gebhart/patrepeval huggingface dataset:
Abstract 4564: Lung cancer serum biomarker discovery using label free LC-MS/MS (2010)

Abstract Lung cancer remains the leading cause of cancer-related death with a 5-year survival rate of less than 15%. Poor survival is largely due to the late stage at which lung cancer is typically diagnosed and the absence of proven imaging and molecular screening modalities for effective early detection. Given the clinical burden from lung cancer, and the relatively favorable survival associated with early stage lung cancer, biomarkers for early detection of lung cancer are of important potential clinical benefit. To identify candidate serum biomarkers for lung cancer, we performed a global proteomic discovery study using LC-MS/MS applied to a set of pooled non-small cell lung cancer (NSCLC) case sera (8 adenocarcinoma and 7 squamous cell carcinoma pools) and matched controls pools. Agilent Human 14 Multiple Affinity Removal spin cartridges were used to deplete the top 14 most abundant serum proteins; the remaining serum proteins were then subjected to trypsin digestion and analyzed in triplicate by nano-LC-ESI-MS/MS. The resulting MS/MS data were searched against the UNIPROT derived human proteome database. A total of 7268 proteins were identified more than 3 times from the combined LC-MS/MS analyses. Both the observed peptide spectral counts and extracted ion chromatograms (EICs) were then used to estimate the relative abundance of proteins across the case/control serum pools. A list of 198 differentially abundant candidate proteins was compiled by applying the Wilcoxon rank sum test to the peptide spectral count data (P&lt;0.02). A MATLABTM based in-house tool was developed to extract ion chromatograms for 5397 peptides attributed to 3221 proteins. A total of 181 peptides from 149 proteins were significantly differentially abundant across the case/control pools (P&lt;0.005 Student's t test). These candidate biomarker proteins include positive acute phase response proteins, key molecules in cell-cell signaling and interaction network, DNA replication/recombination/repair network, and a number of previously identified lung cancer-associated serum proteins such as alpha-1-glycoprotein, ceruloplasmin, leucine-rich-α-glycoproteins, and kinnogen-1. The peptide spectral count and EIC derived abundances of some of these candidate proteins have been confirmed with multiple reaction monitoring (MRM) assays which will serve as targeted quantitative assays to evaluate the classification performance of selected candidate biomarkers in planned sequential independent case/control validation studies. [Supported by Hirtzel Foundation Postdoctoral Fellowship to XZ, P50 CA90440 NCI SPORE in Lung Cancer to JMS, and NCI Early Detection Research Network Biomarker Discovery Laboratory, U01 CA084968 to WLB]. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4564.
Distribution of CD133 reveals glioma stem cells self-renew through symmetric and asymmetric cell divisions (2011)

Malignant gliomas contain a population of self-renewing tumorigenic stem-like cells; however, it remains unclear how these glioma stem cells (GSCs) self-renew or generate cellular diversity at the single-cell level. Asymmetric cell division is a proposed mechanism to maintain cancer stem cells, yet the modes of cell division that GSCs utilize remain undetermined. Here, we used single-cell analyses to evaluate the cell division behavior of GSCs. Lineage-tracing analysis revealed that the majority of GSCs were generated through expansive symmetric cell division and not through asymmetric cell division. The majority of differentiated progeny was generated through symmetric pro-commitment divisions under expansion conditions and in the absence of growth factors, occurred mainly through asymmetric cell divisions. Mitotic pair analysis detected asymmetric CD133 segregation and not any other GSC marker in a fraction of mitoses, some of which were associated with Numb asymmetry. Under growth factor withdrawal conditions, the proportion of asymmetric CD133 divisions increased, congruent with the increase in asymmetric cell divisions observed in the lineage-tracing studies. Using single-cell-based observation, we provide definitive evidence that GSCs are capable of different modes of cell division and that the generation of cellular diversity occurs mainly through symmetric cell division, not through asymmetric cell division.
Personal Health Care Assistant/Companion in Virtual World (2009)

We propose to create a virtual personal health care assistant in the virtual world Second Life that accompanies the user, via an avatar, through interactions with healthcare databases answering the user's avatar's questions. This paper explores various ways to promote healthy in a virtual world environment by integrating several existing technologies.
Evaluation of compact range using a diagonal flat plate (2002)

