gebhart/patrepeval huggingface dataset:
Behavior of Chromium in Soils: VII. Adsorption and Reduction of Hexavalent Forms (1983)

Abstract Based on adsorption studies with Fe(OH) 3 , Cr(OH) 3 , and soils, 10 m M K‐phosphate buffered at pH 7.2 was found to be adequate for characterizing exchangeable Cr(VI). The quantity of Cr(VI) removed from solution by 19 A and 19 B horizon soils from the northeastern United States was partitioned into two fractions, based on the amount of soil‐Cr extracted with the phosphate buffer. The fraction removed by the buffer was termed “exchangeable;” that retained by the soil was termed “nonexchangeable.” The nonexchangeable Cr(VI) not recovered by phosphate had been either reduced to an insoluble form of Cr(III), or had been precipitated or very tightly adsorbed by the soil as anionic Cr(VI). Of 20 µ mol/100 g soil (23 kg/ha) Cr(VI) added, an average of 7.2 was removed by the unlimed 38 soils (mean pH 5.4). Of this quantity, 4.8 µ mol were exchangeable by phosphate. Surface soils generally removed less Cr(VI) than B horizons (5.8 vs. 8.6 µ mol/100 g), and the proportion of Cr(Vi) removed in phosphate‐exchangeable form also was lower. Liming to pH 7 decreased the average quantity of Cr(VI) removed by the soils to 2.6, with exchangeable and nonexchangeable forms each accounting for about 50% of the total. Sulfate and phosphate added with Cr(VI) to two A and two B horizon soils decreased Cr(VI) removal by the soil, with phosphate having a greater effect than sulfate. Although liming decreased Cr(VI) removal by the soils, even less Cr(VI) was held in exchangeable or nonexchangeable form in limed treatments containing the competing anions. Gallic acid rapidly reduced Cr(VI) held by soil colloids in exchangeable form except in limed samples of spodic horizons and a Hydric Dystrandept Ap, all high in amorphous, organically complexed Al and Fe sesquioxides.
Advanced process modules and architectures for half-terahertz SiGe:C HBTs (2009)

The European project DOTFIVE addresses evolutionary scaling of self-aligned selective epitaxial base SiGe:C HBTs, investigates novel SiGe:C HBT architectures, and develops novel process modules to push SiGe BiCMOS towards 500 GHz F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> and 2.5 ps gate delay. In this paper, scaling issues of SiGe:C HBT technology will be addressed. The limitations of the different commonly used architectures will be described, and measures taken in the project to overcome these limitations will be summarized. Initial results indicate that the objectives of the project can be reached.
G(α)i2-deficient mice with colitis exhibit a local increase in memory CD4+ T cells and proinflammatory Th1-type cytokines (1997)

Mice with targeted deletion of the G protein G(alpha)i2 develop an inflammatory bowel disease closely resembling ulcerative colitis. To better define disease pathogenesis, the mucosal immune system in G(alpha)i2-deficient mice was studied. Phenotypic analysis of large intestine lamina propria lymphocytes revealed a large increase in memory CD4+ T cells (CD44high, CD45RBlow, CD62Llow). Furthermore, expression of the mucosal homing receptor integrin beta7 was increased on mucosal, but not systemic, CD4+ T cells. Analysis of cytokine production revealed a marked increase in proinflammatory Th1-type cytokines in inflamed colons, as compared with wild-type mice or G(alpha)i2-deficient mice without colitis. Thus, IFN-gamma and IL-1beta levels were increased 13-fold and 30-fold, respectively, with more modest increases in IL-6 levels (5-fold) and TNF levels (2-fold). Inflamed colons of G(alpha)i2-deficient mice also demonstrated increased IL-12 p40 mRNA levels. No increase in IL-2, IL-4, IL-5, and IL-10 was seen. Large intestinal epithelial cells in G(alpha)i2-deficient mice with colitis were found by immunohistochemistry to express increased levels of both MHC class I and class II Ags. Colitis was associated with increased IgG levels (60-fold increase), predominantly IgG2a (135-fold increase), in large but not small intestinal secretions. This was shown by ELISPOT analysis to result from local production within the lamina propria.
Multioctave, 3–18  μm sub-two-cycle supercontinua from self-compressing, self-focusing soliton transients in a solid (2015)

