gebhart/patrepeval huggingface dataset:
Dielectric relaxation spectroscopy of a nematic liquid crystal doped with ferroelectric Sn 2 P 2 S 6 nanoparticles (2003)

It was found that doping a nematic liquid crystal (LC) with a small amount of ferroelectric nanoparticles strongly affects the dielectric properties of the system. In particular, adding the ferroelectric particles results in a shift of the absorption bands corresponding to the rotation of liquid crystal molecules around their short axes to lower frequencies and in an increase of the amplitude and with of the absorption bands. This suggests that strong interactions occur between the LC molecules and the particles, caused by the large dipole moment and high polarizability of the ferro-particles. The ferroelectric particles affect not only dielectric losses, but also dielectric permittivity of the system. Specifically, the static dielectric permittivity and the dielectric anisotropy of the suspension are more than twice that of the pure LC.
Design innovations to optimize the 3D stackable vertical gate (VG) NAND flash (2012)

The design architecture for 3D vertical gate (VG) NAND Flash is discussed in detail. With the unique structure of 3D VG and its decoding method, we have developed several important design innovations to optimize this technology: (1) “Shift-BL scramble” to average the BL capacitances, providing uniform C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BL</sub> 's for various memory layers; (2) Optimized read waveforms to suppress the hot-carrier induced read disturb in the page reading mode; (3) Novel reverse read with “multi-Vt sensing technique” for different memory layers to compensate the Vt variation due to the layer-to-layer process difference; (4) Program inhibit method and technique to minimize the “Z-directional” self-boosting program disturb in 3D stackable memory. Optimized chip-level performances with excellent memory window for SLC and MLC operations are demonstrated on a 2-layer 3D VG NAND chip.
Nitrolinoleate Inhibits Platelet Activation by Attenuating Calcium Mobilization and Inducing Phosphorylation of Vasodilator-stimulated Phosphoprotein through Elevation of cAMP (2002)

Reactive species formed from nitric oxide (NO) nitrate unsaturated fatty acids such as linoleate (LA) to nitrated derivatives including nitrolinoleate (LNO(2)). The effect of LNO(2) on human platelets was examined to define how nitrated lipids might behave in vivo. LNO(2), but not LA or 3-nitrotyrosine, dose dependently (0.5-10 microm) inhibited thrombin-mediated aggregation of washed human platelets, with concomitant attenuation of P-selectin expression and selective phosphorylation of VASP at the cAMP-dependent protein kinase selective site, serine 157. LNO(2) caused slight mobilization of calcium (Ca(2+)) from intracellular stores but significantly inhibited subsequent thrombin-stimulated Ca(2+) elevations. LNO(2) did not elevate platelet cGMP, and its effects were not blocked with inhibitors of NO signaling (oxyhemoglobin, 1H-[1,2,4]oxadiazole[4,3-a]quinoxalin-1-one. 2-fold elevations in cAMP were found following LNO(2) treatment of platelets, and the adenylyl cyclase inhibitors 2',5'-dideoxyadenosine and SQ22536 partially restored thrombin-stimulated aggregation. Finally, LNO(2) significantly inhibited cAMP hydrolysis to AMP by platelet lysates. These data implicate cAMP in the anti-aggregatory action of LNO(2). The platelet inhibitory actions of LNO(2) indicate that nitration reactions that occur following NO generation in an oxidizing environment can alter the activity of lipids and lend insight into mechanisms by which NO-derived species may modulate the progression of vascular injury.
TheArabidopsisB-Box Zinc Finger Family (2009)

The Arabidopsis thaliana genome encodes >1500 transcription factors, and ∼45% of these belong to families specific to plants ([Riechmann et al., 2000][1]). Comparison of the entire complement of transcription factors of Arabidopsis , Drosophila melanogaster , Caenorhabditis elegans , and
Nonlinear scale-space filtering and multiresolution system (1995)

