gebhart/patrepeval huggingface dataset:
Selection of Test Chemicals for the ECVAM International Validation Study on <i>In Vitro</i> Embryotoxicity Tests (2002)

The European Centre for the Validation of Alternative Methods (ECVAM) has sponsored a large international prevalidation and validation study of three embryotoxicity tests, involving embryonic stem cells, limb bud micromass cultures, and post-implantation whole-embryo cultures. The main objective of the study was to assess the performance of these in vitro tests in discriminating between non-embryotoxic, weakly embryotoxic and strongly embryotoxic compounds. An initial part of the study was to select 20 test substances for the formal validation trial, conducted under blind conditions. A database of in vivo and in vitro developmental toxicity test results was complied on 310 chemicals that had been used in previous validation studies, or suggested for such use, or that had good quality "segment II"-type in vivo data, or for which there were human data. From this database, a shortlist of about 30 candidates was constructed. Because the ECVAM study would not include metabolic activation, chemicals known to require activation for their developmental effects were excluded as candidates, although some known stable metabolites were included. Attempts were made: to include substances of diverse mechanism; to avoid overemphasis on pharmaceuticals; to avoid biologically inert substances as non-embryotoxicants; and to make the list different from those used previously. The candidates were of three categories: Class 3, strongly embryotoxic, was defined as developmentally toxic in all species tested, inducing multiple developmental effects, and with a high A/D ratio. Class 1, non-embryotoxic, was defined as not developmentally toxic at maternally toxic exposures, but which may show some minor embryo/fetal toxicity, which cannot be separated from maternal toxicity. Class 2, weakly embryotoxic, were chemicals of intermediate activity. From this candidate list, chemicals of known receptor (androgen, oestrogen, glucocorticoid, aryl hydrocarbon) mechanisms were excluded, on the basis that simple tests for such activity are already available. In addition, chemicals not freely available were excluded, and an emphasis on human data was applied. The final list of 20 chemicals was: Class 3--6-aminonicotinamide, 5-bromo- 2'-deoxyuridine, hydroxyurea, methylmercury chloride, methotrexate, all-trans-retinoic acid; Class 2--boric acid, dimethadione, lithium chloride, methoxyacetic acid, valproic acid (VPA), 2-propyl-4-pentynoic acid (4-yn-VPA), salicylic acid sodium salt; and Class 1--acrylamide, D-(+)-camphor, dimethyl phthalate, diphenhydramine hydrochloride, 2-ethyl-4- methylpentanoic acid (isobutyl-ethyl-VPA), Penicillin G sodium salt, saccharin sodium hydrate.
'As if this were Narnia or somewhere': What's Real(ly) Fantasy? An Exploration of John Marsden's Tomorrow, When the War Began and Isobelle Carmody's Greylands (1998)

See article
The Antibacterial Activity of Fragrance Ingredients against Legionella pneumophila (2009)

In the current study we investigated the antibacterial activity of fragrance ingredients against Legionella pneumophila, a causative agent of severe pneumonia. Among the 41 different fragrance ingredients tested, we found that the natural fragrance ingredients oakmoss (OM) and birch tar oil (BT), which contain many components, exhibit potent antibacterial activity. The minimum inhibitory concentration (MIC, % (v/v)) of OM and BT were 0.0020 and 0.0024, respectively and were lower than that of cinnamic aldehyde (0.0078), which has been previously shown to possess high antimicrobial activity. In a time-kill assay of OM and BT at MIC and two times MIC, the colony forming units (CFU) of the microbe were reduced to between 10(-3) to 10(-4) of the original CFU after 1 h co-incubation. After this time, the CFU gradually decreased in number, but remained above detection levels even after a 48-h co-incubation, except for BT at two times MIC. In contrast, at a concentration of 0.1% OM and BT (approximately 50 times MIC), CFU were not detected after co-incubation for 1 h. Another 18 fragrance ingredients including ketone, aldehyde, lactone, acid, phenol derivative, aliphatic alcohol and quinoline also exhibited a lesser degree of antibacterial activity against L. pneumophila at a MIC of less than 0.10.
Abstract 4877: High throughput proteomic applications using protein A/G magnetic beads (2011)

