependent DNA replication by p21 is blocked by interaction with the HPV-16 E7 oncoprotein (1997)

p21 inhibits cyclin-dependent kinase (CDK) activity and proliferating cell nuclear antigen (PCNA)-dependent DNA replication by binding to CDK/cyclin complexes and to PCNA through distinct domains. The human papillomavirus (HPV)-16 E7 oncoprotein (16E7) abrogated a DNA damage-induced cell cycle arrest in vivo, despite high levels of p21. Using cell lysates and purified proteins we show that 16E7 prevented p21 both from inhibiting CDK2/cyclin E activity and PCNA-dependent DNA replication, whereas the nononcogenic HPV-6 E7 had reduced effects. Inactivation of both inhibitory functions of p21 was attained through binding between 16E7 and sequences in the carboxy-terminal end of p21 that overlap with the PCNA-binding site and the second p21 cyclin-binding motif. These data imply that the carboxyl terminus of p21 simultaneously modulates both CDK activity and PCNA-dependent DNA replication and that a single protein, 16E7, can override this modulation to disrupt normal cell cycle control.
Combining 3D optical imaging and dual energy absorptiometry to measure three compositional components (2014)

We report on the design of the technique combining 3D optical imaging and dual-energy absorptiometry body scanning to estimate local body area compositions of three compartments. Dual-energy attenuation and body shape measures are used together to solve for the three compositional tissue thicknesses: water, lipid, and protein. We designed phantoms with tissue-like properties as our reference standards for calibration purposes. The calibration was created by fitting phantom values using non-linear regression of quadratic and truncated polynomials. Dual-energy measurements were performed on tissue-mimicking phantoms using a bone densitometer unit. The phantoms were made of materials shown to have similar x-ray attenuation properties of the biological compositional compartments. The components for the solid phantom were tested and their high energy/low energy attenuation ratios are in good correspondent to water, lipid, and protein for the densitometer x-ray region. The three-dimensional body shape was reconstructed from the depth maps generated by Microsoft Kinect for Windows. We used open-source Point Cloud Library and freeware software to produce dense point clouds. Accuracy and precision of compositional and thickness measures were calculated. The error contributions due to two modalities were estimated. The preliminary phantom composition and shape measurements are found to demonstrate the feasibility of the method proposed.
Analysis of vitamin D metabolic markers by mass spectrometry: Current techniques, limitations of the “gold standard” method, and anticipated future directions (2013)

Vitamin D compounds belong to a group of secosteroids, which occur naturally as vitamin D3 in mammals and D2 in plants. Vitamin D is vital for bone health but recent studies have shown a much wider role in the pathologies of diseases such as diabetes, cancer, autoimmune, neurodegenerative, mental and cardiovascular diseases. Photosynthesis of vitamin D in the human skin and subsequent hepatic and renal metabolism generate a wide range of transformation products occurring over a large dynamic range spanning from picomolar to nanomolar levels. This necessitates selective and sensitive analytical methods to quantitatively capture these low concentration levels in relevant tissues such as blood. Ideally, vitamin D assessment would be performed using a universal and standardized analytical method available to clinical laboratories that provides reliable and accurate quantitative results for all relevant vitamin D metabolites with sufficiently high throughput. At present, LC-MS/MS assays are the most promising techniques for vitamin D analysis. The present review focuses on developments in mass spectrometry methodologies of the past 12 years. It will highlight detrimental influences of the biological matrix, epimer contributions, pitfalls of specific mass spectrometry data acquisition routines (in particular multiple reaction monitoring, MRM), influence of ionization source, derivatization reactions, inter-laboratory comparisons on precision, accuracy, and application range of vitamin D metabolites.
Turbulent transport in magnetic confinement: how to avoid it (1996)

From recent tokamak research, there is considerable experimental evidence that superthermal ions slow down and diffuse classically in the presence of turbulent fluctuations that cause anomalous transport of thermal ions. Further more, research on field-reversed configurations at Los Alamos is consistent with the view that kinetic effects suppress instability growth when the ratio of plasma radius to ion orbital radius is small; turbulence is enhanced and confinement degrades when this ratio increases. Motivated by these experiments, we consider a plasma consisting of large-orbit non-adiabatic ions and adiabatic electrons. For such a plasma, it is possible that the anomalous transport characteristic of tokamaks can be avoided and a compact reactor design becomes viable.
Randomised clinical trial: mesalazine and/or probiotics in maintaining remission of symptomatic uncomplicated diverticular disease - a double-blind, randomised, placebo-controlled study (2013)

Both cyclic mesalazine and Lactobacillus casei subsp. DG treatments, particularly when given in combination, appear to be better than placebo for maintaining remission of symptomatic uncomplicated diverticular disease. (ClinicalTrials.gov: NCT01534754).
S‐phase fraction of human brain tumors in situ measured by uptake of bromodeoxyuridine (1986)

One hundred fifty-four patients with brain tumors of various types were given an intravenous infusion of the thymidine analogue bromodeoxyuridine (BUdR), 200 mg/m2, at the time of surgery but before biopsy of the tumor to label S-phase cells. Excised tumor specimens were fixed, sectioned, and stained by immunoperoxidase methods to detect BUdR. The labelling index (LI), or percentage of BUdR-labelled cells, was calculated for each tumor specimen. The LIs of glioblastomas, medulloblastomas, and most highly anaplastic astrocytomas were 5% to 20%. The majority of moderately anaplastic astrocytomas showed LIs of less than 1%, but 30% of them had LIs similar to those of highly malignant gliomas. Most pituitary adenomas and neurinomas showed LIs of less than 1%. Nonmalignant meningiomas had LIs of less than 1%, whereas malignant meningiomas had LIs higher than 2.7%. This is an important observation, because malignant meningiomas are not well-defined histopathologically and their growth rate and rate of recurrence cannot be predicted by current diagnostic procedures. By estimating the proliferative potential of individual tumors more precisely, the BUdR LI supplements histopathological diagnosis, allowing a more accurate estimate of prognosis and facilitating the design of treatment regimens for individual patients.