gebhart/patrepeval huggingface dataset:
Multi-scale multi-dimensional microstructure imaging of oil shale pyrolysis using X-ray micro-tomography, automated ultra-high resolution SEM, MAPS Mineralogy and FIB-SEM (2017)

The complexity of unconventional rock systems is expressed both in the compositional variance of the microstructure and the extensive heterogeneity of the pore space. Visualizing and quantifying the microstructure of oil shale before and after pyrolysis permits a more accurate determination of petrophysical properties which are important in modeling hydrocarbon production potential. We characterize the microstructural heterogeneity of oil shale using X-ray micro-tomography (µCT), automated ultra-high resolution scanning electron microscopy (SEM), MAPS Mineralogy (Modular Automated Processing System) and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). The organic-rich Eocene Green River (Mahogany zone) oil shale is characterized using a multi-scale multi-dimensional workflow both before and after pyrolysis. Observations in 2-D and 3-D and across nm-µm-mm length scales demonstrate both heterogeneity and anisotropy at every scale. Image acquisition and analysis using µCT and SEM reveal a microstructure of alternating kerogen-rich laminations interbedded with layers of fine-grained inorganic minerals. MAPS Mineralogy combined with ultrafast measurements reveal mineralogic textures dominated by dolomite, calcite, K-feldspar, quartz, pyrite and illitic clays along with their spatial distribution, augmenting conventional mineral analysis. From high resolution Backscattered electron (BSE) images, intra-organic, inter-organic-mineral, intra- and inter-mineral pores are observed with varying sizes and geometries. By using FIB milling and SEM imaging sequentially and repetitively, 3-D data sets were reconstructed. By setting 3-D gradient and marker-based watershed transforms, the organic matter, minerals and pore phases (including pore-back artifacts) were segmented and visualized and the pore-size distribution was computed. Following pyrolysis, fractures from the mm-to-µm scales were observed with preferential propagation along the kerogen-rich laminations and coalescence leading to an interconnected fracture network. The application of these techniques to worldwide oil shale deposits will allow significant insights into estimating mechanical and chemical proprieties of oil shale formations for modeling and designing oil shale pyrolysis processes.
Cre‐lox site‐specific recombination between Arabidopsis and tobacco chromosomes (2000)

To create hybrid chromosomes, we tested the Cre-lox system to mediate recombination between Arabidopsis thaliana and Nicotiana tabacum chromosomes. Protoplasts of the two plants were fused to allow site-specific recombination to join a promoter from tobacco to a hygromycin resistance coding-region from Arabidopsis. The expected recombination junction was detected in hygromycin-resistant calli. Analysis of one hybrid suspension cell line revealed the presence of markers corresponding to the north arm of Arabidopsis chromosome III, but not markers from other chromosome arms. However, these markers were not detected in regenerated plants. With a second hybrid cell line we obtained a single hygromycin-resistant progeny from approximately 18 000 self-fertilized seeds of one regenerated plant. Molecular analysis of this hybrid indicated that a small portion of the north arm of Arabidopsis chromosome V is present in the tobacco genome. However, neither the recombination junction nor Arabidopsis DNA was detected in tissue from the plant grown without selection or in the subsequent generation. Thus interspecies transfer of a chromosome arm between plant cells is possible, but maintenance of the hybrid chromosome in a plant is unlikely. The feasibility of site-specific recombination between genomes of different species offers new possibilities for engineering hybrid chromosomes that may be maintained in cell culture.
X-ray lithography for ⩽100 nm ground rules in complex patterns (1997)

Complex patterns with 75–125 nm feature sizes exposed with x-ray lithography are shown. Lithographic results for 75–125 nm lines with varying pitch are compared to simulations of image formation and resist dissolution, showing good qualitative agreement. Exposure dose latitude, nested-to-isolated print bias, image shortening, linewidth change with gap, and linearity of printed linewidth versus mask linewidth are quantified for 11–22.5 μm gaps. Critical dimension control error budgets for resist linewidth uniformity are determined for logic patterns at 75 and 100 nm ground rules. Image shortening is quantified for 75–125 nm ground rule static random access memory-like patterns, indicating hammerheads added to line ends reduce shortening to acceptable levels for ⩾100 nm ground rules at ⩽17.5 μm gaps. With tight gap control and tight mask linewidth control, 100 nm ground rule complex patterns can be printed with good latitude using x-ray lithography.
Effects of Highly Purified Ethyl All-cis-5,8,11,14,17-icosapentaenoate(EPA-E) on Rabbit Platelets. (1993)

