gebhart/patrepeval huggingface dataset:
Use of Doubling Number as an Arithmetic Measure of Plant Cell Growth and Metal-Induced Cell Growth Inhibition (2023)

Cell growth inhibition is generally handled as a measure of toxicity. Shortly, more toxicity implies more growth inhibition. Then, the question arises; How to calculate &amp;amp; evaluate cell growth inhibition in a universal manner? Actually, the method for calculating growth inhibition is not considered to be a central issue, in general. There are various approaches (subtractive, divisionary, and logarithmic) for calculating cell growth. Among these approaches, two of them are highly easy and popular, subtraction-based and division-based calculations. However, these two methods for the calculation of cell growth do not strongly reflect the nature of cell growth. Alternatively, the use of a doubling number-based formulation can provide a better approach and performance in the evaluation of cell growth and cell growth inhibition unless the culture attains the confluent status. Here, we discussed different methods of growth calculation which we applied to the study of “growth inhibition of BY-2 cells under Cd exposure”.
Gas Hydrate Markup Language: Laboratory Data (2007)

Laboratory Hydrate Data is one of the three constituent modules comprising the XML based Gas Hydrate Markup Language (a.k.a. GHML) schema, the others being Field Hydrate data by L&amp;oumul;wner et al. and Hydrate Modeling by Wang et al. This module describes the characteristics of natural and synthetic gas hydrates as they pertain to data acquired via analysis within a laboratory environment. Such data include the preservation history (i.e.: technique, pressurization gas and pressure, etc), Macroscopic data (i.e.: water-sediment ratio, appearance, P-T behavior, etc) as well as that of the Microscopic realm.
Aging and the encoding of event changes: The role of neural activity pattern reinstatement (2019)

Abstract When encountering unexpected event changes, memories of relevant past experiences must be updated to form new representations. Current models of memory updating propose that people must first generate memory-based predictions to detect and register that features of the environment have changed, then encode the new event features and integrate them with relevant memories of past experiences to form configural memory representations. Each of these steps may be impaired in older adults. Using functional MRI, we investigated these mechanisms in healthy young and older adults. In the scanner, participants first watched a movie depicting everyday activities in a day of an actor’s life. They next watched a second nearly identical movie in which some scenes ended differently. Crucially, before watching the last part of each activity, the second movie stopped, and participants were asked to mentally replay how the activity previously ended. Three days later, participants were asked to recall the activities. Neural activity pattern reinstatement in medial temporal lobe (MTL) during the replay phase of the second movie was associated with detecting changes and with better memory for the original activity features. Reinstatements in posterior medial cortex (PMC) additionally predicted better memory for changed features. Compared to young adults, older adults showed a reduced ability to detect and remember changes, and weaker associations between reinstatement and memory performance. These findings suggest that PMC and MTL contribute to change processing by reinstating previous event features, and that older adults are less able to use reinstatement to update memory for changed features.
Bile acids decrease intracellular bilirubin levels in the cholestatic liver: implications for bile acid-mediated oxidative stress (2010)

High plasma concentrations of bile acids (BA) and bilirubin are hallmarks of cholestasis. BA are implicated in the pathogenesis of cholestatic liver damage through mechanisms involving oxidative stress, whereas bilirubin is a strong antioxidant. We evaluated the roles of bilirubin and BA on mediating oxidative stress in rats following bile duct ligation (BDL). Adult female Wistar and Gunn rats intraperitoneally anaesthetized with ketamine and xylazine underwent BDL or sham operation. Cholestatic markers, antioxidant capacity, lipid peroxidation and heme oxygenase (HO) activity were determined in plasma and/or liver tissue 5 days after surgery. HepG2-rNtcp cells were used for in vitro experiments. Plasma bilirubin levels in control and BDL animals positively correlated with plasma antioxidant capacity. Peroxyl radical scavenging capacity was significantly higher in the plasma of BDL Wistar rats (210 ± 12%, P < 0.0001) compared to controls, but not in the liver tissues. Furthermore after BDL, lipid peroxidation in the livers increased (179 ± 37%, P < 0.01), whereas liver HO activity significantly decreased to 61% of control levels (P < 0.001). Addition of taurocholic acid (TCA, ≥ 50 μmol/l) to liver homogenates increased lipid peroxidation (P < 0.01) in Wistar, but not in Gunn rats or after the addition of bilirubin. In HepG2-rNtcp cells, TCA decreased both HO activity and intracellular bilirubin levels. We conclude that even though plasma bilirubin is a marker of cholestasis and hepatocyte dysfunction, it is also an endogenous antioxidant, which may counteract the pro-oxidative effects of BA in circulation. However, in an animal model of obstructive cholestasis, we found that BA compromise intracellular bilirubin levels making hepatocytes more susceptible to oxidative damage.
A Study of Jets From Unsintered-Powder Metal Lined Nonprecision Small-Caliber Shaped Charges (2001)