We derive and demonstrate a nonlinear scale-space filter and its application in generating a nonlinear multiresolution system. For each datum in a signal, a neighborhood of weighted data is used for clustering. The cluster center becomes the filter output. The filter is governed by a single scale parameter that dictates the spatial extent of nearby data used for clustering. This, together with the local characteristic of the signal, determines the scale parameter in the output space, which dictates the influences of these data on the output. This filter is thus adaptive and data driven. It provides a mechanism for (a) removing impulsive noise, (b) improved smoothing of nonimpulsive noise, and (c) preserving edges. Comparisons with Gaussian scale-space filtering and median filters are made using real images. Using the architecture of the Laplacian pyramid and this nonlinear filter for interpolation, we construct a nonlinear multiresolution system that has two features: (1) edges are well preserved at low resolutions, and (2) difference signals are small and spatially localized. This filter implicitly presents a new mechanism for detecting discontinuities differing from techniques based on local gradients and line processes. This work shows that scale-space filtering, nonlinear filtering, and scale-space clustering are closely related and provides a framework within which further image processing, image coding, and computer vision problems can be investigated.
Identification of a Mouse Anti-Rat IgE Monoclonal Antibody, 44.7b, Which Inhibits IgE Binding to RBL Cells (1989)

We have identified a monoclonal antibody specific for rat IgE, 44.7b, which blocks binding of rat IgE to the mast cell-like line RBL. Other monoclonal anti-rat IgE antibodies (MARE1 and B5) did not inhibit IgE binding to these cells. Furthermore, 44.7b did not react with IgE previously bound to these cells. These results indicate that 44.7b binds to an epitope on the IgE molecule which is within the binding site of the mast cell IgE Fc receptor (FcERI). The 44.7b monoclonal antibody did recognize IgE bound to a B lymphocyte cell line indicating that mast cell and B lymphocyte FcERs recognize different regions of the IgE molecule.
Safety of Dietary Supplements: Chronotropic and Inotropic Effects on Isolated Rat Atria. (2002)

We investigated the effects of dietary supplements on atria isolated from male Wistar rats. The examined supplements, which are increasingly used in Japan, those were Ginkgo biloba extract (GBE), catechins, isoflavones, sodium iron chlorophyllin and sodium copper chlorophyllin. GBE at 100-1000 microg/ml significantly increased the beat rate and the contractile force. Catechins at 1-100 microg/ml significantly potentiated the contractile force but did not effect the beat rates. However, isoflavones, sodium iron and sodium copper chlorophyllins did not change the contractile force or the beat rates. To identify the active ingredient of GBE, ginkgolide B, quercetin and amentoflavone on the atria were tested. Ginkgolide B weakened the contractile force. Quercetin potentiated the contractile force at only 30 microg/ml. Amentoflavone significantly increased the beat rate. From these findings, amentoflavone and quercetin were considered to be the principal ingredients of GBE producing the positive chronotropic and inotropic actions, respectively. In the case of catechins, (-)-epigallocatechin gallate (EGCg), one of the principal ingredients, produced inotropic actions. These findings suggest that there are some dietary supplements which affect cardiac function, such GBE and catechins.
Antidepressants and their effect on sleep (2005)

Given the relationship between sleep and depression, there is inevitably going to be an effect of antidepressants on sleep. Current evidence suggests that this effect depends on the class of antidepressant used and the dosage. The extent of variation between the effects of antidepressants and sleep may relate to their mechanism of action. This systematic review examines randomised-controlled trials (RCTs) that have reported the effect that antidepressants appear to have on sleep. RCTs are not restricted to depressed populations, since several studies provide useful information about the effects on sleep in other groups. Nevertheless, the distinction is made between those studies because the participant's health may influence the baseline sleep profiles and the effect of the antidepressant. Insomnia is often seen with monoamine oxidase inhibitors (MAOIs), with all tricyclic antidepressants (TCAs) except amitriptyline, and all selective serotonin reuptake inhibitors (SSRIs) with venlafaxine and moclobemide as well. Sedation has been reported with all TCAs except desipramine, with mirtazapine and nefazodone, the TCA-related maprotiline, trazodone and mianserin, and with all MAOIs. REM sleep suppression has been observed with all TCAs except trimipramine, but especially clomipramine, with all MAOIs and SSRIs and with venlafaxine, trazodone and bupropion. However, the effect on sleep varies between compounds within antidepressant classes, differences relating to the amount of sedative or alerting (insomnia) effects, changes to baseline sleep parameters, differences relating to REM sleep, and the degree of sleep-related side effects.
Crystallization Behavior of Novel Silicon Boron Oxycarbide Glasses (2004)