Abstract Speed and sample purity are key issues for proteomics researchers. Sample and data-processing throughputs are current bottlenecks in proteomic analysis. Magnetic separations can provide greater consistency and automation of proteomic sample preparation. We report here the development of a novel 1µm protein A/G magnetic bead that enables fast and convenient isolation of proteins via immunoenrichment. Thermo Scientific Pierce Protein A/G Magnetic Beads use a recombinant protein A/G that combines the IgG binding domains of both protein A and protein G. Protein A/G contains four Fc-binding domains from protein A and two from protein G, making it a convenient tool for capture of immunoglobulins from a variety of species and isotypes. Recombinant protein A/G was covalently coupled to 1 μm, blocked double-shelled magnetic particles with a polymeric core. The beads had a binding capacity of &gt;60 μg rabbit IgG per mg bead along with low non-specific binding. Using a Thermo Scientific KingFisher Flex Magnetic Particle Processor, antibodies were purified from serum or ascites with high yield using the Pierce Protein A/G Magnetic Beads. The beads were also used to immunoprecipitate and co-immunoprecipitate multiple proteins significant to different phases of the cell cycle, including cyclin B, Cdk1, cyclin E, and cyclin D. U2OS and HeLa cell lines were first synchronized in serum starved media. The media was replaced with enriched media and cells were harvested at 4 hours (beginning of G1 phase), 6 hours (end of G1 phase), and 18 hours (end of G2 phase). Proteins were effectively isolated from the cell lysates using Pierce Protein A/G Magnetic Beads and identified by Western blot. In addition, these beads were successfully used in a chromatin-immunoprecipitation (ChIP) assay to measure binding of RNA Polymerase II to the proximal myc promoter in A431 lung carcinoma cells treated with and without EGF. In Conclusion, the results indicate that Pierce Protein A/G Magnetic Beads can effectively isolate protein targets in a variety of proteomic applications. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4877. doi:10.1158/1538-7445.AM2011-4877
A Robust Lane Detection Method Based on Vanishing Point Estimation (2018)

Although lane detection technology has been developed for decades, however, many challenging issues remain unresolved. In this paper, we propose a robust vanishing point-based lane detection method. Due to the perspective effect, the two parallel straight lines in 3-D space intersect at the 2-D plane. For the lane line extraction, we use lane shape features to extract lane lines. Firstly, we use LSD (line segment detectors) to extract the straight line segments in each frame of image. Secondly, we use a direction priority search method to remove the most of the interference information. This algorithm makes reference to the directional and shape features of lane lines in 2-D images. Finally, using the remaining straight line segments after filtering out the noise straight line to calculate the vanishing point of the lane line, we use a score function to remove non-candidate lane markings, the score function is constructed using the shape features, direction of the line segments. The experimental results show that the validity and robustness of our new algorithm under complex structured road scenes.
Improving non-linear approaches to anomaly detection, class separation, and visualization (2014)

Linear approaches for multivariate data analysis are popular due to their lower complexity, reduced computational time, and easier interpretation. In many cases, linear approaches produce adequate results; however, non-linear methods may generate more robust transformations, features, and decision boundaries. Of course, these non-linear methods present their own unique challenges that often inhibit their use. In this research, improvements to existing non-linear techniques are investigated for the purposes of providing better, timely class separation and improved anomaly detection on various multivariate datasets, culminating in application to anomaly detection in hyperspectral imagery. Primarily, kernel-based methods are investigated, with some consideration towards other methods. Improvements to existing linear-based algorithms are also explored. Here, it is assumed that classes in the data have minimal overlap in the originating space or can be made to have minimal overlap in a transformed space, and that class information is unknown a priori. Further, improvements are demonstrated for global anomaly detection on a variety of hyperspectral imagery, utilizing fusion of spatial and spectral information, factor analysis, clustering, and screening. Additionally, new approaches for n-dimensional visualization of data and decision boundaries are developed.
Stabilizing a 46 MW Multistage Utility Steam Turbine Using Integral Squeeze Film Bearing Support Dampers (2014)

