gebhart/patrepeval huggingface dataset:
Use of a Single-Chain Antibody Library for Ovarian Cancer Biomarker Discovery (2010)

The discovery of novel early detection biomarkers of disease could offer one of the best approaches to decrease the morbidity and mortality of ovarian and other cancers. We report on the use of a single-chain variable fragment antibody library for screening ovarian serum to find novel biomarkers for the detection of cancer. We alternately panned the library with ovarian cancer and disease-free control sera to make a sublibrary of antibodies that bind proteins differentially expressed in cancer. This sublibrary was printed on antibody microarrays that were incubated with labeled serum from multiple sets of cancer patients and controls. The antibodies that performed best at discriminating disease status were selected, and their cognate antigens were identified using a functional protein microarray. Overexpression of some of these antigens was observed in cancer serum, tumor proximal fluid, and cancer tissue via dot blot and immunohistochemical staining. Thus, our use of recombinant antibody microarrays for unbiased discovery found targets for ovarian cancer detection in multiple sample sets, supporting their further study for disease diagnosis.
Stress- and mitogen-induced phosphorylation of the synapse-associated protein SAP90/PSD-95 by activation of SAPK3/p38gamma and ERK1/ERK2 (2004)

SAPK3 (stress-activated protein kinase-3, also known as p38gamma) is a member of the mitogen-activated protein kinase family; it phosphorylates substrates in response to cellular stress, and has been shown to bind through its C-terminal sequence to the PDZ domain of alpha1-syntrophin. In the present study, we show that SAP90 [(synapse-associated protein 90; also known as PSD-95 (postsynaptic density-95)] is a novel physiological substrate for both SAPK3/p38gamma and the ERK (extracellular-signal-regulated protein kinase). SAPK3/p38gamma binds preferentially to the third PDZ domain of SAP90 and phosphorylates residues Thr287 and Ser290 in vitro, and Ser290 in cells in response to cellular stresses. Phosphorylation of SAP90 is dependent on the binding of SAPK3/p38gamma to the PDZ domain of SAP90. It is not blocked by SB 203580, which inhibits SAPK2a/p38alpha and SAPK2b/p38beta but not SAPK3/p38gamma, or by the ERK pathway inhibitor PD 184352. However, phosphorylation is abolished when cells are treated with a cell-permeant Tat fusion peptide that disrupts the interaction of SAPK3/p38gamma with SAP90. ERK2 also phosphorylates SAP90 at Thr287 and Ser290 in vitro, but this does not require PDZ-dependent binding. SAP90 also becomes phosphorylated in response to mitogens, and this phosphorylation is prevented by pretreatment of the cells with PD 184352, but not with SB 203580. In neurons, SAP90 and SAPK3/p38gamma co-localize and they are co-immunoprecipitated from brain synaptic junctional preparations. These results demonstrate that SAP90 is a novel binding partner for SAPK3/p38gamma, a first physiological substrate described for SAPK3/p38gamma and a novel substrate for ERK1/ERK2, and that phosphorylation of SAP90 may play a role in regulating protein-protein interactions at the synapse in response to adverse stress- or mitogen-related stimuli.
Who needs a 20 cm precision farming system? (2002)

The GPS industry has recently focused a great deal of effort on emerging applications in the agriculture industry. The technology is now available to develop accurate navigational devices that will allow the farmer to place the correct amount of fertilizers and chemicals where the field requires it. Computer maps can be generated by soil testing, yield monitoring, and using previous field input information along with accurate positioning devices. These maps can then be used with the variable applicators that are capable of varying the rates as they pass through different parts of the fields. These applicators use a computer to control the rates of nitrogen, phosphate and other essential fertilizers that will provide the correct amount of nutrients for the crop to carry it through the growing season. It is understood that real-time accuracy of 0.02 to 0.20 m is required in the agriculture industry to provide the benefits as mentioned. With recent developments, GPS hardware technology has evolved to the stage where suitable and cost effective accuracy can now be achieved to address this market requirement. Technology is now being implemented into products which are proving accurate to these levels.
Immune response to bacterial dextrans. II. T cell control of antibody isotypes. (1983)