Homogeneous silicon boron oxycarbide (Si‐B‐O‐C) glasses based on SiO x C 4– x and BO y C 3– y mixed environments were obtained by pyrolysis under inert atmosphere of sol–gel‐derived precursors. Their high‐temperature structural evolution from 1000° to 1500°C was followed using XRD, 29 Si and 11 B MAS NMR, and chemical analysis and compared with the behavior of the parent boron‐free Si‐O‐C glasses. The XRD study revealed that, for the Si‐O‐C and the Si‐B‐O‐C systems, high‐temperature annealing led to the crystallization of nanosized β‐SiC into an amorphous SiO 2 ‐based matrix. NMR analysis suggested that the β‐SiC crystallization occurred with a consumption of the mixed silicon and boron oxycarbide units. Finally, by comparing the behavior of the Si‐O‐C and Si‐B‐O‐C glasses, it was shown that the presence of boron increased the crystallization kinetics of β‐SiC.
Three-dimensional Structure and Enzymatic Function of Proapoptotic Human p53-inducible Quinone Oxidoreductase PIG3 (2009)

Tumor suppressor p53 regulates the expression of p53-induced genes (PIG) that trigger apoptosis. PIG3 or TP53I3 is the only known member of the medium chain dehydrogenase/reductase superfamily induced by p53 and is used as a proapoptotic marker. Although the participation of PIG3 in the apoptotic pathway is proven, the protein and its mechanism of action were never characterized. We analyzed human PIG3 enzymatic function and found NADPH-dependent reductase activity with ortho-quinones, which is consistent with the classification of PIG3 in the quinone oxidoreductase family. However, the activity is much lower than that of zeta-crystallin, a better known quinone oxidoreductase. In addition, we report the crystallographic structure of PIG3, which allowed the identification of substrate- and cofactor-binding sites, with residues fully conserved from bacteria to human. Tyr-59 in zeta-crystallin (Tyr-51 in PIG3) was suggested to participate in the catalysis of quinone reduction. However, kinetics of Tyr/Phe and Tyr/Ala mutants of both enzymes demonstrated that the active site Tyr is not catalytic but may participate in substrate binding, consistent with a mechanism based on propinquity effects. It has been proposed that PIG3 contribution to apoptosis would be through oxidative stress generation. We found that in vitro activity and in vivo overexpression of PIG3 accumulate reactive oxygen species. Accordingly, an inactive PIG3 mutant (S151V) did not produce reactive oxygen species in cells, indicating that enzymatically active protein is necessary for this function. This supports that PIG3 action is through oxidative stress produced by its enzymatic activity and provides essential knowledge for eventual control of apoptosis.
The Marshall R. Urist Young Investigator Award. Gene expression during autograft lumbar spine fusion and the effect of bone morphogenetic protein 2. (1998)

A prospective animal study of posterolateral lumbar spine arthrodesis was performed to determine the temporal and spatial pattern of gene expression and to determine the effect of recombinant human bone morphogenetic protein 2 on the gene expression pattern of a healing spine fusion mass. In Group 1, 20 adult New Zealand rabbits underwent L4-L5 posterolateral intertransverse process arthrodesis using autograft alone. Two rabbits were euthanized at each of the following points: 0, 2, and 4 days, and 1, 2, 3, 4, 5, 6, and 10 weeks after surgery. The same surgical technique was used for 16 rabbits in Group II, except that the autograft first was soaked in a solution of recombinant human bone morphogenetic protein 2 before implantation. Ribonucleic acid was extracted from different regions of the fusion mass at each point and analyzed for expression of bone and cartilage related genes using reverse transcription polymerase chain reaction. A reproducible temporal sequence and spatial pattern of gene expression was found in healing spine fusions. In the central portion of the fusion mass a temporal lag in gene expression was observed that parallels the lag in healing within the central zone previously observed in histologic studies. Treatment of bone graft with recombinant human bone morphogenetic protein 2 resulted in an increase in the early expression of bone morphogenetic protein 6 which was associated with expression of higher levels of Type I collagen, osteocalcin, and other bone related genes. These findings suggest that central nonunion may be associated with delayed expression of osteoblast related genes in the central region of the forming fusion mass. The growth factor, recombinant human bone morphogenetic protein 2, increased the level of bone related gene expression throughout the fusion mass, eliminated the delay in healing within the central zone, and may decrease the likelihood of a nonunion.
Post-transcriptional suppression of gene expression in Xenopus embryos by small interfering RNA (2002)