The effects of ethyl all-cis-5,8,11,14,17-icosapentaenoate (EPA-E), highly purified ethyl ester of icosapentaenoic acid (EPA), on rabbit platelets were studied. In in vitro, highly purified EPA (62.5-3000 microM) suppressed the platelet aggregation induced by collagen, arachidonic acid (AA) and adenosine diphosphate (ADP). In ex vivo, a single administration of EPA-E (300 and 1000 mg/kg, p.o.) and repeated administrations (30 and 300 mg/kg/d, p.o.) for 2 weeks showed no effects on collagen-, AA- and ADP-induced platelet aggregation. Repeated administrations (30 and 300 mg/kg/d, p.o.) for 4 weeks suppressed the collagen-induced platelet aggregation, but not the AA- and ADP-induced platelet aggregation. Repeated administrations for 4 weeks also suppressed thromboxane B2 (TXB2) formation induced by collagen, but a single administration and repeated administrations for 2 weeks failed to inhibit TXB2 formation. The EPA level in the platelet phospholipids increased slightly with a single administration, and increased markedly with repeated administrations for 2 and 4 weeks. The AA level in the phospholipids showed practically no changes with a single and repeated administrations. These results suggested that highly purified EPA-E could reduce platelet aggregability by the change of the EPA level in the platelet phospholipids and should allow for a reasonable period of administration.
Flow microsphere immunoassay for the quantitative and simultaneous detection of multiple soluble analytes. (1990)

Publisher Summary This chapter develops a quantitative and highly sensitive assay, named “flow microsphere immunoassay (FMIA),” permitting the simultaneous quantification of several analytes in a sample. The method employs several discrete size classes of plastic microspheres of 5, 7, 10, and 15 pm diameter, each class coated with a specific capture reagent. The four size classes of coated microspheres are mixed together and added to the sample under analysis. Each microsphere acts as an accumulator that removes from the sample and concentrates specific analyte for later measurement. Following incubation in the sample, the microspheres are washed to remove unbound sample and labeled with a fluorescent reagent that reacts only with the microsphere-accumulated analyte, labeling only those microsphere. Following washing, the microsphere suspension is analyzed using a flow cytometer that measures microsphere size and fluorescence. As it passes through the sensor region of a cytometer, the size of each microsphere is measured identifying the microsphere class and, thereby, the capture reagent. Fluorescence of the microsphere is measured; the amplitude of the signal indicates the quantity of the analyte in the sample.
Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region (2006)

We replaced degenerate codons for nine amino acids within the capsid region of the Sabin type 2 oral poliovirus vaccine strain with corresponding nonpreferred synonymous codons. Codon replacements were introduced into four contiguous intervals spanning 97% of the capsid region. In the capsid region of the most highly modified virus construct, the effective number of codons used (N(C)) fell from 56.2 to 29.8, the number of CG dinucleotides rose from 97 to 302, and the G+C content increased from 48.4% to 56.4%. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased in proportion to the number of replacement codons. Plaque areas decreased over an approximately 10-fold range, and virus yields decreased over an approximately 65-fold range. Perhaps unexpectedly, the synthesis and processing of viral proteins appeared to be largely unaltered by the restriction in codon usage. In contrast, total yields of viral RNA in infected cells were reduced approximately 3-fold and specific infectivities of purified virions (measured by particle/PFU ratios) decreased approximately 18-fold in the most highly modified virus. The replicative fitness of both codon replacement viruses and unmodified viruses increased with the passage number in HeLa cells. After 25 serial passages (approximately 50 replication cycles), most codon replacements were retained, and the relative fitness of the modified viruses remained well below that of the unmodified virus. The increased replicative fitness of high-passage modified virus was associated with the elimination of several CG dinucleotides. Potential applications for the systematic modulation of poliovirus replicative fitness by deoptimization of codon usage are discussed.
Einleitung (2009)

Dieses Lehrbuch führt in die Soziologische Theorie nach Talcott Parsons ein. Dieser Großtheoretiker beschloss den ersten Band — Brock/Junge/Krähnke: Soziologische Theorien von Auguste Comte bis Talcott Parsons — der sich mit den Vorläufern, Gründern und Klassikern der Soziologischen Theorie befasste.
How feasible is the use of magnetic field alone for indoor positioning? (2012)