The authors present a method which uses a diagonal flat plate to develop a stray signal criterion based on a tolerable RCS (radar cross section) measurement error. The scattered cross section of a 1.25 ft by 1.25 ft diagonal flat plate has been measured in a compact range with a blended rolled-edge reflector and with a knife-edge reflector. The measured RCS pattern of the plate at 6 GHz is shown, with the ideal plate RCS pattern plotted for comparison. The stray signal from one of the junctions between the rolled edge and the parabolic section is about 6.2 degrees from the axis of the plate. As a result, there should be an error in the plate RCS pattern at approximately=3.1 degrees . It is found that this error is about 0.88 dB for the blended rolled-edge reflector. The knife edge of the modified reflector is located about 12 degrees from the plate axis and, as a result, there is a significant error (5.17 dB) in the plate RCS pattern at theta =6 degrees .< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mechanisms for the Oxygen Radical-Mediated Toxicity of Various Thiol-Containing Compounds in Cultured Mammalian Cells (1994)

Kathryn D. Held, John E. Biaglow, Mechanisms for the Oxygen Radical-Mediated Toxicity of Various Thiol-Containing Compounds in Cultured Mammalian Cells, Radiation Research, Vol. 139, No. 1 (Jul., 1994), pp. 15-23
Analysis of mixtures of glycerol, propylene glycol, and trimethylene glycol (1947)

Summary Procedures have been presented for the determination of glycerol, propylene glycol, and trimethylene glycol in the solutions containing all three and for analysis of sweet water concentrates. The methods are not limited to the products studied, but may be applied to mixtures of other hydroxy compounds which possess similar properties.
The pharmacokinetics of endralazine in essential hypertensives and in normotensive subjects. (1983)

The direct-acting vasodilator, endralazine, in combination with a beta-adrenoceptor blocker significantly reduced the blood pressures of normotensive volunteers and of patients with essential hypertension. The mean terminal elimination half-life for endralazine of 136 min in hypertensive patients did not differ significantly from the 155 min in normotensive subjects. In normal subjects the mean oral bioavailability for endralazine was 75% and the mean clearance was 780 ml/min. There were no significant pharmacokinetic differences between fast and slow acetylators. The administration of endralazine to steady state in the hypertensive patients was associated with an increase in terminal elimination half-life and a decrease in the rate of absorption. However, there was no accumulation of endralazine with chronic dosing.
The transcriptional regulator PLZF induces the development of CD44 high memory phenotype T cells (2008)

Transcriptional pathways controlling the development of CD44(hi) memory phenotype (MP) T cells with "innate-like" functions are not well understood. Here we show that the BTB (bric-a-brac, tramtrack, broad complex) domain-containing protein promyelocytic leukemia zinc finger (PLZF) is expressed in CD44(hi), but not in CD44(lo), CD4(+) T cells. Transgenic expression of PLZF during T cell development and in CD4(+) and CD8(+) T cells induced a T cell intrinsic program leading to an increase in peripheral CD44(hi) MP CD4(+) and CD8(+) T cells and a corresponding decrease of naïve CD44(lo) T cells. The MP CD4(+) and CD8(+) T cells produced IFNgamma upon PMA/ionomycin stimulation, thus showing innate-like function. Changes in the naïve versus memory-like subset distribution were already evident in single-positive thymocytes, indicating PLZF-induced T cell developmental alterations. In addition, CD1d-restricted natural killer T cells in PLZF transgenic mice showed impaired development and were severely reduced in the periphery. Finally, after anti-CD3/CD28 stimulation, CD4(+) transgenic T cells showed reduced IL-2 and IFNgamma production but increased IL-4 secretion as a result of enhanced IL-4 production of the CD44(hi)CD62L(+) subset. Our data indicate that PLZF is a novel regulator of the development of CD44(hi) MP T cells with a characteristic partial innate-like phenotype.
Algorithms for software development version control and change detection (1982)

Simple computer algorithms for processing source program and text data files in order to extract detection, version control, version history, and current status information are described. These algorithms presuppose that it is possible to attach to each record of the source files a 6-character code, placed within delimiters that will cause the compiler, or other using program, to ignore this code field. The code contains a 2-character code for a character-by-character position-sensitive checksum of the record, another for the record number in the file, and a third for the data on which the encoding took place. Once the source file has been thus encoded, it is possible to detect the following transactions on the file since the most recent version coding; (1) addition of new records (having no version code), (2) modification of existing records, (3) deletion of a number of records, (4) movement and/or duplication of existing records, and (5) modification and duplication of records. In addition, it is possible to extract a version history of the number of records created or modified by date. A special file listing program is described which prints the file records without showing the version codes, but places a change bar at the right margin whenever a is detected. The program also provides a list of changed pages and a version history.
Denoising Source Separation (2005)