Strongly coupled nonlinear spatiotemporal dynamics of ultrashort mid-infrared pulses undergoing self-focusing simultaneously with soliton self-compression in an anomalously dispersive, highly nonlinear solid semiconductor is shown to enable the generation of multioctave supercontinua with spectra spanning the entire mid-infrared range and compressible to subcycle pulse widths. With 7.9 μm, 150 fs, 2 μJ, 1 kHz pulses used as a driver, 1.2 cycle pulses of mid-infrared supercontinuum radiation with a spectrum spanning the range of wavelengths from 3 to 18 μm were generated in a 5 mm GaAs plate. Further compression of these pulses to subcycle pulse widths is possible through compensation of the residual phase shift.
The synchronization manifesto: a critique of whole‐culture synchronization (2019)

The field of cell cycle studies is dominated by the incorrect idea that one can treat an entire culture to produce a synchronized culture. If this predominant method cannot work, at all, then an enormous amount of work on the cell cycle must be re-evaluated. Here, criteria are presented for determining whether a culture is 'truly' synchronized. No whole-culture 'synchronization' method has been shown to produce a 'truly' synchronized population of cells rather than a population of cells sharing some singular and particular property within that collection of cells. It is demonstrated and explained why it is impossible to truly synchronize cells using whole-culture methods. Such whole-culture methods produce cells that may have some properties in common for all the cells in a group, but these cells are not actually and truly synchronized. Synchronized cultures can only be produced by a selection method where cells of a particular cell cycle age or size are removed from the cell population and the remainder is discarded. The field of cell cycle analysis is chained to the incorrect idea of whole-culture synchronization methodology. It is important to break the chains that lead to many incorrect results regarding the cell cycle. It must be recognized that an enormous amount of funds, time, energy, and thought is wasted using the methods that do not synchronize cells at all.
Recent progress on transfer-Si solar cells at ipe Stuttgart (2003)

This work reports first results on flexible crystalline thin film Si solar cells prepared by transferring single crystalline Si films onto transparent plastic foils. Despite the high absorbance of the plastic superstrates, our very first cells of 4 cm/sup 2/ size show AM 1.5G efficiencies above 14%, for cell thicknesses of 40 /spl mu/m. For cells transferred behind glass superstrates, we have brought the Si-transfer technique to cell efficiencies above 16%. As a new market for flexible solar cells, we identify solar cells integrated into clothing, for the supply of personal electronics such as personal digital assistants, intelligent wrist watches, radios, compact disc players, mobile phones, and other consumer electronics. Here, we report first results on so-called clothing integrated photovoltaics (ipv) of the ipe Stuttgart.
Chlorpromazine specifically inhibits peripheral and brain TNF production, and up-regulates IL-10 production, in mice. (1994)

We have previously shown that chlorpromazine (CPZ) inhibits tumour necrosis factor (TNF) production and protects against endotoxic shock in mice. In this paper we investigated the effect of pretreatment with CPZ, 4 mg/kg i.p. 30 min before, compared with dexamethasone (DEX; 3 mg/kg) on the induction of other endotoxin (lipopolysaccharide; LPS)-induced cytokines in the serum of mice, i.e. interleukin-1 alpha (IL-1 alpha), IL-6 and IL-10, and TNF. We also studied the effect of CPZ on serum and spleen-associated TNF. Both DEX and CPZ inhibited TNF production, whereas induction of IL-1 and IL-6 was inhibited by DEX but not by CPZ. DEX did not affect IL-10, while CPZ potentiated its induction. CPZ also inhibited spleen-associated TNF induction in LPS-treated mice, suggesting an effect on the synthesis of TNF. CPZ inhibited TNF induction by Gram-positive bacteria (heat-killed Staphylococcus epidermidis) and by anti-CD3 monoclonal antibodies. Intraperitoneal administration of CPZ also inhibited the induction of brain-associated TNF induced by intra-cerebroventricular injection of LPS. Therefore, CPZ is a more specific inhibitor of TNF production than DEX; in particular, CPZ increased the induction of IL-10, which is a 'protective' cytokine known to inhibit LPS toxicity and TNF production. CPZ inhibited TNF production in vivo, irrespective of the TNF stimulus used to induce TNF. Finally, CPZ did not induce the 'rebound' effect of DEX that, when given 24 hr before LPS, potentiates TNF production, but it did inhibit TNF production after 24 hr.
Effects of magnesium deficiency on the pathogenesis of myocardial infarction. (1986)