The use of magnetic field variations for positioning and navigation has been suggested by several researchers. In most of the applications, the magnetic field is used to determine the azimuth or heading. However, for indoor applications, accurate heading determination is difficult due to the presence of magnetic field anomalies. Here location fingerprinting methodology can take advantage of these anomalies. In fact, the more significant the local anomalies, the more unique the magnetic “fingerprint”. In general, the more elements in each fingerprint, the better for positioning. Unfortunately, magnetic field intensity data only consists of three components. Since true north (or magnetic north) is generally unknown, even with help of the accelerometer to detect the direction of the gravity, only two components can be extracted, i.e. the horizontal intensity and the vertical intensity (or total intensity and inclination). Furthermore, moving objects containing ferromagnetic materials and electronic devices may affect the magnetic field. Tests were carried out to investigate the feasibility of using magnetic field alone for indoor positioning. Possible solutions are discussed.
Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model (2010)

Increasing survival of motor neuron 2, centromeric (SMN2) exon 7 inclusion to express more full-length SMN protein in motor neurons is a promising approach to treat spinal muscular atrophy (SMA), a genetic neurodegenerative disease. Previously, we identified a potent 2'-O-(2-methoxyethyl) (MOE) phosphorothioate-modified antisense oligonucleotide (ASO) that blocks an SMN2 intronic splicing silencer element and efficiently promotes exon 7 inclusion in transgenic mouse peripheral tissues after systemic administration. Here we address its efficacy in the spinal cord--a prerequisite for disease treatment--and its ability to rescue a mild SMA mouse model that develops tail and ear necrosis, resembling the distal tissue necrosis reported in some SMA infants. Using a micro-osmotic pump, we directly infused the ASO into a lateral cerebral ventricle in adult mice expressing a human SMN2 transgene; the ASO gave a robust and long-lasting increase in SMN2 exon 7 inclusion measured at both the mRNA and protein levels in spinal cord motor neurons. A single embryonic or neonatal intracerebroventricular ASO injection strikingly rescued the tail and ear necrosis in SMA mice. We conclude that this MOE ASO is a promising drug candidate for SMA therapy, and, more generally, that ASOs can be used to efficiently redirect alternative splicing of target genes in the CNS.
Non-pathogenic bacteria elicit a differential cytokine response by intestinal epithelial cell/leucocyte co-cultures (2000)

The differential recognition of non-pathogenic bacteria by CaCO-2 cells required the presence of underlying leucocytes. These results strengthen the hypothesis that bacterial signalling at the mucosal surface is dependent on a network of cellular interactions.
Heterogeneity of HLA-A,B, Ia-like, and melanoma-associated antigen expression by human melanoma cell lines analyzed with monoclonal antibodies and flow cytometry. (1982)

With the use of monoclonal antibodies, indirect immunofluorescence, and flow cytometry, human melanoma cell lines (Colo 38, M-16, and M-21) were examined for the quantitative level of expression of HLA-A,B antigens, Ia-like antigens, and two human melanoma-associated antigens (MAA) referred to as 280K and 94K MAAs. Each of the melanoma cell lines examined showed tremendous heterogeneity with regard to antigen expression. A detailed study of the heterogeneity of the four antigens listed revealed that variation in cell size could, in part, account for the large differences in antigen expression observed. Cell surface density of HLA-A,B antigens, Ia-like antigens, and the 280K and 94K MAAs remained relatively constant over a wide range of cell sizes that were examined, with the exception that small melanoma cells showed a slightly lower mean surface density of MAA expression than did large cells. A novel method was used to detect the expression of the two MAAs as a function of the Colo 38 cell cycle using dual-laser beam flow cytometry. The results of these experiments show that both the 280K MAA and the 94K MAA are differentially expressed during various stages of the cell cycle, with each antigen being maximally detected during G2 + M.
Mechanisms of cytotoxicity of nicotine in human periodontal ligament fibroblast cultures in vitro (2002)