Abstract : The U.S. Army Research Laboratory (ARL) obtained a sample of powder metal-lined nonprecision shaped charges from Halliburton Energy Services located in Alvarado, TX. These shaped charges, designated as the 4 5/8-in PM OMNI, are designed and manufactured for use as oil-well or gas-well perforators. The agreement with Halliburton Energy Services involved a complete study of these rounds. They were being investigated as a potential shaped charge to be used in the controlled detonation, containment, and decontamination of chemical munitions by the U.S. Army Garrison Directorate of Safety, Health, and the Environment (DSHE) at Aberdeen Proving Ground (APO). ARL is interested in charges of this type due to their design for optimum performance at short standoff, the short charge length and head height, the fact that the charges are inexpensive, and their potential application as precursor charges against specialized targets. The authors also have an interest in modeling the penetration of a powder-metal jet. Thus, the penetration standoff data will provide experimental data to verify a penetration model. This study is the subject of this report.
Response Characteristics of Bisphenols on a Metal–Organic Framework-Based Tyrosinase Nanosensor (2016)

Bisphenols (BPs), which have more than ten kinds of structural analogues, are emerging as the most important endocrine disrupting chemicals that adversely affect human health and aquatic life. A tyrosinase nanosensor based on metal-organic frameworks (MOFs) and chitosan was developed to investigate the electrochemical response characteristics and mechanisms of nine kinds of BPs for the first time. The developed tyrosinase nanosensor showed a sensitive response to bisphenol A, bisphenol F, bisphenol E, bisphenol B, and bisphenol Z, and the responsive sensitivities were highly dependent on their respective log Kow values. However, the nanosensor showed no response to bisphenol S (BPS), bisphenol AP (BPAP), bisphenol AF (BPAF), or tetrabromobisphenol A, although BPS, BPAP, and BPAF have structures similar to those of the responsive BPs. The obtained results reveal that the electrochemical response of different BPs is affected not only by the molecular structure, especially the available ortho positions of phenolic hydroxyl groups, but also by the substituent group properties (electron acceptor or electron donor) on the bisphenol framework. The electronic cloud distribution of the phenolic hydroxyl groups, which is affected by the substituent group, determines whether the available ortho positions of phenolic hydroxyl groups can be oxidized by the tyrosinase biosensor. These response mechanisms are very significant as they can be used for predicting the response characteristics of many BPs and their various derivatives and metabolites on biosensors. The unexpected anti-interference ability of the biosensor to nine heavy metal ions was also discovered and discussed. The MOF-chitosan nanocomposite proves to be a promising sensing platform for the construction of diverse biosensors for selective detection of targets even in the presence of a high concentration of heavy metal ions.
Single-atom trapping and transport in DMD-controlled optical tweezers (2018)

We demonstrate the trapping and manipulation of single neutral atoms in reconfigurable arrays of optical tweezers. Our approach offers unparalleled speed by using a Texas Instruments Digital Micro-mirror Device (DMD) as a holographic amplitude modulator with a frame rate of 20,000 per second. We show the trapping of static arrays of up to 20 atoms, as well as transport of individually selected atoms over a distance of 25{\mu}m with laser cooling and 4{\mu}m without. We discuss the limitations of the technique and the scope for technical improvements.
[Realistic in vitro study of oxygen radical liberation by alveolar macrophages and mononuclear cells of the peripheral blood after short-term exposure to SO2]. (1993)

