gebhart/patrepeval huggingface dataset:
The Chemical Composition of Bitumen in Pyrolyzed Green River Oil Shale: Characterization by 13C NMR Spectroscopy (2013)

During oil shale pyrolysis at high temperature, the conversion of kerogen to oil and gas proceeds dominantly through a mechanism involving bitumen as a reaction intermediate—at low maturities bitumen is formed from decomposition of kerogen, while at high maturities bitumen is transformed primarily to oil and gas. Here, we study the chemical composition of Green River bitumens of a range of maturities by high-field 13C nuclear magnetic resonance (NMR) spectroscopy. Numerous trends in the evolution of bitumen with maturity are observed, some of which are similar to trends previously observed in kerogen while others are not. As found previously for kerogen, bitumen becomes more aromatic (less aliphatic) with increasing maturity. However, in contrast to kerogen, which is primarily consumed during maturation and was found previously to have aliphatic chains that become shorter and/or more branched with maturity, aliphatic chains in bitumen lengthen with maturity in the low maturity regime where bitumen is primarily being formed but then shorten with maturity in the high maturity regime where bitumen is primarily being consumed. The structure of aromatic rings in bitumen is essentially unchanged with maturity, as their size, alkyl substitution, and heteroatom substitution are found to be independent of maturity; in contrast, the size of aromatic rings in kerogen generally increases with maturity. These measurements of the chemical composition of the bitumen intermediate enhance understanding of petroleum generation by oil shale pyrolysis at high temperature.
Use of microsphere-antibody conjugates in microparticle-enhanced nephelometric immunoassay (1992)

A new microparticle-enhanced nephelometric immunoassay has been recently described as a sensitive, accurate, and easy-to-perform competitive immunoassay for various analytes. As initially described, this test is based on the nephelometric quantification of the inhibition, by the antigen to be assayed, of immunoagglutination of microparticle-antigen conjugates. Its applicability as a competitive immunoassay is thus limited by the necessary availability of pure antigens to prepare microparticle-antigen conjugates. In this paper, we report an adaptation of this initial test, where microparticles are coated by monoclonal antibodies, eliminating the need for purified antigens. The new configurations of particle agglutination-based immunoassays described include use of these microparticle-antibody conjugates with microparticle-antigen conjugates, free antigen, and anti-mouse immunoglobulins antiserum. The feasibility of such configurations is studied with human chorionic gonadotropin hormone, human thyroid stimulating hormone, and human myoglobin as antigens. Capture of the analyte by microparticle-antibody conjugates is evidenced by inhibition of their agglutination with microparticle-antigen conjugates and by agglutination in a sandwich assay with a complementary monoclonal antibody or polyclonal antiserum. The use of a second xenogenic antibody enhances the agglutination process and increases the assay sensitivity. Microparticle-antibody conjugates may extend the applications of microparticle-enhanced nephelometric immunoassays to unavailable analytes.
Generation and Assembly of Spheroid-like Particles (2008)

This paper reports a straightforward approach in generating spheroid-like particles and also the orientational orders observed in the self-assembly of these particles. Nonspherical particles, such as spheroid-like particles, are useful in both fundamental studies and industrial applications due to the geometry impact that they bring to the bulk properties of various material systems. Developing processes to generate nonspherical particles is an ongoing quest to meet the need of using such particles in different applications. The approach reported here takes advantage of a controlled chemical etching process. Exposing the spherical silica particles partially to carbon tetrafluoride in a reactive ion plasma-etching chamber transformed the particles from spherical shape into spheroid-like shape. A simple model is proposed to predict the geometry of the resulting nonspherical particles. The shape and dimension of the nonspherical particles generated through such a process matched well with the prediction of the model. The assembly of these spheroid-like particles showed a unique orientational order associated with the alignment of their axes. This approach will help further studies on the fundamental properties of the nonspherical particles, such as packing, rheology, and optical interaction.
Fast and Scalable Distributed Deep Convolutional Autoencoder for fMRI Big Data Analytics (2017)