The isotype distribution of Dextran B 512 (Dex)-specific plaque-forming cells (PFC) and serum antibodies was studied after in vivo immunization in C57BL/6 mice. Although IgG2b and IgG3 could also be detected in most individuals, the majority of non-IgM PFC were of the IgA isotype. All classes other than IgM were T cell-dependent, as shown by their complete absence in athymic "nude" mice. This unusual isotype pattern was further investigated by studying the antibody responses to the same Dex epitope coupled to a protein carrier, and to a different hapten coupled to the carrier Dex or to a protein. The results show that IgA responses are epitope-related and selectively associated with anti-Dex antibodies: no IgA PFC are detected against a hapten coupled to Dex or proteins, while the enhanced levels of helper cell reactivity provided by protein carrier to Dex result in the appearance of IgG1 antibodies in addition to IgA. These results indicate that T cells that modulate isotype patterns in these responses can discriminate between Dex- and DNP-specific B cells in the response to the same carrier. Since the same idiotype is detected on a large fraction of the IgM and IgA anti-Dex response and antiidiotypic helper cells have previously been detected in normal C57BL/6 mice, we suggest that idiotype-specific T cells control the production of IgA antibodies upon immunization with Dex.
Development of breeding populations of rhesus macaques (Macaca mulatta) that are specific pathogen-free for rhesus cytomegalovirus. (2008)

Development of breeding colonies of rhesus macaques (Macaca mulatta) that are specific pathogen-free (SPF) for rhesus cytomegalovirus (RhCMV) is relatively straightforward and requires few modifications from current SPF programs. Infants separated from the dam at or within a few days of birth and cohoused with similarly treated animals remain RhCMV seronegative indefinitely, provided they are never directly or indirectly exposed to a RhCMV-infected monkey. By systematically cohousing seronegative animals into larger social cohorts, breeding populations of animals SPF for RhCMV can be established. The additional costs involved in expanding the current definition of SPF status to include RhCMV are incremental compared with the money already being spent on existing SPF efforts. Moreover, the large increase in research opportunities available for RhCMV-free animals arguably would far exceed the development costs. Potential new areas of research and further expansion of existing research efforts involving these newly defined SPF animals would have direct implications for improvements in human health.
Difference between compositional and grain size effect on the dielectric nonlinearity of Mn and V-doped BaTiO3 multilayer ceramic capacitors (2014)

The difference between compositional and grain size effect on the dielectric nonlinearity was contrasted in Mn and V-doped BaTiO3 multilayer ceramic capacitors utilizing the first order reversal curve (FORC) distribution based on the Preisach model. The high field dielectric constants can be increased either by the adjustment of additive composition, that is, Ba concentration maintaining the same grain size, or by increasing its size. The former compositional effect caused an enhanced dielectric constant in both low and high field region, which can be associated with the increase in the saturation polarization, the reversible and the irreversible FORC distributions near zero bias. The latter grain growth effect, on the other hand, resulted in a decrease of the dielectric constants in the low field but a steep ac field dependence of them, which can be correlated with a decrease of the reversible FORC distribution and a significant increase of the irreversible FORC distribution near origin. These results show that the compositional effect is caused by the increase of the magnitude of the spontaneous polarization and the domain wall density, whereas the grain size effect is caused by the increase in the size of the domain and its wall, which increases the probability of domain pinning by weakly pinning centers but enables its long range motion beyond the threshold field.
<i>POMT2</i> mutations cause α-dystroglycan hypoglycosylation and Walker-Warburg syndrome (2005)

A fourth causative gene for WWS was uncovered. These genes account for approximately one third of the WWS cases. Several more genes are anticipated, which are likely to play a role in glycosylation of alpha-DG.
The Notochordal Cell in the Nucleus Pulposus: A Review in the Context of Tissue Engineering (2003)