Alveolar macrophages (AM) located on the alveolar surface are directly exposed to air pollutants. We evaluated the effect of exposure to SO2 on the oxidative metabolism of AM and peripheral blood mononuclear cells (PBMNC) by measuring the spontaneous and stimulated reactive oxygen-intermediates (ROI) release. AM or PBMNC were placed on a polycarbonate membrane, which was in contact with the surface of a reservoir filled with RPMI 1640 allowing the cells to be supplied with nutrients by capillarity. For SO2 exposure times of 10, 20 and 30 minutes and concentrations of 2.5, 7.5 and 12.5 ppm were chosen. A 10-minute SO2-exposure up to 12.5 ppm induced a dose dependent maximal 3.6 fold increase of spontaneous ROI-production (r = 0.876; p < 0.005). A 30-minute exposure of 12.5 ppm SO2 exhibited a cytotoxic effect inducing the death of 62 +/- 9% of AM and caused a 63% decrease of ROI-release compared to 2.5 ppm SO2-exposure under identical conditions (r = -0.96; p < 0.005). These experiments demonstrate that AM and PBMNC are activated by SO2 and that concentrations in the range of 12.5 ppm SO2 are toxic and induce a decrease in ROI-release after 30 minutes exposure of these cells.
Designing DBMS support for the temporal dimension (1984)

Article Free Access Share on Designing DBMS support for the temporal dimension Authors: V Lum View Profile , P Dadam View Profile , R Erbe View Profile , J Guenauer View Profile , P Pistor View Profile , G Walch View Profile , H Werner View Profile , J Woodfill View Profile Authors Info & Claims SIGMOD '84: Proceedings of the 1984 ACM SIGMOD international conference on Management of dataJune 1984 Pages 115–130https://doi.org/10.1145/602259.602276Online:01 June 1984Publication History 81citation418DownloadsMetricsTotal Citations81Total Downloads418Last 12 Months6Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The Impact of Word Alignment Accuracy on Audio-visual Word Prominence Detection (2014)

To automatically detect prominent syllables or words, most approaches require a segmentation of the speech signal and a subsequent extraction of prosodic features in these segments. In this paper we investigate the impact of the precision of this segmentation on the detection. We perform the segmentation of our audiovisual prosodically rich corpus based on an HMM trained on a large dataset. Thereby, we investigate different training strategies of the HMM. We consider on one hand training without any prior information, i.e. flat start and on the other hand when using partially manually created segmentations. Additionally we also introduce features tailored to detect onsets in the spectrogram. We evaluate the performance of the segmentation on our corpus on one hand by comparing it to manual annotations and on the other hand functionally, i.e. via the impact on the prominent word detection. The results show that the use of manual annotations in the training and the onset features significantly improve the segmentation accuracy. Yet the results of the prominent word detection do not to benefit from the better segmentation. From this we conclude that the extraction of the prosodic features is robust against segmentation errors. Index Terms: segmentation, Gaborfilter, audio-visual, wordprominence, contour, FPCA
European facilities for advanced accelerators development (2022)

Abstract Research on the application of advanced and novel accelerator schemes to high-energy physics requires facilities capable of producing multi-GeV particle beams. We briefly review the challenges faced by advanced accelerators in reaching collider-relevant parameters and give a concise description of relevant European facilities and large scale installations, either in operation or in a state of advanced design, with their main goals. We also emphasize contributions from smaller, mostly university groups or laboratories. These facilities and groups advance the field considerably and address some of the challenges arising in the translation of advanced accelerator concepts to a future high-energy physics machine. We highlight the fact that there is in addition the strong need for a dedicated European facility with a scientific and R&amp;D program specific to the research questions exclusive to a plasma-based e - e + linear collider.
In Vitro Formation of β Cell Pseudoislets Using Islet-Derived Endothelial Cells (2013)