In recent years, analyzing task-based fMRI (tfMRI) data has become an essential tool for understanding brain function and networks. However, due to the sheer size of tfMRI data, its intrinsic complex structure, and lack of ground truth of underlying neural activities, modeling tfMRI data is hard and challenging. Previously proposed data-modeling methods including Independent Component Analysis (ICA) and Sparse Dictionary Learning only provided a weakly established model based on blind source separation under the strong assumption that original fMRI signals could be linearly decomposed into time series components with corresponding spatial maps. Meanwhile, analyzing and learning a large amount of tfMRI data from a variety of subjects has been shown to be very demanding but yet challenging even with technological advances in computational hardware. Given the Convolutional Neural Network (CNN), a robust method for learning high-level abstractions from low-level data such as tfMRI time series, in this work we propose a fast and scalable novel framework for distributed deep Convolutional Autoencoder model. This model aims to both learn the complex hierarchical structure of the tfMRI data and to leverage the processing power of multiple GPUs in a distributed fashion. To implement such a model, we have created an enhanced processing pipeline on the top of Apache Spark and Tensorflow library, leveraging from a very large cluster of GPU machines. Experimental data from applying the model on the Human Connectome Project (HCP) show that the proposed model is efficient and scalable toward tfMRI big data analytics, thus enabling data-driven extraction of hierarchical neuroscientific information from massive fMRI big data in the future.
Post-stroke upper extremity rehabilitation using 5-7 implanted microstimulators: Safety and control systems (2006)

microstimulators were implanted in a feasibility study of rehabilitation of arm function in subjects with stroke. Results of safety, reliability, and efficacy of the system are presented. It was shown that microstimulators could be implanted safely with only minor side effects. The system proved reliable. The motor thresholds showed to be low and stable.
Long-lasting reduction in clonogenic potential of colorectal cancer cells by sequential treatments with 5-azanucleosides and topoisomerase inhibitors (2016)

These results suggest that sequential treatments with DNA demethylating agents and topoisomerase inhibitors may exert clinically relevant anticancer effects.
Cell-free DNA release under psychosocial and physical stress conditions (2018)

The understanding of mechanisms linking psychological stress to disease risk depend on reliable stress biomarkers. Circulating cell-free DNA (cfDNA) has emerged as a potential biomarker of cellular stress, aging, inflammatory processes, and cell death. Recent studies indicated that psychosocial stress and physical exercise might also influence its release. We compared the effects of acute psychosocial and physical exercise stress on cfDNA release by exposing 20 young, healthy men to both an acute psychosocial laboratory stressor and an acute physical exercise stressor. Venous blood and saliva samples were collected before and after stress exposure. Cell-free DNA was extracted from plasma and quantified by qPCR. Furthermore, cfDNA fragment length was analyzed and cfDNA methylation patterns were assayed across time. In addition, release of stress hormones and subjective stress responses were measured. Results showed a twofold increase of cfDNA after TSST and fivefold increase after exhaustive treadmill exercise, with an overabundance of shorter cfDNA fragments after physical exhaustion. Interestingly, cell-free mitochondrial DNA showed similar increase after both stress paradigms. Furthermore, cfDNA methylation signatures-used here as a marker for diverse cellular origin-were significantly different post stress tests. While DNA methylation decreased immediately after psychosocial stress, it increased after physical stress, suggesting different cellular sources of active DNA release. In summary, our results suggest stimulus and cell-specific regulation of cfDNA release. Whereas the functional role of stress-associated cfDNA release remains elusive, it might serve as a valuable biomarker in molecular stress research as a part of the psychophysiological stress response.
A More Efficient Outcome for Alzheimer Disease Research: the Item Response Theory Based Score for the Clinical Dementia Rating (CDR®) (2022)