An understanding of developmental biology can provide useful insights into how different tissue-engineered repairs might be designed. During embryogenesis of the intervertebral disk, the cells of the notochord play a critical role in initiating tissue formation, and may be responsible for development of the nucleus pulposus. In some species, including humans, these notochordal cells may eventually be lost, either through apoptosis or terminal differentiation, and are replaced by chondrocyte-like cells. However, there is some evidence that the notochordal cells may persist in at least some humans. This review discusses some of the potential applications of notochordal cells in tissue engineering of the nucleus pulposus.
Na-K-Cl cotransporter-1 in the mechanism of cell swelling in cultured astrocytes after fluid percussion injury (2011)

Brain edema and associated increased intracranial pressure are major consequences of traumatic brain injury (TBI). An important early component of the edema associated with TBI is astrocyte swelling (cytotoxic edema). Mechanisms for such swelling, however, are poorly understood. Ion channels/transporters/exchangers play a major role in cell volume regulation, and a disturbance in one or more of these systems may result in cell swelling. To examine potential mechanisms in TBI-mediated brain edema, we employed a fluid percussion model of in vitro barotrauma and examined the role of the ion transporter Na(+)-K(+)-2Cl(-)-cotransporter 1 (NKCC1) in trauma-induced astrocyte swelling as this transporter has been strongly implicated in the mechanism of cell swelling in various neurological conditions. Cultures exposed to trauma (3, 4, 5 atm pressure) caused a significant increase in NKCC1 activity (21%, 42%, 110%, respectively) at 3 h. At 5 atm pressure, trauma significantly increased NKCC1 activity at 1 h and it remained increased for up to 3 h. Trauma also increased the phosphorylation (activation) of NKCC1 at 1 and 3 h. Inhibition of MAPKs and oxidative/nitrosative stress diminished the trauma-induced NKCC1 phosphorylation as well as its activity. Bumetanide, an inhibitor of NKCC1, significantly reduced the trauma-induced astrocyte swelling (61%). Silencing NKCC1 with siRNA led to a reduction in trauma-induced NKCC1 activity as well as in cell swelling. These findings demonstrate the critical involvement of NKCC1 in the astrocyte swelling following in vitro trauma, and suggest that blocking NKCC1 activity may represent a useful therapeutic strategy for the cytotoxic brain edema associated with the early phase of TBI.
CCR5, GPR15, and CXCR6 Are Major Coreceptors of Human Immunodeficiency Virus Type 2 Variants Isolated from Individuals with and without Plasma Viremia (2005)

Human immunodeficiency virus type 2 (HIV-2) is generally considered capable of using a broad range of coreceptors. Since HIV-2 variants from individuals with nonprogressive infection were not studied previously, the possibility that broad coreceptor usage is a property of variants associated with progressive infection could not be excluded. To test this, we determined the coreceptor usage of 43 HIV-2 variants isolated from six long-term-infected individuals with undetectable plasma viremia. Using GHOST indicator cells, we showed for the first time that the only coreceptors efficiently used by low-pathogenic HIV-2 variants are CCR5, GPR15 (BOB), and CXCR6 (BONZO). Surprisingly, control HIV-2 variants (n = 45) isolated from seven viremic individuals also mainly used these three coreceptors, whereas use of CCR1, CCR2b, or CCR3 was rare. Nearly a quarter of all HIV-2 variants tested could infect the parental GHOST cells, which could be partially explained by CXCR4 usage. Use of CXCR4 was observed only for HIV-2 variants from viremic individuals. Thirty-eight variants from aviremic and viremic HIV-2-infected individuals were additionally tested in U87 cells. All except one were capable of infecting the parental U87 cells, often with high efficiency. When virus production in parental cells was regarded as background in the coreceptor-transduced cell lines, the results in U87 cells were largely in agreement with the findings in GHOST cells. HIV-2 isolates from aviremic individuals commonly use as coreceptors CCR5, GPR15, and CXCR6, as well as an unidentified receptor expressed by U87 cells. Broad coreceptor usage, therefore, does not appear to be associated with pathogenicity of HIV-2.
[Comparison of the radiosensitivity of chromosomes during the S and G2 periods in regenerating rat liver cells]. (1976)

