gebhart/patrepeval huggingface dataset:
A SIMPLE METHOD OF ISOLATION OF CRYSTALLINE STERCOBILIN OR UROBILIN FROM FECES (1953)

The methods described two decades ago (l-3) for the isolation of crystalline stercobilin or urobilin from feces or urine are relatively slow and cumbersome. It is often desirable to obtain a few mg of crystalline material quickly, either to permit determination of the preponderant type (whether stercobilin, urobilin, or d-urobilin) or calibration of a quantitative method. More recently, the studies of Shemin and associates (4-S), based on the essential nature of glycine and acetate in the biosynthesis of the heme pigments, have made it highly desirable to have at hand a simple method permitting rapid and repeated isolation of stercobilin from feces in order that serial observations of N16 content may be made, following administration of N16-glycine. Of special interest in this connection is the question of exact significance of the early appearance of N15 in the stercobilin molecule, a finding indicating that a certain fraction, varying under normal and pathological conditions, has a derivation other than the hemoglobin of red blood cells which have survived a normal life span (6, 7). Since determinations of the atom per cent excess of N15 in the mass spectrometer require but 10 mg. of pure substance, the method to be described in the following is particularly adapted to studies of this type. This method depends in considerable part on the dehydrogenation of stercobilinogen or urobilinogen with iodine, in petroleum ether solutions, as described in the preceding paper (9). It may be noted that Lichtenstein and Terwen, in 1925 (lo), used petroleum ether to extract a urobilinogen from an aqueous filtrate of a feces-ferrous hydroxide mixture. The petroleum ether was then allowed to stand in the light, with resultant formation and precipitation of an amorphous urobilin. The latter was not crystallized, but was evidently relatively pure. It probably consisted in the main of the levorotatory stercobilin. We have, in fact, been able to isolate crystalline sterco-
Nucleation mechanism of GaN nanowires grown on (111) Si by molecular beam epitaxy (2009)

We have performed a real-time in situ x-ray scattering study of the nucleation of GaN nanowires grown by plasma-assisted molecular beam epitaxy on AlN(0001)/Si(111). The intensity variation of the GaN diffraction peak as a function of time was found to exhibit three different regimes: (i) the deposition of a wetting layer, which is followed by (ii) a supralinear regime assigned to nucleation of almost fully relaxed GaN nanowires, eventually leading to (iii) a steady-state growth regime. Based on scanning electron microscopy and electron microscopy analysis, it is proposed that the granular character of the thin AlN buffer layer may account for the easy plastic relaxation of GaN, establishing that three-dimensional islanding and plastic strain relaxation of GaN are two necessary conditions for nanowire growth.
Frequency of recent retrotransposition events in the human factor IX gene (2001)

Two germline retrotransposition mutations of recent origin were observed in 727 independent mutations (0.28%) in the human factor IX gene (F9) of patients with hemophilia B: 1) a 279 bp insertion in exon H originating from an Alu family of short interspersed elements not previously known to be active and, 2) a 463 bp insertion in exon E of a LINE1 element originating in the maternal grandmother. If the rates of recent germline mutation in F9 are typical of the genome, a retrotransposition event is estimated to occur somewhere in the genome of about one in every 17 children born. Analysis of other estimates for retrotransposition frequency and overall mutation rates suggests that the actual rate of retrotransposition is likely to be in the range of one in every 2.4 to 28 live births.
The Twenty-Year Story of a Plant-Based Vaccine Against Hepatitis B: Stagnation or Promising Prospects? (2013)