The death rate due to myocardial infarction appears to vary with dietary consumption of Mg. This could be due to effects on atherosclerosis, coronary artery spasm, altered pathogenesis of myocardial infarction, increased vulnerability to arrhythmia, or some combination of these. Mg deficiency (MD) has been found to increase the severity of a coronary occlusive event in terms of the amount of necrosis produced by a given occlusion. MD is also associated with increased likelihood of arrhythmia development. In addition, reduced extracellular magnesium concentration (Mgo) is associated with contraction of vascular smooth muscle that may be the equivalent of arterial spasm. In hamsters, MD leads to fibrinoid necrosis thought to be secondary to Ca overload. These 3 effects: coronary artery spasm, cardiac arrhythmia, and increased vulnerability to myocardial necrosis following coronary occlusion, may all be dependent on changes in myocardial and vascular smooth muscle electrolyte metabolism that follow from the reduced Mgo that is associated with MD.
Comparison of the <i>Bordetella pertussis</i> and <i>Bordetella parapertussis</i> Isolates Circulating in Saint Petersburg between 1998 and 2000 with Russian Vaccine Strains (2003)

We analyzed the Bordetella pertussis and Bordetella parapertussis isolates circulating in Saint Petersburg that were collected between 1998 and 2000 and compared them with isolates collected 40 years ago and Russian vaccine strains. The analysis involved serotyping, pulsed-field gel electrophoresis of chromosomal DNA after digestion with XbaI and SpeI, and sequencing of the ptxS1 and prn genes, which encode the S1 subunit of the pertussis toxin and the major adhesin pertactin, respectively. The Russian isolates were classified in five of the six pulsed-field gel electrophoresis groups identified in other European countries. The B. pertussis isolates currently circulating in Saint Petersburg differed from the Russian whole-cell vaccine strains and the isolates collected in the prevaccine era. However, their repartition in the major pulsed-field gel electrophoresis groups was slightly different from that of isolates collected in countries that have had a high level of vaccine coverage for a long time, probably because the level of vaccine coverage in Saint Petersburg has increased only recently, after decreasing until the early 1990s. Most of the B. parapertussis isolates studied were similar to those circulating in France. However, some variants were observed, perhaps because B. parapertussis infections are more common in children in this area.
A statistical selection strategy for normalization procedures in LC‐MS proteomics experiments through dataset‐dependent ranking of normalization scaling factors (2011)

Quantification of LC-MS peak intensities assigned during peptide identification in a typical comparative proteomics experiment will deviate from run-to-run of the instrument due to both technical and biological variation. Thus, normalization of peak intensities across an LC-MS proteomics dataset is a fundamental step in pre-processing. However, the downstream analysis of LC-MS proteomics data can be dramatically affected by the normalization method selected. Current normalization procedures for LC-MS proteomics data are presented in the context of normalization values derived from subsets of the full collection of identified peptides. The distribution of these normalization values is unknown a priori. If they are not independent from the biological factors associated with the experiment the normalization process can introduce bias into the data, possibly affecting downstream statistical biomarker discovery. We present a novel approach to evaluate normalization strategies, which includes the peptide selection component associated with the derivation of normalization values. Our approach evaluates the effect of normalization on the between-group variance structure in order to identify the most appropriate normalization methods that improve the structure of the data without introducing bias into the normalized peak intensities.
Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts prediction (1999)