Radiosensitivity of chromosomes at S and G2 periods was studied by means of autoradiography technique in cells or regenerating liver of rats treated with X-rays at the doses of 150 and 300 r. The experiments were made so that the interval between irradiation and mitosis in S and G2 cells was equal. The results have shown that under the experimental conditions there are significant differences in the yield of chromosome aberrations between the labelled and intact cells. This withnesses for the existence of differences in radiosensitivity of chromosomes at different periods of mitotic cycle.
Are Short Chain Fatty Acids in Gut Microbiota Defensive Players for Inflammation and Atherosclerosis? (2017)

Intestinal flora (microbiota) have recently attracted attention among lipid and carbohydrate metabolism researchers. Microbiota metabolize resistant starches and dietary fibers through fermentation and decomposition, and provide short chain fatty acids (SCFAs) to the host. The major SCFAs acetates, propionate and butyrate, have different production ratios and physiological activities. Several receptors for SCFAs have been identified as the G-protein coupled receptor 41/free fatty acid receptor 3 (GPR41/FFAR3), GPR43/FFAR2, GPR109A, and olfactory receptor 78, which are present in intestinal epithelial cells, immune cells, and adipocytes, despite their expression levels differing between tissues and cell types. Many studies have indicated that SCFAs exhibit a wide range of functions from immune regulation to metabolism in a variety of tissues and organs, and therefore have both a direct and indirect influence on our bodies. This review will focus on SCFAs, especially butyrate, and their effects on various inflammatory mechanisms including atherosclerosis. In the future, SCFAs may provide new insights into understanding the pathophysiology of chronic inflammation, metabolic disorders, and atherosclerosis, and we can expect the development of novel therapeutic strategies for these diseases.
Resonant tunneling in coupled quantum dots (1992)

Resonant tunneling in GaAs-AlGaAs triple barrier diodes is studied as a function of the diode diameter between d=8 μm and d=100 nm. We observe, only in the very small diodes, a novel spikelike fine structure in the current-voltage characteristics within the conventional resonant tunneling peaks. These spikes are assigned to resonant tunneling between coupled quantum dots. Furthermore, a much stronger quenching of the conventional resonance peaks at lower bias is observed with decreasing diode diameters as compared to the higher bias peaks. This effect is clearly reproducible and may be an indication that the low bias peaks employ different tunneling mechanisms than the high bias peaks.
Implementation of integrated membrane processes for pilot scale development of fractionated milkcomponents (2000)

Numerous opportunities for the separation and fractionation of milk and whey components are presented as a result of continuing developments in filtration membranes modules and processes. The preparation of sufficient quantities of selected protein groups for functionality studies and food application tests requires considerable amounts of starting material, particularly in the case of whey-based constituents. Adequate amounts of membrane filtration surface area are, therefore, needed in order to expedite processing time, limit conditions for microbial growth and increase productivity from a product development point of view. With this objective in mind, a series of large pilot plant membrane separation systems based on microfiltration, ultrafiltration and electrodialysis were recently installed and commissioned. Rapid ultrafiltration of whey for the generation of high protein concentrates under a wide variety of conditions, including 'cold' filtration, is facilitated by a Memtech spiral wound membrane plant with a maximum surface area of 144 m 2 that is accommodated within 3 modules mounted in parallel. Designed to operate on a continuous feed-and-bleed principle, product is heated while pumping via a plate-heater to the plant's balance tank in order to raise temperature to the desired operating condition. Magnetic flow meters mounted on the feed, permeate and diafiltration water lines enable the volume concentration ratio to be controlled throughout a run. Defatting of rennet whey by microfiltration using a Tetra Pak Alcross M, Type 2 19 Special, crossflow microfiltration (MF) plant fitted with a 0.1 m pore size ceramic membrane with a filtration area of 13.3 m 2 trebled flux rate during ultrafiltration at 12 C under steady state conditions. High protein whey protein concentrates (ca. 80% total protein) were processed in the defatted and nondefatted state at either 50 C or 12C for functional characterisation. Preliminary analyses indicate that all 4 WPC's produced weak gels. Native phosphocasein was prepared from skim milk using the above MF plant. Partial demineralisation of skim milk prior to MF was facilitated using an Ionics (Ionics Inc.) Electromat ED, featuring a 100-cell pair Mark III electrodialysis membrane stack. Electrodialysis resulted in improvements in the heat stability profile of phosphocasein, at the expense of rennet coagulation properties which were totally eliminated even in the presence of added calcium.
Accuracy of CT‐based thickness measurement of thin structures: Modeling of limited spatial resolution in all three dimensions (2002)