Abstract Background CDR sum of boxes (CDR‐SB) is widely used as a primary outcome in Alzheimer disease (AD) research due to its reliability and accuracy. However, it is an ordinal rank measure instead of a continuous measure and therefore may not be able to capture subtle changes in cognition. Additionally, it weights each domain equally, without accounting for the patterns of the responses scores across CDR items. To generate a more optimal score, we developed a bi‐factor model based on the item response theory (IRT) which can account for different response pattern, item difficulty and discrimination level to provide an improved estimate of the dementia severity. We demonstrated the superiority of the IRT score in two independent cohorts. Method Baseline item level CDR data from 2949 participants enrolled in the WashU Knight ADRC study were used to develop the IRT model. The best fitting IRT model was then applied to the longitudinal item level CDR data in both the Knight ADRC and DIAN‐TU‐001 (142 participants) studies to generate the IRT scores (a continuous measure) for each participant at each visit. Result Correlations between the CDR IRT score and SB were consistent at different visits (0.89 ∼ 0.92 for DIAN‐TU cohort, 0.92 ∼ 0.94 for Knight ADRC cohort). The IRT score had a much larger effect size (&gt; 60% for the DIAN‐TU cohort and &gt; 40% for the Knight ADRC cohort) than that of CDR‐SB when comparing converter to stable cognitively normal participants. For CDR‐SB of 0 group, the IRT score was significantly associated with some of the clinical/cognitive outcomes and biomarkers. For CDR‐SB &gt; 0 group, the IRT score had slightly higher correlations with other outcomes than CDR‐SB. The IRT score correlated better with the estimated age from dementia onset in the DIAN cohort. Using IRT score as the primary outcome in clinical trials could save 10% ∼ 30% of the sample size compared to that of using CDR‐SB. Conclusion The CDR IRT score could potentially be used as a more efficient outcome in AD research to gain precision in detecting cognitive decline and improve power (or reduce sample size).
Semi-lossless text compression (2004)

This paper discusses the semilossless text compression. The data compression method is classified into lossless and lossy methods. Lossless methods include usually those applied on text files or other data for which no loss of information can be tolerated, lossy techniques are generally applied to image files as well as to video and audio data, for which the overall knowledge a user might extract does not seem significantly reduced even if a part of the data is omitted.
Analysis of Mouse Brain Transcriptome After Experimental Duvenhage Virus Infection Shows Activation of Innate Immune Response and Pyroptotic Cell Death Pathway (2018)

Rabies is an important neglected disease, characterized by invariably fatal encephalitis. Several studies focus on understanding the pathogenic mechanisms of the prototype lyssavirus rabies virus (RABV) infection, and little is known about the pathogenesis of rabies caused by other lyssaviruses. We sought to characterize the host response to Duvenhage virus infection and compare it with responses observed during RABV infection by gene expression profiling of brains of mice with the respective infections. We found in both infections differentially expressed genes leading to increased expression of type I interferons (IFNs), chemokines, and proinflammatory cytokines. In addition several genes of the IFN signaling pathway are up-regulated, indicating a strong antiviral response and activation of the negative feedback mechanism to limit type I IFN responses. Furthermore we provide evidence that in the absence of significant neuronal apoptotic death, cell death of neurons is mediated via the pyroptotic pathway in both infections. Taken together, we have identified several genes and/or pathways for both infections that could be used to explore novel approaches for intervention strategies against rabies.
Antifungal Activity ofMucuna pruriensSeed Extractives and L-dopa (2011)

The seeds of Mucuna pruriens (L.) D.C. (Leguminosae) were extracted first with hexane, then with ethyl acetate, and finally with methanol. The solvents were removed to get the respective extractives. These were assessed for the mycelial growth inhibition of three phytopathogenic fungi—Colletotrichum gloeosporioides, Colletotrichum capsici, and Fusarium solani—by the poisoned-food technique. Methanol extractive showed highest activity against all the three test organisms. L-dopa [3-(3,4-Dihydroxyphenyl)-L-alanine], which was qualitatively detected in the ethyl acetate and methanol extractives and quantitatively assessed in the seeds, showed antifungal activity against all the three test organisms, showing that it is one of the active principles in these extractives.
A full-scale demonstration of in situ chemical oxidation through recirculation at the X-701B site (1997)