CASP3 saw a substantial increase in the volume of ab initio 3D prediction data, with 507 datasets for fifteen selected targets and sixty-one groups participating. As with CASP2, methods ranged from computationally intensive strategies that attempt to recreate the physical and chemical forces involved in protein folding to the more recent knowledge-based approaches. These exploit information from the structure databases, extracting potentially similar fragments and/or distance constraints derived from multiple sequence alignments. The knowledge-based approaches generally gave more consistently successful predictions across the range of targets, particularly that of the Baker group (Bystroff and Baker, J Mol Biol 1998;281:565-577; Simons et al. Proteins Suppl 1999;3:171-176), which used a fragment library. In the secondary structure prediction category, the most successful approaches built on the concepts used in PHD (Rost et al. Comput Appl Biosci 1994;10:53-60), an accepted standard in this field. Like PHD, they exploit neural networks but have different strategies for incorporating multiple sequence data or position-dependent weight matrices for training the networks. Analysis of the contact data, for which only six groups participated, suggested that as yet this data provides a rather weak signal. However, in combination with other types of prediction data it can sometimes be a useful constraint for identifying the correct structure.
miRNA, siRNA, piRNA and Argonautes: News in small matters (2010)

Since the discovery of the first microRNA (miRNA) family member lin-4 in Caenorhabditis elegans by Lee et al. and RNA interference (RNAi) by Andrew Fire and his colleagues in the 1990s, the new field of regulatory non-coding RNAs has enormously gained momentum and importance. Small regulatory RNAs comprise small interfering RNAs (siRNAs), miRNAs and Piwi-associated small RNAs (piRNAs). Generated from double-stranded RNAs (dsRNAs), siRNAs trigger sequence-specific mRNA decay also known as RNA interference (RNAi). miRNAs in association with Argonaute (AGO ) and GW182 proteins, forming the RNA-induced silencing complex (RISC), mediate fine tuning of gene expression and are involved in various biological key processes. An estimate of 500-1,000 miRNA genes exist in vertebrates and plants and about 100 in invertebrates. Each miRNA is predicted to target hundreds of mRNAs thus influencing key regulatory mechanisms of the cell. Consequently, deregulated miRNA expression has been suggested to contribute to the initiation and progression of human cancer and other diseases. piRNAs associated with Piwi proteins protect the animal germline from mobile genetic elements, thereby acting as a small RNA-based immune system.
Compact digitally tunable laser (2003)

We present a new design for a digitally tunable laser using two waveguide grating routers with different free spectral range. For an N-channel device, both the number of required amplifiers and the number of required grating arms scale as the square root of N, resulting in a more compact device than previously demonstrated and better scaleability. Contrary to previously demonstrated devices with a reduced number of amplifiers, all wavelength channels are multiplexed together in one common channel, allowing for a higher output power. Tuning speeds below 10 ns are envisioned. Experimental results are presented.
Determination of the linear frequency response of single pipelines using persistent transient excitation: a numerical investigation (2013)

The linear frequency response of a fluid-filled pipeline extracted by fluid transient waves can be used to detect leaks in pipelines. This research conducts numerical analysis on how to accurately determine the linear frequency response diagram (FRD) of single pipelines using persistent transient pressure signals. Two types of persistent signals, the maximum-length binary sequence and the inverse-repeat sequence (IRS), are compared in terms of the accuracy in estimating the linear response of a pipeline at resonant frequencies. The IRS is found to be more appropriate for identifying the linear portion of the FRD of a pipeline, since its antisymmetric property can supress part of the nonlinear response. Numerical simulations are conducted to verify the findings.
Syntenin-1 Is a New Component of Tetraspanin-Enriched Microdomains: Mechanisms and Consequences of the Interaction of Syntenin-1 with CD63 (2006)