Measurement of the width of thin structures such as the cortical shell of the vertebral body or femoral neck with computed tomography (CT) is limited by the spatial resolution of the CT system. Limited spatial resolution exists both within the CT image plane and perpendicular to it and can be described by the in-plane point spread function (PSF) and the across-plane slice sensitivity profile (SSP), respectively. The goal of this study was to confirm that errors of thickness measurement of thin structures critically depend on the spatial positioning of the object and the spatial resolution limitations of CT in all three dimensions, and to assess the size of the errors themselves. We compared computer models that incorporated both effects to experimentally assessed cortical thicknesses of the European Spine Phantom. Analysis included varying CT slice width, the orientation of measurement and angle beta of misalignment of longitudinal scanner and phantom axes. Agreement of models with measurements was good in all configurations with an overall error of 0.17 mm. This showed that PSF and SSP are adequate system characteristics to predict deviation of measured values from true widths. Errors between measurements and true cortical thickness values delta(true) averaged to 1.5 mm were strongly positively correlated with slice width d and beta. When the across-plane partial volume effect was eliminated, limited in-plane resolution still accounted for overestimation of delta(true) by 0.68 (137%), 0.27 (27%), and 0.06 mm (4%) for delta(true)=0.5, 1.0, and 1.5 mm, respectively. For delta(true) of 1.0 mm and above, it was shown that although the absolute cortical thickness values might not be accurately measurable, relative differences between two values are reflected in measurement. Implications for cortical thickness measurement are that the spinal cortical shell is too thin, whereas accurate assessment at locations of the femoral neck exhibiting a thicker cortical shell of both difference and absolute values should be possible with CT even for larger misalignment angles, especially when a smaller CT slice width is chosen.
Optical and Magnetooptical Properties of FePt–SiO[sub 2] Magnetic Nanocomposites (2005)

The magnetic, optical, and magnetooptical properties of granular (FePt)1−x (SiO2)x nanocomposites in the disordered state and after heat treatment were studied. The magnetooptical response of samples in which the concentration of the metallic component approached the percolation threshold was observed to become considerably enhanced. Modeling transverse Kerr effect (TKE) spectra in a straightforward effective medium approximation provided a qualitative fit to the experimental data over a broad concentration range. The dependences of the Kerr effect on the SiO2 concentration in the nanocomposite are not monotonic and exhibit a sharp break near the percolation threshold. An analysis of the field dependences of the TKE and magnetization curves revealed that structural changes associated with ordering in annealed FePt films occur only in nanocomposites with fairly large grains.
Tissue regulatory T cells (2020)

Foxp3<sup>+</sup> CD4<sup>+</sup> regulatory T cells (Tregs) are an immune cell lineage endowed with immunosuppressive functionality in a wide array of contexts, including both anti-pathogenic and anti-self responses. In the past decades, our understanding of the functional diversity of circulating or lymphoid Tregs has grown exponentially. Only recently, the importance of Tregs residing within non-lymphoid tissues, such as visceral adipose tissue, muscle, skin and intestine, has been recognized. Not only are Tregs critical for influencing the kinetics and strength of immune responses, but the regulation of non-immune or parenchymal cells, also fall within the purview of tissue-resident or infiltrating Tregs. This review focuses on providing a systematic and comprehensive comparison of the molecular maintenance, local adaptation and functional specializations of Treg populations operating within different tissues.