Double-stranded RNA (dsRNA) induces gene-specific silencing in organisms from fungi to animals, a phenomenon known as RNA interference (RNAi). RNAi represents an evolutionarily conserved system to protect against aberrant expression of genes and a powerful tool for gene manipulation. Despite reports that RNAi can be induced in vertebrates, severe sequence-non-specific effects of long dsRNA have been documented in various systems. It has recently been shown in cultured mammalian cells that small interfering RNAs (siRNAs) of 21-23 nt can mediate RNAi but bypass the non-specific response induced by longer dsRNAs. However, the effectiveness of siRNAs has not been demonstrated in living vertebrates. In addition, the mechanism of siRNA suppression of gene expression in vertebrate cells remains to be elucidated. Here we show that synthetic 21 nt siRNAs can specifically inhibit the expression of exogenously introduced as well as endogenous genes in the embryos of Xenopus laevis. siRNAs significantly reduced the steady-state amount of both the mRNA and protein of the cognate gene target. Moreover, co-injection of siRNA with the target RNA transcript specifically suppressed the activity of the latter. Taken together, our findings establish siRNA-mediated post-transcriptional suppression of gene expression in Xenopus embryos.
Accuracy and predictability of intraocular lens power calculation after photorefractive keratectomy (2000)

The smaller of the actual or the refraction-derived keratometric value is recommended for calculating IOL power in post-PRK eyes.
Thymic dendritic cell precursors: relationship to the T lymphocyte lineage and phenotype of the dendritic cell progeny. (1996)

Successive T-precursors isolated from adult mouse thymus were examined for their developmental potential, by transfer to irradiated Ly 5-disparate recipients. The earliest, "low CD4" precursors formed T, B, and dendritic cells (DC), but not myeloid cells, in accordance with earlier studies. Surprisingly, the next downstream CD4-8-3 44+25+ precursor population still formed DC as well as T cells although it no longer formed B or myeloid cells. Further down-stream, the CD4-8 3-44-25+ population formed only T cells. The thymic and splenic DC progeny of the early thymic precursors all expressed high levels of CD8 alpha, in contrast with normal splenic DC and the splenic DC progeny of bone marrow stem cells, which consisted of both CD8 and CD8+ DC. A common precursor of T cells and of a subclass of DC is proposed, with CD8 alpha as a marker of the lymphoid-related DC lineage.
Purification and Characterization of Two Muconate Cycloisomerase Isozymes from Aniline-assimilatingFrateuriaSpecies ANA-18 (1998)

Two muconate cycloisomerases (MC I and MC II, EC 5.5.1.1) were purified to homogeneity from an aniline-grown Frateuria sp. ANA-18. MC I and MC II were similar in molecular mass, optimal pH, and pH stability but different in thermostability, and some other enzymatic properties. NH2-terminal amino acid sequences were different between the two isozymes, indicated that these are encoded by different genes. Different inducible production of MC I and MC II suggested that two catechol branches involved in the beta-ketoadipate pathway function in Frateuria sp. ANA-18.
High incidence of translocations t(11;14)(q13;q32) and t(4;14)(p16;q32) in patients with plasma cell malignancies. (1998)

Abnormalities involving the 14q32 region are recurrent chromosomal changes in plasma cell malignancies. Recent preliminary molecular analyses found IGH rearrangements in almost 100% of human myeloma cell lines and in 75% of patients. However, no systematic study analyzing the nature of the partner chromosomal regions have been reported thus far. To define the exact incidence of illegitimate IGH rearrangements and the respective incidence of partner genes cloned to date, we analyzed 141 patients with either multiple myeloma (MM, n = 127) or primary plasma cell leukemia (PCL, n = 14) using fluorescence in situ hybridization. The overall incidence of illegitimate recombinations was 57% (80 of 141 patients). Analysis of this incidence according to Durie and Salmon stage, patients' status, i.e., MM versus primary PCL and diagnosis versus relapse, immunoglobulin type and subtype, and beta2-microglobulin value, did not show any correlation. To analyze the nature of the partner chromosomal region, we selected probes specific for the following genes: FGFR3 (4p16), MYC (8q24), CCND1 (11q13), MAF (16q23), and BCL2 (18q21). These probes, combined with differentially labeled 14q32 probes, were used for dual-color fluorescence in situ hybridization on interphase plasma cells. Among the 80 patients with illegitimate IGH rearrangement, we identified 23 IGH-CCND1 fusion cases [i.e., t(11;14)], 17 IGH-FGFR3 fusion cases [i.e., t(4;14)], 3 IGH-MYC fusion cases [i.e., t(8;14)], and only one IGH-MAF fusion case. No IGH-BCL2 fusion case was detected. In 37 of 80 patients, none of these partner genes was involved. Analysis of cases with specific translocations according to their bioclinical features at diagnosis did not show any correlation. This study demonstrated that CCND1 and FGFR3 genes are involved together in about 50% of MM and primary PCL patients with illegitimate IGH rearrangements.
Nosocomial bloodstream infection in critically ill patients. Excess length of stay, extra costs, and attributable mortality (1994)