Tetraspanins are clustered in specific microdomains (named tetraspanin-enriched microdomains, or TERM) in the plasma membrane and regulate the functions of associated transmembrane receptors, including integrins and receptor tyrosine kinases. We have identified syntenin-1, a PDZ domain-containing protein, as a new component of TERM and show that syntenin-1 specifically interacts with the tetraspanin CD63. Detailed biochemical and heteronuclear magnetic resonance spectroscopy (NMR) studies have demonstrated that the interaction is mediated by the C-terminal cytoplasmic region of the tetraspanin and the PDZ domains of syntenin-1. Upon interaction, NMR chemical shift perturbations were predominantly localized to residues around the binding pocket of PDZ1, indicating a specific mode of recognition of the cytoplasmic tail of CD63. In addition, the C terminus of syntenin-1 has a stabilizing role in the CD63-syntenin-1 association, as deletion of the last 17 amino acids abolished the interaction. The CD63-syntenin-1 complex is abundant on the plasma membrane, and the elevated expression of the wild-type syntenin-1 slows down constitutive internalization of the tetraspanin. Furthermore, internalization of CD63 was completely blocked in cells expressing a syntenin-1 mutant lacking the first 100 amino acids. Previous results have shown that CD63 is internalized via AP-2-dependent mechanisms. Hence, our data indicate that syntenin-1 can counteract the AP-2-dependent internalization and identify this tandem PDZ protein as a new regulator of endocytosis.
The fibroblast growth factor receptor is not required for herpes simplex virus type 1 infection (1992)

The early events mediating herpes simplex virus type 1 (HSV-1) infection include virion attachment to cell surface heparan sulfates and subsequent penetration. Recent evidence has suggested that the high-affinity fibroblast growth factor (FGF) receptor mediates HSV-1 entry. This report presents three lines of experimental evidence showing that the high-affinity FGF receptor is not required for HSV-1 infection. First, rat L6 myoblasts lacking FGF receptors were as susceptible to HSV-1 infection as L6 cells genetically engineered to express the FGF receptor. Second, a soluble FGF receptor fragment that inhibited FGF binding and receptor activation did not inhibit HSV-1 infection. Finally, basic FGF (but not acidic FGF) inhibited HSV-1 infection in L6 cells lacking FGF receptors, presumably by blocking cell surface heparan sulfates also required for HSV-1 infection. These results show that the high-affinity FGF receptor is not required for HSV-1 infection but instead that specific low-affinity basic FGF binding sites are used for HSV-1 infection.
Expression of the Bovine Leukemia Virus Envelope Glycoprotein (gp51) by Recombinant Baculovirus and Its Use in an Enzyme-Linked Immunosorbent Assay (2004)

The gene encoding the major envelope glycoprotein (gp51) with its signal sequence, represented by an additional NH2-terminal 33-residue amino acid sequence of bovine leukemia virus (BLV), was inserted into a baculovirus transfer vector. A recombinant virus expressing a secreted gp51 protein in insect cells was isolated. The recombinant gp51 expressed was characterized by using an anti-BLV monoclonal antibody by both Western blotting analysis and enzyme-linked immunosorbent assay (ELISA). The secreted gp51 was used as an antigen, and an ELISA with recombinant gp51 (rgp51) was developed for the detection of BLV antibodies. This new procedure was compared with a previous ELISA method for the detection of BLV antibodies and an agar gel immunodiffusion test performed with an unpurified BLV antigen preparation. The comparative testing of field samples showed that the ELISA with rgp51 is more specific and also suitable for the testing of pooled sera.
The problems with Criterion A: A comment on Morey et al. (2022). (2022)

The alternative model of personality disorder (American Psychiatric Association, 2013), introduced in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, represents a significant advancement in our understanding of personality disorders. Despite this advancement, nearly 10 years after its introduction, considerable debate remains regarding the conceptualization, operationalization, and ultimately the utility of personality impairment (i.e., Criterion A). Morey et al. (2022) review the impetus for, conceptualization of, the current state of our understanding of Criterion A, and conclude that Criterion A is a valid and clinically useful component of the alternative model of personality disorder. In our commentary, we present a more pessimistic view and review literature critical of Criterion A not included in the main text of their review. We conclude that Criterion A, as currently operationalized by the Level of Personality Functioning Scale, does not provide the functionality or utility as suggested by Morey and colleagues in their review. Instead, we suggest that pathological traits are well-positioned to capture severity of dysfunction and likely carry the most clinically useful information. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
[Effects of antisense N-myc gene on nerve growth factor-induced differentiation of neuroblastoma cell line]. (1999)

Antisense N-myc transfection could specifically inhibit the expression of N-myc and promoted the nerve growth factor-induced differentiation of neuroblastoma cell line. Transfection of antisense N-myc could also enhance the process of apoptosis of the tumor cells.