gebhart/patrepeval huggingface dataset:
Rate of Absorption for CO2 Absorption Systems Using a Wetted Wall Column (2017)

Knowledge on the absorption rate of CO2 in absorption systems is essential for accurate equipment design. This work is focused on determining the rate of absorption for novel absorption systems using a wetted wall column. This is a widely used method for determining the absorption flux of carbon dioxide in amine solutions. Two absorption systems were investigated, namely aqueous solutions of monoethanolamine (MEA), which is considered a benchmark amine solution, and solutions of 2-amino-2-methyl-1-propanol (AMP) in the organic solvent N-methyl-2-pyrrolidone (NMP). Aqueous solutions of MEA have been widely researched for CO2 capture whereas solutions of AMP in NMP are novel absorption systems that have been reported as promising alternatives for CO2 capture, based on its ability to be regenerated at lower temperatures. Experiments were performed with a wetted wall column in order to investigate the CO2 absorption rate of the previously mentioned amine solutions. Different amine concentrations for the aqueous MEA were investigated, 1.5 and 7 m, as well as for solutions of AMP in NMP, 1.5 and 5 m. From the experiments the overall flux of CO2 could be evaluated and used to calculate the mass transfer coefficients. The results showed a higher flux and higher liquid side mass transfer of CO2 for AMP in NMP compared to aqueous MEA.
Contribution of DNA and tissue microarray technology to the identification and validation of biomarkers and personalised medicine in breast cancer. (2007)

Completion of the human genome project has revolutionised translational medicine. High-throughput technology now permits investigators to systematically interrogate the genome, transcriptome, proteome and metabolome. It is expected that these advances will eventually be translated into new more sensitive diagnostic tests and less toxic therapeutics. A major shift is expected in clinical oncology over the next few decades as we start to move away from currently practiced, population-based approaches to personalised medicine. In this emerging approach, the molecular and pathophysiological characteristics of an individual patient and tumour will be measured and tailored therapeutic regimens will be administered based on these profiles. One of the key steps in this process will be the identification and validation of biomarkers. Whilst great advances have been made in the discovery of putative biomarkers, disappointingly few have been translated into clinically applicable assays. It is widely believed that this is due to a lack of well-designed, thorough validation studies. Here, we review the role of DNA microarrays and tissue microarrays in the validation of biomarkers in breast cancer, with emphasis on their potential application to determine mode of personalised therapy in the future.
Adenosine A3 Receptor Suppresses Prostate Cancer Metastasis by Inhibiting NADPH Oxidase Activity (2009)

Prostate cancer is the most commonly diagnosed and second most lethal malignancy in men, due mainly to a lack of effective treatment for the metastatic disease. A number of recent studies have shown that activation of the purine nucleoside receptor, adenosine A(3) receptor (A(3)AR), attenuates proliferation of melanoma, colon, and prostate cancer cells. In the present study, we determined whether activation of the A(3)AR reduces the ability of prostate cancer cells to migrate in vitro and metastasize in vivo. Using severe combined immunodeficient mice, we show that proliferation and metastasis of AT6.1 rat prostate cancer cells were decreased by the administration of A(3)AR agonist N(6)-(3-iodobenzyl) adenosine-5'-N-methyluronamide. In vitro studies show that activation of A(3)AR decreased high basal nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity present in these cells, along with the expression of Rac1 and p47(phox) subunits of this enzyme. Inhibition of NADPH oxidase activity by the dominant-negative RacN17 or short interfering (si)RNA against p47(phox) reduced both the generation of reactive oxygen species and the invasion of these cells on Matrigel. In addition, we show that membrane association of p47(phox) and activation of NADPH oxidase is dependent on the activity of the extracellular signal-regulated kinase (ERK)1/2 mitogen-activated protein kinase pathway. We also provide evidence that A(3)AR inhibits ERK1/2 activity in prostate cancer cells through inhibition of adenylyl cyclase and protein kinase A. We conclude that activation of the A(3)AR in prostate cancer cells reduces protein kinase A-mediated stimulation of ERK1/2, leading to reduced NADPH oxidase activity and cancer cell invasiveness.
Phase II Trial of Single-Agent Bevacizumab Followed by Bevacizumab Plus Irinotecan at Tumor Progression in Recurrent Glioblastoma (2008)

We conclude that single-agent bevacizumab has significant biologic and antiglioma activity in patients with recurrent glioblastoma.
Graphene Sensors (2011)