β cell pseudoislets (PIs) are used for the in vitro study of β-cells in a three-dimensional (3-D) configuration. Current methods of PI induction require unique culture conditions and extensive mechanical manipulations. Here we report a novel co-culture system consisting of high passage β-cells and islet-derived endothelial cells (iECs) that results in a rapid and spontaneous formation of free-floating PIs. PI structures were formed as early as 72 h following co-culture setup and were preserved for more than 14 d. These PIs, composed solely of β-cells, were similar in size to that of native islets and showed an increased percentage of proinsulin-positive cells, increased insulin gene expression in response to glucose stimulation, and restored glucose-stimulated insulin secretion when compared to β-cells cultured as monolayers. Key extracellular matrix proteins that were absent in β-cells cultured alone were deposited by iECs on PIs and were found in and around the PIs. iEC-induced PIs are a readily available tool for examining β cell function in a native 3-D configuration and can be used for examining β-cell/iEC interactions in vitro.
A 76-mm/sup 2/ 8-Mb chain ferroelectric memory (2001)

This paper demonstrates the first 8-Mb chain ferroelectric RAM (chain FeRAM) with 0,25-/spl mu/m 2-metal CMOS technology. A small die of 76 mm/sup 2/ and a high average cell/chip area efficiency of 57.4 % have been realized by introducing not only chain architecture but also four new techniques: 1) a one-pitch shift cell realizes small cell size of 5.2 /spl mu/m/sup 2/; 2) a new hierarchical wordline architecture reduces row-decoder and plate-driver areas without an extra metal layer; 3) a small-area dummy cell scheme reduces dummy capacitor size to 1/3 of the conventional one; and 4) a new array activation scheme reduces dataline and second amplifier areas. As a result, the chain architecture with these new techniques reduces die size to 65% of that of the conventional FeRAM. Moreover a ferroelectric capacitor overdrive scheme enables sufficient polarization switching, without overbias memory cell array. This scheme lowers the minimum operation voltage by 0.23 V, and enables 2.5-V V/sub dd/ operation. Thanks to fast cell plateline drive of chain architecture, the 8-Mb chain FeRAM has achieved the fastest random access time, 40 ns, and read/write cycle time, 70 ns, at 3.0 V so far reported.
What is the best surgical approach for ectopia lentis in Marfan syndrome? (2015)

The surgical management of ectopia lentis (EL) in Marfan syndrome (MFS) represents a challenge to the ophthalmologist. We reviewed the literature on the surgical management of ectopia lentis in MFS patients from the classical pars plana lensectomy (PPL) to the most innovative scleral- and iris-fixated intraocular lens (IOL) surgical techniques. The results with the innovative approaches have been satisfactory but with a relatively short follow-up period and several complications associated, and the need of a highly experienced and skilled surgeon. We suggest that PPL approach with postsurgical aphakia is the safest surgical approach to ectopia lentis in MFS on a routinely basis. El manejo quirúrgico de ectopia lentis en Síndrome de Marfan representa un reto para el oftalmólogo. Realizamos una revisión de la literatura sobre el tratamiento quirúrgico de ectopia lentis en pacientes con Síndrome de Marfan incluyendo el manejo clásico con lensectomía pars plana y afaquia postquirúrgica así como como el uso de lentes intraoculares fijados a iris o esclera. Los resultados con estos últimos han sido satisfactorios, pero con un periodo de seguimiento corto y diferentes complicaciones, además de que requieren de un cirujano con gran experiencia. Sugerimos que lensectomia pars plana es el abordaje quirúrgico más seguro de ectopia lentis en Síndrome de Marfan en la práctica diaria.
High Prevalence of Biofilms on Retrieved Implants from Aseptic Pseudarthrosis Cases (2020)

In the absence of the clinical presentation of infection, impregnated bacteria could form a biofilm around an implant, and this biofilm can remain undetected via contemporary diagnostic methods, including swabbing. Implant biofilm is frequently present in "aseptic" pseudarthrosis cases.
Self-homodyne tomography of a twin-beam state (1998)

