gebhart/patrepeval huggingface dataset:
Histone demethylase KDM2B inhibits the chondrogenic differentiation potentials of stem cells from apical papilla. (2015)

Mesenchymal stem cells (MSCs) are a reliable resource for tissue regeneration, but the molecular mechanism underlying directed differentiation remains unclear; this has restricted potential MSC applications. Histone methylation, controlled by histone methyltransferases and demethylases, may play a key role in MSCs differentiation. Previous studies determined that KDM2B can regulate the cell proliferation and osteo/dentinogenic differentiation of MSCs. It is not known whether KDM2B is involved in the other cell lineages differentiation of MSCs. Here we used the stem cells from apical papilla (SCAPs) to study the role of KDM2B on the chondrogenic differentiation potentials in MSCs. In this study, Gain- and loss-of-function assays were applied to investigate the role of KDM2B on the chondrogenic differentiation. Alcian Blue Staining and Quantitative Analysis were used to investigate the synthesis of proteoglycans by chondrocytes. Real-time RT-PCR was used to detect the expressions of chondrogenesis related genes. The Alcian Blue staining and Quantitative Analysis results revealed that overexpression of KDM2B decreased the proteoglycans production, and real-time RT-PCR results showed that the expressions of the chondrogenic differentiation markers, COL1, COL2 and SOX9 were inhibited by overexpression of KDM2B in SCAPs. On the contrary, depletion of KDM2B increased the proteoglycans production, and inhibited the expressions of COL1, COL2 and SOX9. In conclusion, our results indicated that KDM2B is a negative regulator of chondrogenic differentiation in SCAPs and suggest that inhibition of KDM2B might improve MSC mediated cartilage regeneration.
Rock-salt-type lithium metal sulphides as novel positive-electrode materials (2014)

One way of increasing the energy density of lithium-ion batteries is to use electrode materials that exhibit high capacities owing to multielectron processes. Here, we report two novel materials, Li2TiS3 and Li3NbS4, which were mechanochemically synthesised at room temperature. When used as positive-electrode materials, Li2TiS3 and Li3NbS4 charged and discharged with high capacities of 425 mA h g(-1) and 386 mA h g(-1), respectively. These capacities correspond to those resulting from 2.5- and 3.5-electron processes. The average discharge voltage was approximately 2.2 V. It should be possible to prepare a number of high-capacity materials on the basis of the concept used to prepare Li2TiS3 and Li3NbS4.
Motor neuropathy due to docetaxel and paclitaxel (1996)

Paclitaxel and docetaxel are novel chemotherapeutic agents that promote the polymerization and inhibit the depolymerization of microtubules. Sensory neuropathy is common with these agents, particularly paclitaxel. We evaluated 64 patients treated with these drugs; 54 were followed prospectively. Eleven (17%, including six of the 54 prospectively followed patients) developed muscle weakness that was predominantly proximal. The weakness was idiosyncratic, occurring at any stage of treatment, had a variable course, and was reversible upon cessation of drug. All patients developed symptoms or signs of taxane-induced sensory neuropathy. Weakness was likely neuropathic in origin; electrodiagnostic studies suggested a distal axonopathy in some patients and proximal denervation (anterior horn cell or nerve root) in other.
Enhancing Bioremediation with Enzymatic Processes: A Review (2006)

The use of extracellular enzymes has been standard in many industries for many years; only recently have they been studied as a means for enhancing bioremediation. Extracellular enzymes are either secreted from organisms such as white rot fungi or are produced during a fermentation process and possess the ability to break down bonds within organic compounds and/or catalyze their transformation into less toxic and more biodegradable forms. Unlike many microbes, enzymes remain effective in a wide range of pH and temperature ranges, particularly if they are immobilized on some carrier, and they can degrade a wide variety of compounds. Enzymes from white rot fungi have been shown to be effective degraders of TNT, phenols, PCBs, PAHs, and dyes; enzymes such as protease, lipase, and cellulase have demonstrated the ability to reduce pathogen counts, reduce the solids content, and increase deflocculation in sludge. Currently, high production costs inhibit the widespread use of extracellular enzymes for remediation, but bench studies and field studies have shown enzymatic treatment to be feasible options for bioremediation. This paper will explore the current state of use of extracellular enzymes in enhancing the bioremediation of recalcitrant substances and wastewater, as well as the benefits and disadvantages associated with the use of such enzymes.
Clone Detection Using Abstract Syntax Suffix Trees (2006)