In 1996, researchers at Oak Ridge National Laboratory (ORNL) proposed an oxidant delivery technique involving injection and recirculation of the oxidant solution into a contaminated aquifer through multiple horizontal and vertical wells. This technique would be applicable to saturated, hydraulically conductive formations. In the spring of 1997, the Department of Energy (DOE) at the Portsmouth Gaseous Diffusion Plant (PORTS) agreed to collaborate with the DOE`s Subsurface Contaminants Focus Area to conduct a field-scale treatability study using in situ chemical oxidation through recirculation (ISCOR). PORTS agreed to support the demonstration at the X-701B site where the technology can potentially be used to remediate TCE-contaminated groundwater and sediments. The ISCOR field demonstration took advantage of existing infrastructure and extensive site characterization data generated from previous field demonstrations at X-701B. The field test was implemented using a pair of previously installed horizontal wells that transect an area of DNAPL contamination. Groundwater was extracted from one horizontal well, pumped to an existing pump and treat facility, dosed with KMnO{sub 4}, and re-injected into a parallel horizontal well approximately 90 ft away. The field demonstration lasted approximately one month. Treatment effectiveness was determined by comparing contaminant levels in pre-treatment, during, and post-treatment groundwater samples and pre- and post-treatment soil samples.
The contractile state of cat and dog heart in relation to the interval between beats. (1980)

We induced atrioventricular dissociation and initiated ventricular pacing in intact dogs and isolated cat hearts. Left ventricular pressure, its time derivative (dP/t), and action potentials were recorded. When a test pulse was introduced at varying intervals after a period of steady pacing, an optimum contractile response was obtained at an average interval of 720 msec. A similar optimum interval was obtained after pacing at various frequencies and after paired pulse stimulation but was shortened to 560 msec after infusion of epinephrine. The magnitude of the optimum contractile response increased with an increase in the frequency of prior pacing which was accompanied by an increase in the time the cell membrane was depolarized. The optimum contractile response following paired pulse stimulation was greater than that following regular pacing, with the same number of stimuli per minute and the same time of membrane depolarization. The results are explicable in terms of intracellular calcium ion recirculation with separate compartments for release to and uptake from the contractile proteins. A negative feedback control of Ca2+ inflow to the cell by intracellular Ca2+ content is postulated to explain the effect of paired pulse stimulation and shortening of action potential duration following an increase in regular pacing frequency.
Fungicidal activity of indole derivatives against some plant pathogenic fungi (2010)

Fungicidal activity of six prepared indole derivatives in addition to indole-3-acetic acid and indole-3-butyric acid was in vitro evaluated against Fusarium calmorum, Pythium debarianum, Rhizoctonia solani and Macrofomina phaseoli fungi. The toxicity appeared to be a function of both the treated fungus and the tested concentration. IC50 values were calculated and the structure activity relationship (SAR) was illustrated. 2-Phenylindole and 1-acetylindole-3-butyric acid exhibited persuasive fungicidal activities, so their effects were examined in vivo against polyphenoloxidase (PPO), peroxidase (PO), DNA, RNA and sugar contents. Polyphenoloxidase in R. solani systematically responded to 2-phenylindole concentrations with IC50 value of 80.3 μg/ml. 1-Acetylindole-3-butyric acid was more effective than 2-phenylindole with IC50 values of 41.5 and 80.2 μg/ml comparing with 87.6 and 117.1 μg/ml on F. calmorum and M. phaseoli, respectively. While against P. debarianum, the enzyme was inhibited by 1-acetylindole-3-butyric acid with IC50 equaled 45.6 μg/ml. Effect of the tested compounds on peroxidase was differed among the tested fungi. The peroxidase extracted from P. deparianum was less inhibited. Changing in sugar, DNA and RNA contents of the tested fungi were exhibited that explains the disturbance of the fungal cell physiology and developing deformed and dead cells.
Abstract 070: Canonical Wnt Signaling Mediates Enhanced Renal Afferent Arteriolar Reactive Oxygen Species and Contractility in Diabetic Mice (2017)