A new algorithmic framework called denoising source separation (DSS) is introduced. The main benefit of this framework is that it allows for easy development of new source separation algorithms which are optimised for specific problems. In this framework, source separation algorithms are constucted around denoising procedures. The resulting algorithms can range from almost blind to highly specialised source separation algorithms. Both simple linear and more complex nonlinear or adaptive denoising schemes are\nconsidered. Some existing independent component analysis algorithms are reinterpreted within DSS framework and new, robust blind source separation algorithms are suggested. Although DSS algorithms need not be explicitly based on objective functions, there is often an implicit objective function that is optimised. The exact relation between the denoising procedure and the objective function is derived and a useful approximation of the objective function is presented. In the experimental section, various DSS schemes are applied extensively to artificial data, to real magnetoencephalograms and to simulated CDMA mobile network signals. Finally, various extensions to the proposed DSS algorithms are considered. These include nonlinear observation mappings, hierarchical models and overcomplete, nonorthogonal feature spaces. With these extensions, DSS appears to have relevance to many existing models of neural information processing.\n
Marginal fitness contributions of nonessential genes in yeast (1998)

Analysis of the complete genome sequence of Saccharomyces cerevisiae confirms and extends earlier evidence that a majority of yeast genes are not essential, at least under laboratory conditions. Many fail to yield a discernible mutant phenotype even when disrupted. Genes not subject to natural selection would accumulate inactivating mutations, so these "cryptic" genes must have functions that are overlooked by the standard methods of yeast genetics. Two explanations seem possible: (i) They have important functions only in environments not yet duplicated in the laboratory and would have conditional phenotypes if tested appropriately. (ii) They make small, but significant, contributions to fitness even under routine growth conditions, but the effects are not large enough to be detected by conventional methods. We have tested the second "marginal benefit" hypothesis by measuring the fitnesses of a random collection of disruption mutants in direct competition with their wild-type progenitor. A substantial majority of mutant strains that lack obvious defects nevertheless are at a significant selective disadvantage just growing on rich medium under normal conditions. This result has important implications for efforts to understand the functions of novel genes revealed by sequencing projects.
Growth and Body Composition at Diagnosis and Postcure in Children with Cushing’s Syndrome (2009)

Pediatric Cushing’s syndrome is rare, but causes considerable morbidity and suffering. This rare endocrine condition presents a challenge to the pediatrician for diagnosis and optimal therapy. There are few pediatric endocrinologists with sufficient experience to manage these cases in isolation and we recommend close consultation with an experienced adult endocrinologist. Early diagnosis of pediatric Cushing’s syndrome will limit its morbidity. Suppression of normal linear growth is a feature in most patients at diagnosis and presents a challenge after cure. Body composition is also disturbed because of abnormal weight gain, reduced muscle mass and frequently subnormal bone mineral density. Successful cure of Cushing’s syndrome can be achieved in over 90% of patients treated in experienced units. Satisfactory postcure catch-up growth in Cushing’s disease patients frequently requires growth hormone therapy. Restoration of normal body composition is more difficult to achieve. These features will be discussed and data presented related to their status at diagnosis and after cure in the pediatric patient with Cushing’s syndrome will be presented.
Modeling resistivity anomalies from localized voids under irregular terrain (1980)

Abstract In applying earth resistivity methods to the problem of locating and delineating subsurface structures, surface elevation variations along the surveyed terrain introduce distortions in the soundings. The analysis presented here is aimed at characterizing such terrain variations in the detection of relatively small subsurface targets such as caves, sinks, and tunnels in otherwise homogeneous earth materials. The analytical approach involves, first, the development of a suitable earth resistivity model for localized three-dimensional subsurface anomalies in a homogeneous flat half-space. Next, in order to apply the half-space resistivity model to irregular terrain, a Schwarz-Christoffel transformation is utilized to map the terrain surface variations into an equivalent flat half-space. The technique is illustrated by calculating the resistivity response of three tunnels located below a hill with 40-m valleys on either side.
Evidence of a specialized transport mechanism for the intestinal absorption of baclofen (1989)

Absorption of the spasmolytic drug baclofen in three selected intestinal segments of living anaesthetized rats in situ, is shown to be a specialized transport mechanism obeying Michaelis-Menten kinetics. Equation parameters were calculated through different procedures, whose features are discussed. A computer method based on the integrated form of Michaelis-Menten equation which reproduces the entire time course of drug absorption from the data found in three intestinal perfusion series at different initial concentrations, yielded Vm and Km values of 12.0 mg h-1 and 8.0 mg, respectively, in the mean segment of the small intestine, a rather selective absorption site for baclofen. Lesser but comparable absorption rates were found in the proximal and distal segments of the small intestine, whereas in colon, drug absorption was negligible. Baclofen transport was significantly reduced in the presence of the enzymatic inhibitor sodium azide. If these results were extrapolated to humans, they would explain the excellent bioavailability profiles reported for baclofen at normal doses in spite of its physicochemical properties, which do not favour passive diffusion. Based on the same principle, the administration of usual doses at shorter time intervals could be recommended, instead of high, when higher plasma levels at steady-state are needed. On the other hand, more than 8-h sustained-release preparations of baclofen should, probably, be avoided.
Intrinsic speckle noise in off-axis particle holography (2004)