The attributable mortality from nosocomial bloodstream infection is high in critically ill patients. The infection is associated with a doubling of the SICU stay, an excess length of hospital stay of 24 days in survivors, and a significant economic burden.
Quality Requirements for Critical Assay Reagents Used in Bioanalysis of Therapeutic Proteins: What Bioanalysts Should Know About Their Reagents (2011)

Ligand-binding assays are the standard technology used for bioanalysis of therapeutic proteins, for example, for drug quantification (pharmacokinetics assays) and immunogenicity testing (antidrug antibody assays). Besides the selection of the most suitable technology platform (e.g., ELISA, electrochemiluminescence assays and surface plasmon resonance assays) and assay procedure, a pivotal prerequisite for good assay performance on any technology platform is the design, production and characterization of high quality reagents. To enable bioanalytical project support over the complete product life cycle, an appropriate long-term reagent supply is needed. This perspective describes our opinion on the requirements for generation and QC of critical reagents used in ligand-binding assays for drug quantification and antidrug antibody detection to enable high-quality assays and long-term supply, including reagent batch switches. The critical parameters during reagent design, production and long-term supply, along with the appropriate analytical methods for QC testing and appropriate certification, are discussed.
Plasma amino acid and metabolite signatures tracking diabetes progression in the UCD-T2DM rat model (2016)

Elevations of plasma concentrations of branched-chain amino acids (BCAAs) are observed in human insulin resistance and type 2 diabetes mellitus (T2DM); however, there has been some controversy with respect to the passive or causative nature of the BCAA phenotype. Using untargeted metabolomics, plasma BCAA and other metabolites were assessed in lean control Sprague-Dawley rats (LC) and temporally during diabetes development in the UCD-T2DM rat model, i.e., prediabetic (PD) and 2 wk (D2W), 3 mo (D3M), and 6 mo (D6M) post-onset of diabetes. Plasma leucine, isoleucine, and valine concentrations were elevated only in D6M rats compared with D2W rats (by 28, 29, and 30%, respectively). This was in contrast to decreased plasma concentrations of several other amino acids in D3M and/or D6M relative to LC rats (Ala, Arg, Glu, Gln, Met, Ser, Thr, and Trp). BCAAs were positively correlated with fasting glucose and negatively correlated with plasma insulin, total body weight, total adipose tissue weight, and gastrocnemius muscle weight in the D3M and D6M groups. Multivariate analysis revealed that D3M and D6M UCD-T2DM rats had lower concentrations of amino acids, amino acid derivatives, 1,5-anhydroglucitol, and conduritol-β-opoxide and higher concentrations of uronic acids, pantothenic acids, aconitate, benzoic acid, lactate, and monopalmitin-2-glyceride relative to PD and D2W UCD-T2DM rats. The UCD-T2DM rat does not display elevated plasma BCAA concentrations until 6 mo post-onset of diabetes. With the acknowledgement that this is a rodent model of T2DM, the results indicate that elevated plasma BCAA concentrations are not necessary or sufficient to elicit an insulin resistance or T2DM onset.
Circulating Deoxyribonucleic Acid As Prognostic Marker in Non–Small-Cell Lung Cancer Patients Undergoing Chemotherapy (2004)

Our data demonstrate that quantification of plasma DNA is an accurate technique amenable to standardization, which might complement current methods for the prediction of patient survival. This approach might be considered for evaluation in large prospective studies.