Background: Canonical Wnt signaling is involved in oxidative stress and diabetes but its role in diabetic renal microvascular dysfunction is unclear. We tested the hypothesis that enhanced canonical Wnt signaling in renal afferent arterioles from diabetic mice increases reactive oxygen species (ROS) and contractions to endothelin-1 (ET-1). Methods: Diabetic or control C57Bl/6 mice received vehicle or sulindac (40 mg·kg -1 ·day -1 ) to block canonical Wnt signaling for 4 weeks. ET-1 contractions were measured in diameter changes and H 2 O 2 and O 2 .- by fluorescence microscopy. Arteriolar protein expression and enzymatic activity were examined by standard methods. Results: Compared to control, diabetic mouse afferent arteriole had significantly increased O 2 .- (+84%) and H 2 O 2 (+91%) and enhanced sensitivity to ET-1 at 10 -8 mol·l -1 (-72±4% versus -43±4%, P&lt;0.05) accompanied by significantly (P&lt;0.005) reduced protein expressions and activities for catalase and superoxide dismutase 2 (SOD2). Incubation of afferent arterioles from normal or diabetic mice with PEG-SOD reduced responses to ET-1 whereas incubation with PEG-catalase reduced sensitivity to ET-1 selectively in arterioles from diabetic mice. The arteriolar protein expressions for canonical Wnt signaling indicated overactivation of this pathway in diabetic mice (2.6-fold increase in p-GSK-3β/GSK-3β and 3.3-fold decrease in p-β-catenin/β-catenin). Sulindac given to diabetic mice normalized the canonical Wnt signaling protein and arteriolar O 2 .- , H 2 O 2 and ET-1 contractions while doubling (P&lt;0.05) microvascular catalase and SOD2. Conclusions: Increased ROS, notably H 2 O 2 , mediated by canonical Wnt signaling contributes to enhanced afferent arteriolar sensitivity to ET-1 in diabetes. Thus, antioxidant pharmacological strategies targeting canonical Wnt signaling may improve vascular function in diabetic nephropathy.
Properties of Pluripotent Human Embryonic Stem Cells BG01 and BG02 (2004)

Human ES (hES) cell lines have only recently been generated, and differences between human and mouse ES cells have been identified. In this manuscript we describe the properties of two human ES cell lines, BG01 and BG02. By immunocytochemistry and reverse transcription polymerase chain reaction, undifferentiated cells expressed markers that are characteristic of ES cells, including SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, and OCT-3/4. Both cell lines were readily maintained in an undifferentiated state and could differentiate into cells of all three germ layers, as determined by expression of beta-tubulin III neuron-specific molecule (ectoderm), cardiac troponin I (cardiomyocytes, mesoderm), and alpha-fetoprotein (endoderm). A large-scale microarray (16,659 genes) analysis identified 373 genes that were expressed at three-fold or higher levels in undifferentiated BG01 and BG02 cells as compared with pooled human RNA. Ninety-two of these genes were also highly expressed in four other hES lines (TE05, GE01, GE09, and pooled samples derived from GE01, GE09, and GE07). Included in the list are genes involved in cell signaling and development, metabolism, transcription regulation, and many hypothetical proteins. Two focused arrays designed to examine transcripts associated with stem cells and with the transforming growth factor-beta superfamily were employed to examine differentially expressed genes. Several growth factors, receptors, and components of signaling pathways that regulate embryonic development, in particular the nodal signaling pathway, were detected in both BG01 and BG02. These data provide a detailed characterization and an initial gene expression profile for the BG01 and BG02 human ES cell lines.
Direct activation of glomerular endothelial cells by anti-moesin activity of anti-myeloperoxidase antibody (2011)

The endothelial CXC chemokines, KC and MIP-2, contribute to infiltration of neutrophils in MPO-ANCA-associated vasculitis involving glomerulonephritis. The activation of glomerular endothelial cells by anti-MPO IgG appeared to directly involve a signaling through moesin.