A 46 MW 5500 rpm multistage single casing utility steam turbine experienced strong subsynchronous rotordynamic vibration of the first rotor mode; preventing full load operation of the unit. The root cause of the vibration stemmed from steam whirl forces generated at secondary sealing locations in combination with a flexible rotor-bearing system. Several attempts were made to eliminate the subsynchronous vibration by modifying bearing geometry and clearances, which came short of enabling full load operation. The following paper presents experimental tests and analytical results focused on stabilizing a 46 MW 6230 kg utility steam turbine experiencing subsynchronous rotordynamic instability. The paper advances an integral squeeze film damper (ISFD) solution, which was implemented to resolve the subsynchronous vibration and allow full load and full speed operation of the machine. The present work addresses the bearing-damper analysis, rotordynamic analysis, and experimental validation through waterfall plots, and synchronous vibration data of the steam turbine rotor. Analytical and experimental results show that using ISFD improved the stability margin by a factor of 12 eliminating the subsynchronous instability and significantly reducing critical speed amplification factors. Additionally, by using ISFD the analysis showed significant reduction in interstage clearance closures during critical speed transitions in comparison to the hard mounted tilting pad bearing configuration.
Hyperspectral image compressive projection algorithm (2009)

We describe a compressive projection algorithm and experimentally assess its performance when used with a Hyperspectral Image Projector (HIP). The HIP is being developed by NIST for system-level performance testing of hyperspectral and multispectral imagers. It projects a two-dimensional image into the unit under test (UUT), whereby each pixel can have an independently programmable arbitrary spectrum. To efficiently project a single frame of dynamic realistic hyperspectral imagery through the collimator into the UUT, a compression algorithm has been developed whereby the series of abundance images and corresponding endmember spectra that comprise the image cube of that frame are first computed using an automated endmember-finding algorithm such as the Sequential Maximum Angle Convex Cone (SMACC) endmember model. Then these endmember spectra are projected sequentially on the HIP spectral engine in sync with the projection of the abundance images on the HIP spatial engine, during the singleframe exposure time of the UUT. The integrated spatial image captured by the UUT is the endmember-weighted sum of the abundance images, which results in the formation of a datacube for that frame. Compressive projection enables a much smaller set of broadband spectra to be projected than monochromatic projection, and thus utilizes the inherent multiplex advantage of the HIP spectral engine. As a result, radiometric brightness and projection frame rate are enhanced. In this paper, we use a visible breadboard HIP to experimentally assess the compressive projection algorithm performance.
The impact of FLT3 internal tandem duplication mutant level, number, size, and interaction with NPM1 mutations in a large cohort of young adult patients with acute myeloid leukemia (2007)

An internal tandem duplication in the fms-like tyrosine kinase 3 gene (FLT3/ITD) is associated with poor prognosis in acute myeloid leukemia (AML), but the impact of mutant level, size, and interaction with nucleophosmin 1 (NPM1) mutations remains controversial. We evaluated these characteristics in a large cohort of young adult AML patients. There was a highly significant trend for worsening in relapse risk (RR) and overall survival (OS) with increasing FLT3/ITD mutant level (P < .001 for both), and even in the low level mutant group (1%-24% of total FLT3 alleles), RR was significantly worse than in the FLT3 wild-type (WT) group (P < .001). In multivariate analysis, mutant level was the most powerful prognostic factor for RR. Mutant size and number had no significant impact on outcome. The beneficial impact of an NPM1 mutation on RR and OS was seen in FLT3/ITD(+) as well as FLT3/WT patients; both markers were highly significant independent predictors of outcome (P < .001). Stratification using both markers identified 3 prognostic groups: good (FLT3/ITD(-)NPM1(+)), intermediate (FLT3/ITD(-)NPM1(-) or FLT3/ITD(+)NPM1(+)), and poor (FLT3/ITD(+)NPM1(-)). Patients with high FLT3/ITD mutant level (greater than 50%) or FLT3/ITD(+) in the absence of an NPM1 mutation may be good candidates for more experimental therapeutic approaches.
Immuno-PET Imaging of <sup>89</sup>Zr Labeled Anti-PD-L1 Domain Antibody (2018)