Hepatitis B persists as a common human disease despite effective vaccines having been employed for almost 30 years. Plants were considered as alternative sources of vaccines, to be mainly orally administered. Despite 20-year attempts, no real anti-HBV plant-based vaccine has been developed. Immunization trials, based on ingestion of raw plant tissue and conjugated with injection or exclusively oral administration of lyophilized tissue, were either impractical or insufficient due to oral tolerance acquisition. Plant-produced purified HBV antigens were highly immunogenic when injected, but their yields were initially insufficient for practical purposes. However, knowledge and technology have progressed, hence new plant-derived anti-HBV vaccines can be proposed today. All HBV antigens can be efficiently produced in stable or transient expression systems. Processing of injection vaccines has been developed and needs only to be successfully completed. Purified antigens can be used for injection in an equivalent manner to the present commercial vaccines. Although oral vaccines require improvement, plant tissue, lyophilized or extracted and converted into tablets, etc., may serve as a boosting vaccine. Preliminary data indicate also that both vaccines can be combined in an effective parenteral-oral immunization procedure. A partial substitution of injection vaccines with oral formulations still offers good prospects for economically viable and efficacious anti-HBV plant-based vaccines.
Transition rates of Tb3+ in TbP5O14, TbLiP4O12, and TbAl3(BO3)4: An evaluation for laser applications (1983)

The properties of Tb3+ in crystals of three stoichiometric Tb compounds, viz., TbP5O14, TbLiP4O12, and TbAl3(BO3)4 have been studied by spectroscopic absorption and emission methods to evaluate these materials as hosts for Tb3+ laser applications. The absorption spectra between 50000 and 200 cm−1 at 300 °K, the emission spectra between 27000 and 14000 cm−1 at 300 °K, and the fluorescence decay characteristics of 5D4 emission at 300 and 5 °K are given. Because of cross relaxation, the 5D3 and 5G6 emissions in all three materials were concentration-quenched strongly with a similar behavior observed in other hosts. Quenching in the 5D4 states was negligible except for TbAl3(BO3)4 where moderate quenching was observed due to energy transfer to nonradiative traps. Transition rates between various states were calculated by using the Judd–Ofelt approach and a first order wavefunction set, and good fit was obtained between the calculated and experimental parameters. The transition rates were then used to find the emission cross sections of various lines.
Mechanisms of stimulation of interleukin-1 beta and tumor necrosis factor-alpha by Mycobacterium tuberculosis components. (1993)

The granulomatous immune response in tuberculosis is characterized by delayed hypersensitivity and is mediated by various cytokines released by the stimulated mononuclear phagocytes, including tumor necrosis factor-alpha (TNF alpha) and IL-1 beta. We have demonstrated that Mycobacterium tuberculosis cell wall component lipoarabinomannan (LAM), mycobacterial heat shock protein-65 kD, and M. tuberculosis culture filtrate, devoid of LPS as assessed by the Amebocyte Lysate assay, stimulate the production of TNF alpha and IL-1 beta proteins and mRNA from mononuclear phagocytes (THP-1 cells). The effect of LAM on the release of these cytokines was specific, as only LAM stimulation was inhibited by anti-LAM monoclonal antibody. Interestingly, we found that LAM and Gram-negative bacterial cell wall-associated endotoxin LPS may share a similar mechanism in their stimulatory action as demonstrated by inhibition of TNF alpha and IL-1 beta release by monoclonal antibodies to CD14. Anti-CD14 monoclonal antibody MY4 inhibited both TNF alpha and IL-1 beta release with LAM and LPS but no effect was observed with other mycobacterial proteins. An isotype antibody control did not inhibit release of cytokines under the same experimental conditions. M. tuberculosis and its components upregulated IL-1 beta and TNF alpha mRNAs in THP-1 cells. Nuclear run-on assay for IL-1 beta demonstrated that LAM increased the transcription rate. The induction of IL-1 beta was regulated at the transcriptional level, in which these stimuli acted through cis-acting element(s) on the 5' flanking region of the IL-1 beta genomic DNA. M. tuberculosis cell wall component LAM acts similarly to LPS in activating mononuclear phagocyte cytokine TNF alpha and IL-1 beta release through CD14 and synthesis at the transcriptional level; both cytokines are key participants in the host immune response to tuberculosis.
<title>Diagnosis of subdural and intraparenchymal intracranial hemorrhage using a microwave-based detector</title> (2000)

A novel method for identifying and localizing brain hemorrhage is presented. The method uses electromagnetic waves in the microwave and RF region and a modified algorithm previously used for the estimation of the angle of arrival of radar signals. Results are presented applying this device for detecting subdural and intraparenchymal hemorrhages in anesthetized pig.
An infectious recombinant equine arteritis virus expressing green fluorescent protein from its replicase gene (2007)