In holographic imaging of particle fields, the interference among coherent wave fronts associated with particle scattering gives rise to intrinsic speckle noise, which sets a fundamental limit on the amount of information that particle holography can deliver. It has been established that the intrinsic speckle noise is especially severe in in-line holography because of superposition of virtual image waves, the direct transmitted wave, and the real image. However, at sufficiently high particle number densities, such as those typical in holographic particle image velocimetry (HPIV) applications, intrinsic speckle noise also arises in off-axis particle holography from self-interference among wave fronts that form the real image of particles. To overcome the latter problem we have constructed a mathematical model that relates the first- and second-order statistical properties of the intrinsic speckle noise to relevant holographic system parameters. Consistent with our experimental data, the model provides a direct estimate of the information capacity of particle holography. We show that the noise-limited information capacity can be expressed as the product of particle number density and the extent of the particle field along the optical axis. A large angular aperture of the hologram contributes directly to achievement of high information capacity. We also show that filtering in either digital or optical form is generally ineffective in removing the intrinsic speckle noise from the particle image as a result of the similar spectral properties of the two. These findings emphasize the importance of angular aperture in designing holographic particle imaging systems.
Use of Carbodiimides as Stabilizing Agents to Deliver Water—Labile Active Ingredients in Liquid Systems Including Aqueous Medium—Amitraz as a Case Study (2005)

Abstract Several active ingredients such as sulfonylureas and diimidines (Amitraz) are unstable in water. They undergo hydrolysis producing metabolites that are no longer biologically active. The rate of hydrolysis is a function of several factors, such as the solvent system, access to water, pH, temperature, ionic strength, and the types of emulsifiers used in the liquid matrices. Some of the active ingredients undergo rapid hydrolysis even with the residual water present in the emulsifier system in an organic emulsifiable concentrate formulation. It is therefore difficult to formulate such active ingredients in liquid delivery systems. Use of carbodiimides like Stabaxol I® (bis-2,6-diisopropylphenylcarbodiimide) as a water scavenger to stabilize oil-based formulations for Amitraz is well documented and is commercially practiced. We have found that unique combinations of carbodiimides with specific solvent-emulsifier-polymer blends in a buffered system can produce stable microemulsions of Amitraz in water. Such aqueous formulations with 200–500 ppm Amitraz in &gt;99 % water, were stable with 95 % retention on accelerated storage at 50°C for two weeks. This data translates to greater than two years stability at room temperature. Such formulations may be extended to deliver sulfonylureas. We also observed that the concentrate and the matrix containing Stabaxol I® and emulsifiers can produce gels on storage, adversely affecting physical stability. We have identified several additives and alternatives to prevent gel formation enabling long-term storage stability of the matrix and the concentrate. Examples with supporting data will be provided. A rationale and proposed mechanism for the enhanced stability and potential biological activity will be discussed.
The Future of Nuclear Power (2000)

A RECENT NEW YORK TIMES ARTICLE quoted a German official who stated that if the world does not reduce the emission of carbon monoxide and dioxide by one percent per year for the next fifty years, the potential for global warming could be disastrous. The late Bill Lee, Chairman Emeritus of Duke Power, recently made the following observation: Each night over half a billion smoky fires burn for warmth or for cooking, fueled by twigs and dung, both contributing to human and environmental deprivation.
Reversible Storage of Molecular Hydrogen by Sorption into Multilayered TiO<sub>2</sub> Nanotubes (2005)

The sorption of hydrogen between the layers of the multilayered wall of nanotubular TiO2 was studied in the temperature range of -195 to 200 degrees C and at pressures of 0 to 6 bar. Hydrogen can intercalate between layers in the walls of TiO2 nanotubes forming host-guest compounds TiO2 x xH2, where x < or = 1.5 and decreases at higher temperatures. The rate of hydrogen incorporation increases with temperature and the characteristic time for hydrogen sorption in TiO2 nanotubes is several hours at 100 degrees C. The rate of intercalate formation is limited by the diffusion of molecular hydrogen inside the multilayered walls of the TiO2 nanotube. 1H NMR-MAS and XRD data confirm the incorporation of hydrogen between the layers in the walls of TiO2 nanotubes. The nature and possible applications of the observed intercalates are considered.