A self-homodyne detection scheme is proposed to perform two-mode tomography on a twin-beam state at the output of a nondegenerate optical parametric amplifier. This scheme has been devised to improve the matching between the local oscillator and the signal modes, which is the main limitation to the overall quantum efficiency in conventional homodyning. The feasibility of the measurement is analyzed on the basis of Monte Carlo simulations, studying the effect of nonunit quantum efficiency on detection of the correlation and the total photon-number oscillations of the twin-beam state.
Impact of Cytosine 5-Halogens on the Interaction of DNA with Restriction Endonucleases and Methyltransferase (2006)

Growing evidence from both prokaryotes and eukaryotes indicates that pyrimidine 5-methyl groups can have profound biological consequences that are mediated by the affinity of DNA-protein interactions. The presence of the 5-methyl group could potentially create a steric block preventing the binding of some proteins whereas the affinity of many other proteins is substantially increased by pyrimidine methylation. In this paper, we have constructed a series of oligonucleotides containing cytosine and a series of 5-substituted cytosine analogues including all halogens. This set of oligonucleotides has been used to probe the relationship between the size of the substituent and its capacity to modulate cleavage by the methylation-sensitive restriction endonucleases MspI and HpaII. Additionally, we have examined the impact of the halogen substitution on the corresponding bacterial methyltransferase (M.HpaII). We observed that MspI cleavage is only subtly affected by substituted cytosine analogues at the inner position of the CCGG recognition site. In contrast, HpaII cleaves cytosine-containing oligonucleotides completely whereas 5-fluorocytosine-containing oligonucleotides are cleaved at a reduced rate. The presence of the larger halogens Cl, Br, or I as well as a methyl group completely prevents cleavage by HpaII. These data suggest that the steric wall is encountered by HpaII slightly beyond the fluorine substituent, at about 2.65 A from the pyrimidine C5-position. It is known that 5-fluorocytosine in an oligonucleotide can form a covalent irreversible suicide complex with either prokaryotic or eukaryotic methyltransferases. Kinetic data reported here suggest that the 5-fluorocytosine-containing oligonucleotide can also inhibit M.HpaII by formation of a reversible, noncovalent complex. Our results indicate that although a 5-Cl substituent has electronic properties similar to 5-F, 5-chlorocytosine duplexes neither form a complex with M.HpaII nor inhibit enzymatic methylation. Emerging data suggest that halogenation of cytosine can occur in DNA in vivo from inflammation-mediated reactive molecules. The results reported here suggest that the inadvertent halogenation of cytosine residues in DNA could alter the affinity of sequence-specific DNA-binding proteins.
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility (2017)

Kawasaki disease (KD) is the most common acquired pediatric heart disease. We analyzed Whole Genome Sequences (WGS) from a 6-member African American family in which KD affected two of four children. We sought rare, potentially causative genotypes by sequentially applying the following WGS filters: sequence quality scores, inheritance model (recessive homozygous and compound heterozygous), predicted deleteriousness, allele frequency, genes in KD-associated pathways or with significant associations in published KD genome-wide association studies (GWAS), and with differential expression in KD blood transcriptomes. Biologically plausible genotypes were identified in twelve variants in six genes in the two affected children. The affected siblings were compound heterozygous for the rare variants p.Leu194Pro and p.Arg247Lys in Toll-like receptor 6 (TLR6), which affect TLR6 signaling. The affected children were also homozygous for three common, linked (r2 = 1) intronic single nucleotide variants (SNVs) in TLR6 (rs56245262, rs56083757 and rs7669329), that have previously shown association with KD in cohorts of European descent. Using transcriptome data from pre-treatment whole blood of KD subjects (n = 146), expression quantitative trait loci (eQTL) analyses were performed. Subjects homozygous for the intronic risk allele (A allele of TLR6 rs56245262) had differential expression of Interleukin-6 (IL-6) as a function of genotype (p = 0.0007) and a higher erythrocyte sedimentation rate at diagnosis. TLR6 plays an important role in pathogen-associated molecular pattern recognition, and sequence variations may affect binding affinities that in turn influence KD susceptibility. This integrative genomic approach illustrates how the analysis of WGS in multiplex families with a complex genetic disease allows examination of both the common disease-common variant and common disease-rare variant hypotheses.