Thus far, systems developed for heterologous gene expression from the genomes of nidoviruses (arteriviruses and coronaviruses) have relied mainly on the translation of foreign genes from subgenomic mRNAs, whose synthesis is a key feature of the nidovirus life cycle. In general, such expression vectors often suffered from relatively low and unpredictable expression levels, as well as genome instability. In an attempt to circumvent these disadvantages, the possibility to express a foreign gene [encoding enhanced green fluorescent protein (eGFP)] from within the nidovirus replicase gene, which encodes two large polyproteins that are processed proteolytically into the non-structural proteins (nsps) required for viral RNA synthesis, has now been explored. A viable recombinant of the arterivirus Equine arteritis virus, EAV-GFP2, was obtained, which contained the eGFP insert at the site specifying the junction between the two most N-proximal replicase-cleavage products, nsp1 and nsp2. EAV-GFP2 replication could be launched by transfection of cells with either in vitro-generated RNA transcripts or a DNA launch plasmid. EAV-GFP2 displayed growth characteristics similar to those of the wild-type virus and was found to maintain the insert stably for at least eight passages. It is proposed that EAV-GFP2 has potential for arterivirus vector development and as a tool in inhibitor screening. It can also be used for fundamental studies into EAV replication, which was illustrated by the fact that the eGFP signal of EAV-GFP2, which largely originated from an eGFP-nsp2 fusion protein, could be used to monitor the formation of the membrane-bound EAV replication complex in real time.
Increased oxidative damage in nuclear and mitochondrial DNA in Alzheimer's disease (2005)

Increasing evidence suggests that oxidative stress is associated with normal aging and several neurodegenerative diseases, including Alzheimer's disease (AD). Here we quantified multiple oxidized bases in nuclear and mitochondrial DNA of frontal, parietal, and temporal lobes and cerebellum from short postmortem interval AD brain and age-matched control subjects using gas chromatography/mass spectrometry with selective ion monitoring (GC/MS-SIM) and stable labeled internal standards. Nuclear and mitochondrial DNA were extracted from eight AD and eight age-matched control subjects. We found that levels of multiple oxidized bases in AD brain specimens were significantly (p < 0.05) higher in frontal, parietal, and temporal lobes compared to control subjects and that mitochondrial DNA had approximately 10-fold higher levels of oxidized bases than nuclear DNA. These data are consistent with higher levels of oxidative stress in mitochondria. Eight-hydroxyguanine, a widely studied biomarker of DNA damage, was approximately 10-fold higher than other oxidized base adducts in both AD and control subjects. DNA from temporal lobe showed the most oxidative damage, whereas cerebellum was only slightly affected in AD brains. These results suggest that oxidative damage to mitochondrial DNA may contribute to the neurodegeneration of AD.
Mismatch-targeted transposition of Mu: A new strategy to map genetic polymorphism (2002)

Phage Mu DNA transposes to duplex target DNA sites with limited sequence specificity. Here we demonstrate that Mu transposition exhibits a strong target site preference for all single-nucleotide mismatches. This finding has implications for the mechanism of transposition and provides a powerful tool for genomic research. A single mismatch could be detected as a preferred target of Mu transposition in the presence of 300,000-fold excess of nonmismatched sites. We demonstrate the detection of both heterozygous and homozygous mutations in the cystic fibrosis transmembrane conductance regulator gene and single nucleotide polymorphism in HLA region by Mu transposition mismatch analysis procedure.
Performance of the COBAS AMPLICOR HCV MONITOR Test, Version 2.0, an Automated Reverse Transcription-PCR Quantitative System for Hepatitis C Virus Load Determination (2000)