This paper reviews the potential of graphene as a material for fabricating various types of sensors. Graphene is a monolayer of carbon atoms which exhibits some remarkable electronic and mechanical properties and many of these properties lend themselves to sensor applications. The review attempts to be comprehensive in sensor types covering chemical and electrochemical sensors, magnetic and electric field sensors, optical sensors together with mass and strain sensors. The fact that graphene offers some advantages over this entire range of sensing modalities is an indication of its versatility and importance.
Engineering and production of streptokinase in a Bacillus subtilis expression-secretion system (1994)

Streptokinase is one of the major blood-clot-dissolving agents used in many medical treatments. With the cloned streptokinase gene (skc) available, production of the secreted streptokinase from various Bacillus subtilis strains was studied. The use of the six-extracellular-protease-deficient strain, WB600, greatly improved the production yield of the secreted streptokinase. A modified skc which has the original skc promoter and signal sequence replaced with the B. subtilis levansucrase promoter and signal sequence was also constructed. B. subtilis carrying either the wild-type or the modified skc produces streptokinase at a comparable level. Even with WB600 as the expression host, a C-terminally-processed streptokinase was also observed. Through region-specific combinatorial mutagenesis around the C-terminal processing sites, streptokinase derivatives resistant to C-terminal degradation were engineered. One of the derivatives showed a 2.5-fold increase in specific activity and would potentially be a better thrombolytic agent.
Effective conductivity, dielectric constant, and diffusion coefficient of digitized composite media via first-passage-time equations (1999)

We generalize the Brownian motion simulation method of Kim and Torquato [J. Appl. Phys. 68, 3892 (1990)] to compute the effective conductivity, dielectric constant and diffusion coefficient of digitized composite media. This is accomplished by first generalizing the first-passage-time equations to treat first-passage regions of arbitrary shape. We then develop the appropriate first-passage-time equations for digitized media: first-passage squares in two dimensions and first-passage cubes in three dimensions. A severe test case to prove the accuracy of the method is the two-phase periodic checkerboard in which conduction, for sufficiently large phase contrasts, is dominated by corners that join two conducting-phase pixels. Conventional numerical techniques (such as finite differences or elements) do not accurately capture the local fields here for reasonable grid resolution and hence lead to inaccurate estimates of the effective conductivity. By contrast, we show that our algorithm yields accurate estimates of the effective conductivity of the periodic checkerboard for widely different phase conductivities. Finally, we illustrate our method by computing the effective conductivity of the random checkerboard for a wide range of volume fractions and several phase contrast ratios. These results always lie within rigorous four-point bounds on the effective conductivity.
Oncogenic Point Mutations in the Human Retinoblastoma Gene: Their Application to Genetic Counseling (1989)

Mutations of the retinoblastoma gene, most of which cannot be detected by conventional Southern blotting, are known to cause both the nonhereditary and hereditary forms of retinoblastoma and have been implicated in the development of other cancers. Nonhereditary retinoblastoma is caused by a somatic mutation. Hereditary retinoblastoma is caused by a germ-cell mutation, most often a new one, and thus there is usually no family history of the disease. Unlike patients with the nonhereditary disease, those with the hereditary form are at risk for additional retinoblastomas, and their progeny are at risk for the tumors. We used a sensitive technique of primer-directed enzymatic amplification, followed by DNA sequence analysis, to identify mutations as small as a single nucleotide change in tumors from seven patients with simplex retinoblastoma (with no family history of the disease). In four patients the mutation involved only the tumor cells, and in three it involved normal somatic cells as well as tumor cells but was not found in either parent; thus, these mutations appeared to be new, germ-cell mutations. In addition, we found point mutations in cells from a bladder carcinoma, a small-cell carcinoma of the lung, and another retinoblastoma. We conclude that the technique that we have described can distinguish hereditary from nonhereditary retinoblastoma and that it is useful in risk estimation and genetic counseling.
Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases (2012)

The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.
Local Entrainment of Alpha Oscillations by Visual Stimuli Causes Cyclic Modulation of Perception (2014)