Recently, various immuno-PET tracers based on monoclonal antibodies (mAbs), engineered scaffold proteins, and peptides were developed to target either programmed cell death protein 1 (PD-1) or programmed cell death ligand 1 (PD-L1), showing promise in assessment of immune checkpoints. We sought to develop an immunotherapeutic agent based PET probe that enables real-time assessment of PD-L1 expression and evaluation of antibody drug biodistribution to select eligible candidates for anti-PD-1/PD-L1 immunotherapies. KN035, a 79.6 kDa size anti-PD-L1 domain antibody under analysis in clinical trials, was used to develop the immuno-PET probe, <sup>89</sup>Zr-Df-KN035. Immuno-PET studies were performed to monitor PD-L1 levels in nude mice bearing LN229 xenografts with positive expression for PD-L1, and to evaluate the whole-body biodistribution in healthy non-human primates (NHPs). LN229 xenografts were markedly visualized from 24 h after injection of <sup>89</sup>Zr-Df-KN035, with elevated accumulation persisting for up to 120 h. Tumor radioactivity was notably reduced in the presence of excess KN035. Mouse ex vivo biodistribution studies performed at 24 and 120 h revealed tumor-to-muscle ratios as high as 5.64 ± 0.65 and 7.70 ± 1.37, respectively. In the NHP model, PET imaging demonstrated low background. The liver and kidney showed moderate accumulation with the highest SUV<sub>mean</sub> value of 1.15 ± 0.15 and 2.13 ± 0.10 at 72 h, respectively. The spleen, lymph nodes, and salivary glands were also slightly visualized. In conclusion, <sup>89</sup>Zr-Df-KN035, a novel anti-PD-L1 domain antibody-based probe, shows the feasibility of noninvasive in vivo evaluation of PD-L1 expression. This work further provides a template for immunotherapeutic agent based imaging to evaluate human PD-L1 expression and to augment our understanding of therapeutic agent biodistribution, leading to better therapeutic strategies in the future.
Regulation of microRNA processing in development, differentiation and cancer (2008)

microRNA (miRNA) is a class of small, noncoding, regulatory RNAs. The approximately 21 nt mature miRNA is processed from larger precursor molecules following a coordinated series of events. In theory, miRNA processing may be regulated at any of these steps. A growing body of evidence has demonstrated various steps in the miRNA biogenesis process for which regulation occurs. RNA editing of miRNA precursors, SNPs or mutations in the miRNA precursors, regulation by RNA binding proteins, alterations in the levels of key processing proteins, as well as a number of unknown mechanisms contribute to the regulation of miRNA processing. This article reviews the available literature on the regulation of miRNA processing that occurs within normal cells, during development or in diseases such as cancer.
Sex differences in regional distribution of fat cell size and lipoprotein lipase activity in morbidly obese patients. (1987)

Adipose tissue distribution is an important predictor of obesity-associated morbidity and mortality. A central ('male') fat distribution is associated with increases in intra-abdominal adipose tissue which might be of metabolic importance. Although many recent studies have pointed out significant regional differences in the size and metabolism of subcutaneous fat cells intra-abdominal depots have not been systematically examined. We compared fat cell sizes (FCS) and lipoprotein lipase activity (LPLA) of two internal (omental, mesenteric) and four subcutaneous (SQ) sites (femoral, gluteal, abdominal, epigastric) in morbidly obese patients (26 premenopausal women and 14 men). Men had larger internal FCS than women while women had larger SQ FCS in the gluteal and femoral depots. Mesenteric FCS were largest of all sites in men. In women, omental fat cells were the smallest of all sites sampled but omental fat cells were as large as SQ sites in men. A more central distribution of fat in women (high waist/hip ratio) was associated with large mesenteric fat cells. Calculation of total fat cell number based on SQ FCS only, revealed sex differences that were eliminated by also using intra-abdominal FCS in the calculation. Averaged across all six sites, women had higher LPLA than men. Higher LPL activities were found in the lower-body subcutaneous sites with enlarged fat cells in women. However, the relative enlargement of intra-abdominal FCS in men was not associated with increased LPLA. In conclusion, sex- and site-specific variations in the distribution of FCS and LPLA in internal and SQ fat depots emphasize the importance of analyzing these depots in studies of fat cell number and adipose tissue metabolism.
Antitumor-Active Cobalt−Alkyne Complexes Derived from Acetylsalicylic Acid:  Studies on the Mode of Drug Action (2004)