The use of tobacco products significantly contributes to the progression of periodontal disease and poor response to healing following periodontal therapy. The purpose of this study was to determine the effects of nicotine, a major component of cigarette smoking, on human periodontal ligament fibroblast (PDLF) growth, proliferation, and protein synthesis to elucidate its role in periodontal destruction associated with its use. Human PDLFs were derived from three healthy individuals undergoing extraction for orthodontic reasons. At a concentration higher than 2.5 mM, nicotine was found to be cytotoxic to human PDLFs (P < 0.05). Nicotine also significantly inhibited cell proliferation and decreased protein synthesis in a dose-dependent manner. At concentrations of 50 and 200 microM, nicotine suppressed the growth of PDLFs by 48% and 86% (P < 0.05), respectively. A 10-mM concentration level of nicotine significantly inhibited the protein synthesis to only 44% of these in the untreated control (P < 0.05). Furthermore, the effects of antioxidants (superoxide dismutase (SOD); catalase and 2-oxothiazolidine-4-carboxylic acid (OTZ) and buthionine sulfoximine (BSO) were added to search for the possible mechanism of action, as well as a method for the prevention, of cigarette smoking-associated periodontal diseases. The addition of OTZ, a precursor of cysteine that metabolically promotes GSH synthesis, acted as a protective effect on the nicotine-induced cytotoxicity. However, SOD and catalase did not decrease the nicotine-induced cytotoxicity. In contrast, the addition of BSO, a cellular GSH synthesis inhibitor, enhanced the nicotine-induced cytotoxicity. These results indicate that thiol depletion could be the mechanism for nicotine cytotoxicity. The levels of nicotine tested inhibited cell growth, proliferation, and protein synthesis on human PDLFs. This suggests that nicotine itself might augment the destruction of periodontium associated with cigarette smoking. In addition, these inhibitory effects were associated with intracellular thiol levels. Factors that induce glutathione synthesis of human PDLF may be used for further chemoprevention of cigarette smoking-related periodontal diseases.
Repetitive Mild Brain Trauma Accelerates Aβ Deposition, Lipid Peroxidation, and Cognitive Impairment in a Transgenic Mouse Model of Alzheimer Amyloidosis (2002)

Traumatic brain injury (TBI) increases susceptibility to Alzheimer's disease (AD), but it is not known how TBI contributes to the onset or progression of this common late life dementia. To address this question, we studied neuropathological and behavioral consequences of single versus repetitive mild TBI (mTBI) in transgenic (Tg) mice (Tg2576) that express mutant human Abeta precursor protein, and we demonstrate elevated brain Abeta levels and increased Abeta deposition. Nine-month-old Tg2576 and wild-type mice were subjected to single (n = 15) or repetitive (n = 39) mTBI or sham treatment (n = 37). At 2 d and 9 and 16 weeks after treatment, we assessed brain Abeta deposits and levels in addition to brain and urine isoprostanes generated by lipid peroxidation in these mice. A subset of mice also was studied behaviorally at 16 weeks after injury. Repetitive but not single mTBI increased Abeta deposition as well as levels of Abeta and isoprostanes only in Tg mice, and repetitive mTBI alone induced cognitive impairments but no motor deficits in these mice. This is the first experimental evidence linking TBI to mechanisms of AD by showing that repetitive TBI accelerates brain Abeta accumulation and oxidative stress, which we suggest could work synergistically to promote the onset or drive the progression of AD. Additional insights into the role of TBI in mechanisms of AD pathobiology could lead to strategies for reducing the risk of AD associated with previous episodes of brain trauma and for preventing progressive brain amyloidosis in AD patients.
Power assist method for HAL-3 estimating operator's intention based on motion information (2004)

This paper describes the recognition method and the control method to realize the power assist which reflects operator's intention by grasping the interaction between operator's intention and motion information. The basic control method for HAL had been performed by using myoelectricity which reflects operator's intention. As the application of the basic method, we considered the control method of power assist based on another information by considering the relation between myoelectricity and another information of motion, and the recognition method for the control method. We adopted phase sequence control which generated a series of assist motions by the transition of some fundamental motions called phase. The result of experiments showed the effective power assist which reflected operator's intention by using this control method.
Visualization and quantification of capillary drainage in the pore space of laminated sandstone by a porous plate method using differential imaging X‐ray microtomography (2017)

Abstract The experimental determination of capillary pressure drainage curves at the pore scale is of vital importance for the mapping of reservoir fluid distribution. To fully characterize capillary drainage in a complex pore space, we design a differential imaging‐based porous plate (DIPP) method using X‐ray microtomography. For an exemplar mm‐scale laminated sandstone microcore with a porous plate, we quantify the displacement from resolvable macropores and subresolution micropores. Nitrogen (N 2 ) was injected as the nonwetting phase at a constant pressure while the porous plate prevented its escape. The measured porosity and capillary pressure at the imaged saturations agree well with helium measurements and experiments on larger core samples, while providing a pore‐scale explanation of the fluid distribution. We observed that the majority of the brine was displaced by N 2 in macropores at low capillary pressures, followed by a further brine displacement in micropores when capillary pressure increases. Furthermore, we were able to discern that brine predominantly remained within the subresolution micropores, such as regions of fine lamination. The capillary pressure curve for pressures ranging from 0 to 1151 kPa is provided from the image analysis compares well with the conventional porous plate method for a cm‐scale core but was conducted over a period of 10 days rather than up to few months with the conventional porous plate method. Overall, we demonstrate the capability of our method to provide quantitative information on two‐phase saturation in heterogeneous core samples for a wide range of capillary pressures even at scales smaller than the micro‐CT resolution.
Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis (2005)

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.