Prestimulus oscillatory neural activity in the visual cortex has large consequences for perception and can be influenced by top-down control from higher-order brain regions. Making a causal claim about the mechanistic role of oscillatory activity requires that oscillations be directly manipulated independently of cognitive instructions. There are indications that a direct manipulation, or entrainment, of visual alpha activity is possible through visual stimulation. However, three important questions remain: (1) Can the entrained alpha activity be endogenously maintained in the absence of continuous stimulation?; (2) Does entrainment of alpha activity reflect a global or a local process?; and (3) Does the entrained alpha activity influence perception? To address these questions, we presented human subjects with rhythmic stimuli in one visual hemifield, and arhythmic stimuli in the other. After rhythmic entrainment, we found a periodic pattern in detection performance of near-threshold targets specific to the entrained hemifield. Using magnetoencephalograhy to measure ongoing brain activity, we observed strong alpha activity contralateral to the rhythmic stimulation outlasting the stimulation by several cycles. This entrained alpha activity was produced locally in early visual cortex, as revealed by source analysis. Importantly, stronger alpha entrainment predicted a stronger phasic modulation of detection performance in the entrained hemifield. These findings argue for a cortically focal entrainment of ongoing alpha oscillations by visual stimulation, with concomitant consequences for perception. Our results support the notion that oscillatory brain activity in the alpha band provides a causal mechanism for the temporal organization of visual perception.
ISOLATION AND CHARACTERIZATION OF STEM/ PROGENITOR CELLS FROM HUMAN AMNION – POSSIBLE APPLICATION OF NEURAL REPAIR IN THE FUTURE (2006)

Objectives: Fetal membranes, which contained amnion and chorion, serve multiple and disparate roles in human pregnancy. Amnion is the major strength component of fetal membranes, allowing the containment of the amniotic fluid and the avoidance of premature rupture of membrane. In recent years, one kind of somatic stem cells was fully discussed, and that was mesenchymal stem cell. At the beginning, mesenchymal stem cell was focused on their ability to differentiate into bone, cartilage, adipose tissues, etc, and maybe those tissues could easily apply to clinical transplantation in the future. But in 1998, bone marrow isolated mesenchymal stem cells were found to undergo neuronal differentiation when they were co-cultured with brain tissue. As a result, mesenchymal stem cells may have the potential to differentiate into different tissues. Methods: In this study, we collected samples from chorion of a placenta obtained from an elective cesarean section. First, we had found adequate procedure to get two kinds of amniotic cells separately and we compared their characteristics and morphology. Second, we performed serial dilution to find if any stem cell or progenitor cell clone from single cell which had the capacity to self-renew and differentiate into multiple lineages. Third, after we have already isolated this clone, we analyzed its characterizations and also compared with those of other somatic stem cells.
The analytical bootstrap (2014)

Sampling is one of the most commonly used techniques in Approximate Query Processing (AQP)-an area of research that is now made more critical by the need for timely and cost-effective analytics over "Big Data". Assessing the quality (i.e., estimating the error) of approximate answers is essential for meaningful AQP, and the two main approaches used in the past to address this problem are based on either (i) analytic error quantification or (ii) the bootstrap method. The first approach is extremely efficient but lacks generality, whereas the second is quite general but suffers from its high computational overhead. In this paper, we introduce a probabilistic relational model for the bootstrap process, along with rigorous semantics and a unified error model, which bridges the gap between these two traditional approaches. Based on our probabilistic framework, we develop efficient algorithms to predict the distribution of the approximation results. These enable the computation of any bootstrap-based quality measure for a large class of SQL queries via a single-round evaluation of a slightly modified query. Extensive experiments on both synthetic and real-world datasets show that our method has superior prediction accuracy for bootstrap-based quality measures, and is several orders of magnitude faster than bootstrap.
S4L: Self-Supervised Semi-Supervised Learning (2019)

This work tackles the problem of semi-supervised learning of image classifiers. Our main insight is that the field of semi-supervised learning can benefit from the quickly advancing field of self-supervised visual representation learning. Unifying these two approaches, we propose the framework of self-supervised semi-supervised learning (S4L) and use it to derive two novel semi-supervised image classification methods. We demonstrate the effectiveness of these methods in comparison to both carefully tuned baselines, and existing semi-supervised learning methods. We then show that S4L and existing semi-supervised methods can be jointly trained, yielding a new state-of-the-art result on semi-supervised ILSVRC-2012 with 10% of labels.
Genome Editing in Plants: An Overview of Tools and Applications (2017)

The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants.
Discovery and Optimization of Anthranilic Acid Sulfonamides as Inhibitors of Methionine Aminopeptidase-2:  A Structural Basis for the Reduction of Albumin Binding (2006)

Methionine aminopeptidase-2 (MetAP2) is a novel target for cancer therapy. As part of an effort to discover orally active reversible inhibitors of MetAP2, a series of anthranilic acid sulfonamides with micromolar affinities for human MetAP2 were identified using affinity selection by mass spectrometry (ASMS) screening. These micromolar hits were rapidly improved to nanomolar leads on the basis of insights from protein crystallography; however, the compounds displayed extensive binding to human serum albumin and had limited activity in cellular assays. Modifications based on structural information on the binding of lead compounds to both MetAP2 and domain III of albumin allowed the identification of compounds with significant improvements in both parameters, which showed good cellular activity in both proliferation and methionine processing assays.
Centrosome aberrations in acute myeloid leukemia are correlated with cytogenetic risk profile (2002)