A clinical evaluation of an automated quantitative PCR assay, the COBAS AMPLICOR HCV MONITOR test, version 2.0 (v2.0), was carried out to assess the performance of this test in comparison with that of the previous, manual version, the AMPLICOR HCV MONITOR test, and with that of nested PCR. Serial dilutions of serum samples infected with genotype 1b, 2a, or 3, as well as synthetic RNA transcripts and serum samples derived from 87 patients with chronic hepatitis C and infected with genotype 1a, 1b, 2a, 2b, 3a, 3b, 4, or 5, were analyzed to determine the ability of the system to efficiently quantify various hepatitis C virus (HCV) genotypes. These experiments showed that the COBAS AMPLICOR HCV MONITOR test, v2.0, has mean intra-assay, interassay, and interoperator coefficients of variation that range from 22 to 34.5% and a 3-logarithm dynamic range, which spans from 10(3) to 10(6) copies/ml. Compared to the previous, manual version of the test, the COBAS AMPLICOR HCV MONITOR test, v2.0, showed an improved efficacy for all genotypes, especially genotypes 2, 3, and 4, whose estimated concentrations were on average 1 logarithm higher. When used to monitor patients under treatment, however, both versions showed the same patterns of viremia, indicating that the COBAS AMPLICOR HCV MONITOR test, v2.0, and the AMPLICOR HCV MONITOR test were equally effective at detecting relative viremia changes in serial samples. As expected, the automated test was less sensitive than nested PCR; among specimens from a cohort of patients treated with interferon, nested PCR identified three more viremic specimens, which probably contained very low concentrations of HCV RNA.
CubifAE-3D: Monocular Camera Space Cubification on Autonomous Vehicles for Auto-Encoder based 3D Object Detection (2020)

We introduce a method for 3D object detection using a single monocular image. Depth data is used to pre-train an RGB-to-Depth Auto-Encoder (AE). The embedding learnt from this AE is then used to train a 3D Object Detector (3DOD) CNN which is used to regress the parameters of 3D object poses after the encoder from the AE generates a latent embedding from the RGB image. We show that we can pre-train the AE using paired RGB and depth images from simulation data once and subsequently only train the 3DOD network using real data, comprising of RGB images and 3D object pose labels (without the requirement of dense depth). Our 3DOD network utilizes a particular $cubification$ of 3D space around the camera, where each cuboid is tasked with predicting N object poses, along with their class and confidence values. The AE pre-training and this method of dividing the 3D space around the camera into cuboids give our method its name - CubifAE-3D. We demonstrate results for monocular 3D object detection on the Virtual KITTI 2, KITTI, and nuScenes datasets for Autnomous Vehicle (AV) perception.
Chemotherapy: induction of stress responses (2006)

Eukaryotic cells, from yeast to mammals, respond and adapt to environmental and microenvironmental stressors by evolutionary conserved multicomponent endogenous systems that utilise a network of signal transduction pathways to regulate the adaptive and protective phenotype. The balance between cell survival and cell death is decisive for sensitivity or resistance to DNA-damaging chemotherapeutic agents. Anticancer drugs may themselves act as stressors to induce adaptive signals that could limit their clinical value. Related research has been focused on the modulation of the expression and function of the heat shock proteins, the unfolded protein response, the mechanisms of subcellular translocation of signalling components, the genomic and non-genomic actions of drugs and endogenous functional components like hormonal pathways, the input of inflammation and alterations in the microenvironmental milieu and on the control of the cell cycle and proliferation. The outcome seems to be driven by the first-line responses that support cellular integrity and by specific mechanisms that depend on the type of cell and the nature, and duration and severity of the noxious stimulus. Data obtained from experimental organisms like the yeast have added valuable information on the basic conservation in cellular stress-related processes in eukaryotes and on the consequences that may accompany the adaptive and protective phenotype during the stress response to anticancer agents. Understanding the complex molecular pathways mediating these processes has started to contribute to the reevaluation of the current therapeutic regiments and to revolutionise the approaches for improved anticancer therapy.
Behavior of Polyethylene Oxide Based Nonionic Surfactants in Silicon Processing Using Alkaline Solutions (1995)