Cobalt−alkyne complexes are drugs with remarkable cytotoxicity. From the complexes tested up to now we selected the aspirin derivative [2-acetoxy-(2-propynyl)benzoate]hexacarbonyldicobalt (Co-ASS) as the lead compound. To get more insight into the mode of action, we systematically modified the alkyne ligand and determined the cytotoxic properties of the resulting cobalt complexes. Further investigations were performed on the drug lipophilicity, the cellular uptake into MCF-7 and MDA-MB 231 breast cancer cells, the DNA-binding efficacy, and the nuclear drug content. The ability to inhibit glutathione reductase and cyclooxygenase (COX) enzymes, the binding to the estrogen receptor, and the induction of apoptotic processes were examined for selected compounds. Interestingly, the most antitumor active compounds were potent COX inhibitors (COX-1 and COX-2). The presented results indicate that cobalt−alkyne complexes of the Co-ASS type, represent a new class of organometallic cytostatics with a mode of drug action in which COX inhibition probably plays a major role.
Low-loss transmission through tightly bent standard telecommunication fibers (2000)

This letter presents a principle of low-loss light transmission through tightly bent standard telecommunication optical fibers. The design is based on selective launching and filtering of the fundamental mode in standard graded index multimode fiber. The proposed system has demonstrated significantly better macrobend tolerance than commercially available bend resistant fibers.
Inversion of DTS Logs To Measure Zonal Coverage During and After Wellbore Treatments With Coiled Tubing (2011)

Abstract Distributed temperature sensing (DTS) is a fiber-optic technology that provides continuous temperature profiles along the length of a well. When placing the fiber inside a coiled tubing (CT), one can monitor the temperature evolution while pumping, as well as during a shut-in period. This evolution, in turn, yields some indications about the fluid placement performance or zonal coverage. So far, interpretation of such DTS traces has mostly been qualitative. The work presented here demonstrates how DTS data can be used, coupled with an inversion algorithm and a forward model of fluid injection into a reservoir, to quantify the intake profile of treatment fluid along the wellbore. Recent field cases of matrix acidizing treatments in carbonate reservoirs are analyzed to illustrate the workflow and how it may yield valuable information.
MAPK and heat shock protein 27 activation are associated with respiratory syncytial virus induction of human bronchial epithelial monolayer disruption (2007)

Respiratory syncytial virus (RSV) is the major cause of bronchiolitis in infants, and a common feature of RSV infections is increased lung permeability. The accumulation of fluid in the infected lungs is caused by changes in the endothelial and epithelial membrane integrity. However, the exact mechanisms of viral-induced fluid extravasation remain unclear. Here, we report that infection of human epithelial cells with RSV results in significant epithelial membrane barrier disruption as assessed by a decrease in transepithelial electrical resistance (TEpR). This decrease in TEpR, which indicates changes in paracellular permeability, was mediated by marked cellular cytoskeletal rearrangement. Importantly, the decrease in TEpR was attenuated by using p38 MAPK inhibitors (SB-203580) but was partially affected by JNK inhibitor SP-600125. Interestingly, treatment of A549 cells with MEK1/2 inhibitor (U-0126) led to a decrease in TEpR in the absence of RSV infection. The changes in TEpR were concomitant with an increase in heat shock protein 27 (Hsp27) phosphorylation and with actin microfilament rearrangement. Thus our data suggest that p38 MAPK and Hsp27 are required for RSV induction of human epithelial membrane permeability.
Comorbidity of Anxiety and Depression (1990)

Many factors obscure the diagnosis of psychogenic disorders, especially anxiety and depression. The factors involved include an overlap of symptoms, discrepancies in diagnostic criteria, and the unreliability of self- and observer-reporting. Differentiation among the various personality disorders is, however, extremely important, both for identifying the most appropriate treatment plan for a given patient and for evaluating the therapeutic activity of newly developed pharmacologic agents. Emerging factors that may have an impact on differential diagnoses of anxiety and depression include age at onset, family history, and personality traits associated with different types of psychopathology.
Can Epinephrine Inhalations Be Substituted for Epinephrine Injection in Children at Risk for Systemic Anaphylaxis? (2000)

Despite expert coaching, because of the number of epinephrine inhalations required and the bad taste of the inhalations, most children were unable to inhale sufficient epinephrine to increase their plasma epinephrine concentrations promptly and significantly. Therefore, we urge caution in recommending epinephrine inhalation as a substitute for epinephrine injection for out-of-hospital treatment of anaphylaxis symptoms in children.