Reusing software through copying and pasting is a continuous plague in software development despite the fact that it creates serious maintenance problems. Various techniques have been proposed to find duplicated redundant code (also known as software clones). A recent study has compared these techniques and shown that token-based clone detection based on suffix trees is extremely fast but yields clone candidates that are often no syntactic units. Current techniques based on abstract syntax trees-on the other hand-find syntactic clones but are considerably less efficient. This paper describes how we can make use of suffix trees to find clones in abstract syntax trees. This new approach is able to find syntactic clones in linear time and space. The paper reports the results of several large case studies in which we empirically compare the new technique to other techniques using the Bellon benchmark for clone detectors
Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs (2010)

These results confirm the high prevalence of constitutively decreased TGFBR1 allelic expression among patients with colorectal cancer. The association of this phenotype with TGFBR1*6A, rs7034462 and rs1156875 suggests an association between TGFBR1 SNPs and colorectal cancer, which warrants additional studies.
A 1.7mm-Square 3.2kV Low Leakage Current Si MOSFET (2006)

We proposed a new termination structure to minimize the chip size of high breakdown voltage vertical DMOSFETs and to manufacture them using a MEMS process. As a result, we were able to realize a fully functional 1.7 mm square silicon DMOSFET with a breakdown voltage of 3200 V, a leakage current of 1.2 nA at 200 V and an on-state resistance of 165Omega
THz generation and detection using 1550-nm pulses from a fiber laser (2000)

Summary form only given.We have demonstrated THz emission and detection using a 1550-nm fiber laser. The phase-matching condition of DAST and GaAs were studied, as well as the electro-optical properties of a GaAs sensor for free space THz wave detection.
CD40 ligand and IFN-γ synergistically restore IL-12 production in HIV-infected patients (1998)

IL-12 production in HIV-infected (HIV+) individuals is severely impaired after stimulation by bacterial products or T cell-dependent stimuli. Because CD40-CD40 ligand (CD40L) interactions are the major mechanism involved in the T cell-dependent activation of antigen-presenting cells, we investigated whether this pathway was functional in HIV+ donors. CD40 expression was increased on freshly isolated monocytes from HIV+ individuals compared to HIV donors. However, equivalent CD40 expression was obtained in the two groups after cytokine stimulation. Since CD40 expression was intact in HIV+ donors' cells, we determined whether IL-12 production could be restored by providing exogenous T cell-dependent stimuli, CD40L and IFN-gamma, at the time of bacterial stimulation. IL-12 production was not altered by CD40L alone, was increased by IFN-gamma, and was synergistically restored to normal values by IFN-gamma + CD40L. This combination was more efficient for enhancing IL-12 production than granulocyte-macrophage colony-stimulating factor + CD40L or neutralizing anti-IL-10 antibody + CD40L. CD40L did not affect IL-10 production, whereas IFN-gamma significantly decreased it. This study demonstrates that the defect in IL-12 production by leukocytes from HIV+ donors can be overcome in vitro if the interacting cells are provided with the right T cell-dependent co-stimuli.
Rapid Estimation of Amylase Activity of Serum by Turbidimetry (1955)

Abstract The method of Waldron for turbidimetric measurement of amylase activity of duodenal contents has been adapted to measurement of amylase activity of serum. The speed and simplicity of the method make it suitable particularly when results are needed quickly. Comparison of the results obtained by the turbidimetric method with those of a saccharogenic method showed that high amylase activities could be established dependably by the turbidimetric method.
Purification of an active plasminogen activator inhibitor immunologically related to the endothelial type plasminogen activator inhibitor from the conditioned media of a human melanoma cell line. (1986)

24 established melanoma cell cultures were screened for their secretion of plasminogen activators and plasminogen activator inhibitors into the culture medium by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by conventional and reverse fibrin autography. Among the cell lines investigated, 22 cell lines predominantly secreting tissue type plasminogen activator (t-PA) and four cell lines additionally secreting urokinase were found. The conditioned media of two cell lines (KRFM and MJZJ) were found to contain plasminogen activator inhibitor (PAI) activity at a Mr position of approximately 50,000. The PAI of one of the two melanoma cell (MJZJ)-conditioned media found to contain PAI activity was purified to apparent homogeneity employing concanavalin A-Sepharose chromatography, gel filtration on Sephadex G-150, chromatography on Affi-Gel blue, and affinity chromatography on a Sepharose 4B immobilized monoclonal anti-t-PA IgG column. The purified melanoma PAI was found to be a single chain protein, acid stable, immunologically related to the endothelial derived PAI. In contrast to endothelial PAI, melanoma PAI presented itself in the conditioned media of the melanoma cells and in the purified preparation to an appreciable extent in its active form.
Conditional Anomaly Detection (2007)