The adsorption of polyethylene oxide (PEO) based nonionic surfactants onto hydrophobic silicon from an alkaline solution was investigated using an in situ attenuated total reflection Fourier transform infrared spectroscopy technique. The adsorption/desorption profiles of surfactants were affected by the type and length of the hydrophobic group and the lengths of hydrophilic PEO chains. Complete wetting of hydrophobic silicon was measured at surfactant concentrations in the range of 50 to 200 ppm. Surfactant adsorption was controlled by hydrophobic attractions between the hydrophobic moiety of surfactant and the silicon surface. The addition of surfactant to alkaline solutions dramatically reduced the etch rate of silicon and resulted in a smoother silicon surface. Oxidizing treatments followed by buffered oxide etching (BOE) were effective in the complete removal of adsorbed surfactant.
GABA as an inhibitory neurotransmitter in human cerebral cortex (1989)

1. The possible role of gamma-aminobutyric acid (GABA) as an inhibitory neurotransmitter in the human cerebral cortex was investigated with the use of intracellular recordings from neocortical slices maintained in vitro. 2. Electrical stimulation of afferents to presumed pyramidal cells resulted in an initial excitatory postsynaptic potential (EPSP) followed by fast and slow inhibitory postsynaptic potentials (IPSPs). The early IPSP had an average reversal potential of -68 mV, was associated with a mean 67-nS increase in membrane conductance, was reduced by the GABAA antagonist bicuculline, was sensitive to the intracellular injection of Cl-, and was mimicked by the GABAA agonist muscimol. 3. The late IPSP, in contrast, had an average reversal potential of -95 mV, was associated with a mean 12-nS increase in membrane conductance, was reduced by the GABAB antagonist phaclofen, and was mimicked by the GABAB agonist baclofen. 4. Block of the early IPSP by bicuculline or picrotoxin led to the generation of paroxysmal epileptiform activity, which could be further enhanced by reduction of the late IPSP. 5. These data strongly support the hypothesis that GABA is a major inhibitory neurotransmitter in the human cerebral cortex and that GABAergic IPSPs play an important role in controlling the excitability and responsiveness of cortical neurons.
A video-based rendering acceleration algorithm for interactive walkthroughs (2000)

We present a new approach for faster rendering of large synthetic environments using video-based representations. We decompose the large environment into cells and pre-compute video based impostors using MPEG compression to represent sets of objects that are far from each cell. At runtime, we decode the MPEG streams and use rendering algorithms that provide nearly constant-time random access to any frame. The resulting system has been implemented and used for an interactive walkthrough of a model of a house with 260,000 polygons and realistic lighting and textures. It is able to render this model at 16 frames per second (an eightfold improvement over simpler algorithms) on average on a Pentium II PC with an off-the-shelf graphics card.
The use of twin screw extruders for feeding coal against pressures of up to 1500 PSI (1977)

Recent tests with a twin-screw, co-rotating extruder which was successfully used to convey and feed coal against pressures of up to 1500 psi are described. Intermeshing and self-wiping, co-rotating twin-screws give greatly improved conveying and pressure built-up capabilities and avoid hangup and eventual decomposition of coal particles in the screw flights. The conveying action of intermeshing, self-wiping, co-rotating extruder systems approaches that of a positive displacement pump. With this feature, it is possible to maintain very accurate control over all aspects of product conveyance in the extruder, i.e., intake, conveyance and pressure buildup.
Quantitative and Qualitative Evaluation of Geometric Deconvolution of Distortion in Limited-View Computed Tomography (1985)

Images reconstructed using a set of a few projections spanning a narrow angular range suffer from a systematic geometric distortion due to the point spread function of the reconstruction process. This distortion can be removed by deconvolving a complementary set of projections calculated from the initial reconstruction. Homomorphic deconvolution and inverse filtering techniques were used for this purpose. A second reconstruction is computed from the union of both sets of projections. Although the distortion is removed, the results are noisy due to problems associated with inverse filtering. Two-dimensional (2-D) filtering of the second reconstruction is performed to reduce the noise, while preserving the reduction in geometric distortion. Results obtained using several 2-D filters were compared visually and by point noise content, distortion, and projection error measures. Quantitative measures of geometric distortion removal for test images are also described.