Genetic instability is a common feature in acute myeloid leukemia (AML). Centrosome aberrations have been described as a possible cause of aneuploidy in many human tumors. To investigate whether centrosome aberrations correlate with cytogenetic findings in AML, we examined a set of 51 AML samples by using a centrosome-specific antibody to pericentrin. All 51 AML samples analyzed displayed numerical and structural centrosome aberrations (36.0% +/- 16.6%) as compared with peripheral blood mononuclear cells from 21 healthy volunteers (5.2% +/- 2.0%; P <.0001). In comparison to AML samples with normal chromosome count, the extent of numerical and structural centrosome aberrations was higher in samples with numerical chromosome changes (50.5% +/- 14.2% versus 34.3% +/- 12.2%; P <.0001). When the frequency of centrosome aberrations was analyzed within cytogenetically defined risk groups, we found a correlation of the extent of centrosome abnormalities to all 3 risk groups (P =.0015), defined as favorable (22.5% +/- 7.3%), intermediate (35.3% +/- 13.1%), and adverse (50.3% +/- 15.6%). These results indicate that centrosome defects may contribute to the acquisition of chromosome aberrations and thereby to the prognosis in AML.
GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues (2005)

Quantitative gene expression data are often normalized to the expression levels of control or so-called "housekeeping" genes. An inherent assumption in the use of housekeeping genes is that expression of the genes remains constant in the cells or tissues under investigation. Although exceptions to this assumption are well documented, housekeeping genes are of value in fully characterized systems. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most commonly used housekeeping genes used in comparisons of gene expression data. To investigate the value of GAPDH as a housekeeping gene in human tissues, the expression of GAPDH mRNA was measured in a panel of 72 different pathologically normal human tissue types. Measurements were obtained from 371,088 multiplexed, quantitative real-time RT-PCRs with specific target genes. Significant differences in the expression levels of GAPDH mRNA were observed between tissue types and between donors of the same tissue. A 15-fold difference in GAPDH mRNA copy numbers was observed between the highest and lowest expressing tissue types, skeletal muscle and breast, respectively. No specific effect of either age or gender was observed on GAPDH mRNA expression. These data provide an extensive analysis of GAPDH mRNA expression in human tissues and confirm previous reports of the marked variability of GAPDH expression between tissue types. These data establish comparative levels of expression and can be used to add value to gene expression data in which GAPDH is used as the internal control.
Nuclear magnetic resonance imaging with hyper-polarized noble gases (1997)

This is the final report of a six-month, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The nuclei of noble gases can be hyper polarized through a laser-driven spin exchange to a degree many orders of magnitude larger than that attainable by thermal polarization without requiring a strong magnetic field. The increased polarization from the laser pumping enables a good nuclear magnetic resonance (NMR) signal from a gas. The main goal of this project was to demonstrate diffusion-weighted imaging of such hyper-polarized noble gas with magnetic resonance imaging (MRI). Possible applications include characterizing porosity of materials and dynamically imaging pressure distributions in biological or acoustical systems.
Review on the immunogenicity and safety of PCV-13 in infants and toddlers (2011)

Pneumococcal polysaccharide-protein conjugate vaccines (PCVs) generally protect against vaccine-serotype-specific pneumococcal disease. Additional serotypes included in the new 13-valent PCV (PCV-13) formulation and not in the first-generation 7-valent PCV (PCV-7) formulations are 1, 3, 5, 6A, 7F and 19A. Importantly, serotype 1 is associated with a high proportion and burden of pneumococcal disease in low-income countries, whilst serotype 19A emerged as the dominant disease-causing serotype following widespread PCV-7 immunization in the USA. In this article we present the available data on the immunogenicity and safety of PCV-13 in infants and children. Noninferiority studies indicate a similar immunogenicity profile between PCV-13 and PCV-7 recipients against most of the common serotypes. A favorable immunogenicity profile was also observed for at least five of the additional serotypes in PCV-13. An attenuated anamnestic response to serotype 3 was reported in five out of 14 studies. PCV-13 was demonstrated to have a similar acceptable safety profile to PCV-7 and no interference in immunogenicity of other concomitantly administered childhood vaccines was observed among PCV-13 recipients.