When anomaly detection software is used as a data analysis tool, finding the hardest-to-detect anomalies is not the most critical task. Rather, it is often more important to make sure that those anomalies that are reported to the user are in fact interesting. If too many unremarkable data points are returned to the user labeled as candidate anomalies, the software can soon fall into disuse. One way to ensure that returned anomalies are useful is to make use of domain knowledge provided by the user. Often, the data in question includes a set of environmental attributes whose values a user would never consider to be directly indicative of an anomaly. However, such attributes cannot be ignored because they have a direct effect on the expected distribution of the result attributes whose values can indicate an anomalous observation. This paper describes a general purpose method called conditional anomaly detection for taking such differences among attributes into account, and proposes three different expectation-maximization algorithms for learning the model that is used in conditional anomaly detection. Experiments with more than 13 different data sets compare our algorithms with several other more standard methods for outlier or anomaly detection
Economic impact of COPD: Empirical and model-based studies on the cost-effectiveness of treatment options (2011)

Chronic obstructive pulmonary disease (COPD) is a disease characterized by progressive\\nairflow limitation that is not fully reversible and is accompanied by extra-pulmonary\\neffects that can lead to important co-morbidities. The treatment of COPD is associated\\nwith substantial healthcare costs, which are expected to increase in the future. Therefore\\nthe need for information on efficient treatment options in terms of both effects and\\ncosts is high. This thesis aims to investigate the costs and cost-effectiveness of treatment\\noptions for COPD to contribute to evidence-based policy making. This introduction\\nprovides background information on COPD and describes the disease characteristics,\\nepidemiology, the social and economic burden and the available treatment options and\\ntheir potential cost-effectiveness.
The effect of group level variables on fertility in a rural Indian sample (1977)

This paper studies reproductive behaviour (ideal family size, completed family size and family planning acceptance) in a rural Indian area which was rapidly industrialising. Two castes and eleven villages were sampled. It was found that family planning was quite common and that fertility differentials among couples were related to the couples’ unique socioeconomic characteristics as well as to two group level variables (caste and village). The latter result was shown to be statistically significant, for all three measures of reproductive behaviour, even after many unique socioeconomic characteristics and attitudes of each couple were accounted for statistically.
Incremental learning with support vector machines (2002)

Support vector machines (SVMs) have become a popular tool for machine learning with large amounts of high dimensional data. In this paper an approach for incremental learning with support vector machines is presented, that improves the existing approach of Syed et al. (1999). An insight into the interpretability of support vectors is also given.
Development of a Pyrotechnic Shock Simulation Apparatus for Spacecraft Applications (2012)

This report details the research, design, construction, and testing of a pyrotechnic shock simulation apparatus for spacecraft applications. The apparatus was developed to be used in the Space Environments Lab at California Polytechnic State University. It will be used for testing spacecraft components with dimensions up to 24”x12”x12” as well as CubeSats. Additionally, it may be used as an instructional or demonstrational tool in the Aerospace Department’s space environments course. The apparatus functions by way of mechanical impact of an approximately 20 lb stainless steel swinging hammer. Tests were performed to verify the simulator’s functionality. Suggestions for improvement and further progress are also given.
Off-axis reflection zone plate for quantitative soft x-ray source characterization (1997)

A compact system for high-resolution spectroscopy and quantitative photon flux and brilliance measurements of pulsed soft x-ray sources is described. The calibrated system combines a novel elliptical off-axis reflection zone plate with charge-coupled device detection for simultaneous spectral and spatial measurements. Experiments on a water-window droplet-target laser-plasma source demonstrate λ/Δλ⩾1000 spectral resolution and absolute flux and brilliance measurements. © 1997 American Institute of Physics.
Hyper-spectral image processing applications on the SIMD Pixel Processor for the digital battlefield (2003)

Future military scenarios will rely on advanced imaging sensor technology beyond the visible spectrum to gain total battlefield awareness. Real-time processing of these data streams requires tremendous computational workloads and I/O throughputs. This paper presents three applications for hyper-spectral data streams, vector quantization, region autofocus, and K-means clustering, on the SIMD Pixel Processor (SIMPil). In SIMPil, an image sensor array (focal plane) is integrated on top of a SIMD computing layer to provide direct coupling between sensors and processors, alleviating I/O bandwidth bottlenecks while maintaining low power consumption and portability. Simulation results with sustained operation throughputs of 500-1500 Gops/sec support real-time performance and promote focal plane processing on SIMPil.
« The uneasy burden of race » (2011)

“One of the most insidious crimes occurring in this democracy is that of designating another, politically weaker, less socially acceptable, people as the receptacle for one’s self-disgust, for one’s infantile rebellions, for one’s own fears of, and retreats from, reality.” Ralph Ellison, Shadow and Act (1964) Près de 25 années après sa première publication, la lettre ouverte sur les musiques noires adressée un jour de mai 1987 par le musicologue anglais Philip Tagg à ses collègues universitai...
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences (2000)

PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features such as exons of genes and repetitive elements, and colors can be used to clarify and enhance the display. The web site also provides a plot of the locations of those segments in both species (similar to a dot plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions and cis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are often detectable as similar, noncoding sequences in species that diverged as much as 100-300 million years ago, such as humans and mice, Caenorhabditis elegans and C. briggsae, or Escherichia coli and Salmonella spp. PipMaker supports analysis of unfinished or "working draft" sequences by permitting one of the two sequences to be in unoriented and unordered contigs.
Reduction and Sulfonylation of Olefins by Solutions of Diisopropylethylamine and Sulfur Dioxide (1993)

Abstract Solutions of diisopropylethylamine and SO2 deliver sulfones from acrylates and reduce olefins substituted by two carbonyl moieties in α and β positions.
An Initial Experimental Study Of Rotating Micromechanical Liquid O-ring Pressure Seals (2005)

Shrinking macroscopic concepts of machinery to microscopic scales presents several interesting challenges. One of these is the achievement of shaft pressure seals on rotating micromachines. This study investigates the feasibility of using surface tension to create a liquid o-ring. A simplified experimental setup using readily available materials to control contact angles is utilized. Based on results of stationary and relative motion experiments performed in this study, the use of surface tension to create a liquid o-ring appears feasible.
Quantum Shannon Theory (2016)

This is the 10th and final chapter of my book on Quantum Information, based on the course I have been teaching at Caltech since 1997. An earlier version of this chapter (originally Chapter 5) has been available on the course website since 1998, but this version is substantially revised and expanded. Topics covered include classical Shannon theory, quantum compression, quantifying entanglement, accessible information, and using the decoupling principle to derive achievable rates for quantum protocols. This is a draft, pre-publication copy of Chapter 10, which I will continue to update. See the URL on the title page for further updates and drafts of other chapters, and please send me an email if you notice errors.
The Mouse Fetoprotein Transcription Factor (FTF) Gene Promoter Is Regulated by Three GATA Elements with Tandem E Box and Nkx Motifs, and FTF in Turn Activates the Hnf3β, Hnf4α, and Hnf1α Gene Promoters (2001)

Fetoprotein transcription factor (FTF) is an orphan nuclear receptor that activates the alpha(1)-fetoprotein gene during early liver developmental growth. Here we sought to define better the position of FTF in transcriptional cascades leading to hepatic differentiation. The mouse FTF gene was isolated and assigned to chromosome 1 band E4 (one mFTF pseudogene was also found). Exon/intron mapping shows an mFTF gene structure similar to that of its close homologue SF1, with two more N-terminal exons in the mFTF gene; exon mapping also delimits several FTF mRNA 5'- and 3'-splice variants. The mFTF transcription initiation site was located in adult liver at 238 nucleotides from the first translation initiator codon, with six canonical GATA, E box, and Nkx motifs clustered between -50/-140 base pairs (bp) from the cap site; DNA/protein binding assays also pinpointed an HNF4-binding element at +36 bp and an FTF-binding element at -257 bp. Transfection assays and point mutations showed that the mFTF promoter is activated by GATA, HNF4alpha, FTF, Nkx, and basic helix-loop-helix factors, with marked cooperativity between GATA and HNF4alpha. A tandem GATA/E box activatory motif in the proximal mFTF promoter is strikingly similar to a composite motif coactivated by differentiation inducers in the hematopoietic lineage; a tandem GATA-Nkx motif in the distal mFTF promoter is also similar to a composite motif transducing differentiation signals from transforming growth factor-beta-like receptors in the cardiogenic lineage. Three genes encoding transcription factors critical to early hepatic differentiation, Hnf3beta, Hnf4alpha, and Hnf1alpha, each contain dual FTF-binding elements in their proximal promoters, and all three promoters are activated by FTF in transfection assays. Direct DNA binding action and cooperativity was demonstrated between FTF and HNF3beta on the Hnf3beta promoter and between FTF and HNF4alpha on the Hnf1alpha promoter. These combined results suggest that FTF is an early intermediary between endodermal specification signals and downstream genes that establish and amplify the hepatic phenotype.
<i>O</i>-Alkoxyamidine Prodrugs of Furamidine:  In Vitro Transport and Microsomal Metabolism as Indicators of in Vivo Efficacy in a Mouse Model of <i>Trypanosoma brucei rhodesiense</i> Infection (2004)

Five O-alkoxyamidine analogues of the prodrug 2,5-bis[4-methoxyamidinophenyl]furan were synthesized and evaluated against Trypanosoma brucei rhodesiense in the STIB900 mouse model by oral administration. The observed in vivo activity of these prodrugs demonstrates that compounds with an O-methoxyamidine or O-ethoxyamidine group effectively cured all trypanosome-infected mice, whereas prodrugs with larger side-chains did not completely cure the mice. Permeability across Caco-2 cell monolayers and microsomal metabolism were used to identify the underlying mechanisms of prodrug efficacy.