gebhart/patrepeval huggingface dataset:
Hyperosmotic stress activates Rho: differential involvement in Rho kinase-dependent MLC phosphorylation and NKCC activation (2003)

Hyperosmotic stress initiates adaptive responses, including phosphorylation of myosin light chain (MLC) and concomitant activation of Na+-K+-Cl- cotransporter (NKCC). Because the small GTPase Rho is a key regulator of MLC phosphorylation, we investigated 1) whether Rho is activated by hyperosmotic stress, and if so, what the triggering factors are, and 2) whether the Rho/Rho kinase (ROK) pathway is involved in MLC phosphorylation and NKCC activation. Rho activity was measured in tubular epithelial cells by affinity pulldown assay. Hyperosmolarity induced rapid (<1 min) and sustained (>20 min) Rho activation that was proportional to the osmotic concentration and reversed within minutes upon restoration of isotonicity. Both decreased cell volume at constant ionic strength and elevated total ionic strength at constant cell volume were capable of activating Rho. Changes in [Na+] and [K+] at normal total salinity failed to activate Rho, and Cl- depletion did not affect the hyperosmotic response. Thus alterations in cellular volume and ionic strength but not individual ion concentrations seem to be the critical triggering factors. Hyperosmolarity induced mono- and diphosphorylation of MLC, which was abrogated by the Rho-family blocker Clostridium toxin B. ROK inhibitor Y-27632 suppressed MLC phosphorylation under isotonic conditions and prevented its rise over isotonic levels in hypertonically stimulated cells. ML-7 had a smaller inhibitory effect. In contrast, it abolished the hypertonic activation of NKCC, whereas Y-27632 failed to inhibit this response. Thus hyperosmolarity activates Rho, and Rho/ROK pathway contributes to basal and hyperosmotic MLC phosphorylation. However, the hypertonic activation of NKCC is ROK independent, implying that the ROK-dependent component of MLC phosphorylation can be uncoupled from NKCC activation.
Interleukin‐18 levels in induced sputum are reduced in asthmatic and normal smokers (2004)

IL-18 is detectable in induced sputum samples from both asthmatic and normal subjects. Cigarette smoking significantly reduces sputum IL-18 levels. This effect is more pronounced in asthmatics than in normal subjects.
Electronic structure of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">FePO</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>,</mml:mo></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">LiFePO</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>,</mml:mo></mml:math>and related materials (2003)

The electronic structures of ${\mathrm{FePO}}_{4}$ and $\mathrm{Li}M{\mathrm{PO}}_{4},$ where $M=\mathrm{Mn},$ Fe, Co, and Ni, are studied within the framework of density-functional theory. These materials have interesting magnetic properties and have promising technological interest as cathode materials in rechargeable batteries. A comparison of results for various spin configurations suggests that the ferromagnetic configuration, while not seen experimentally, can serve as a useful approximation for studying general features of the electronic structure. The partial densities of states and contour plots of electron densities show that covalent bonding between Fe $3d$ and $\mathrm{O}2p$ orbitals is greater in ${\mathrm{FePO}}_{4}$ than in ${\mathrm{LiFePO}}_{4}.$ Nevertheless, ${\mathrm{LiFePO}}_{4}$ is calculated to have a greater binding energy than its ${\mathrm{FePO}}_{4}$ and Li metal components; the corresponding open circuit voltage for the cathode discharge is calculated to be 3.2 V, which is comparable to (although smaller than) the experimentally measured value.
Preprogrammed and Programmed Cell Death Mechanisms of Apoptosis: UV‐Induced Immediate and Delayed Apoptosis (1996)

Equitoxic doses (10% clonogenic survival) of UV radiation (UVR) from the three waveband regions, i.e. UVA1 (340-400 nm), UVB (290-320 nm) and UVC (200-290 nm), were shown to induce immediate or delayed apoptosis in L5178Y-R murine lymphoma cells. Membrane and DNA damage were shown to be the most probable initiators of UVA1-induced immediate or UVR-induced delayed apoptosis, respectively. These UV-induced apoptotic processes appeared to utilize two different "core" biochemical mechanisms; however, one core mechanism could be initiated at two distinct sites (e.g. membrane or DNA) and result in disparate kinetics. In an attempt to resolve this mechanistic issue, the dependence on macromolecular synthesis of each UV-induced apoptotic mechanism was investigated. In the absence of UVR, inhibition of either transcription (actinomycin D) or translation (cycloheximide) induced apoptosis in a concentration- and time-dependent manner. These results suggest that an apoptotic mechanism exists that does not require macromolecular synthesis postinsult (constitutive). The UVR data demonstrate that UVA1-induced immediate apoptosis utilizes this constitutive mechanism (preprogrammed), while UVR-induced delayed apoptosis utilizes the well-known inducible mechanism (programmed). Therefore, there are two different core biochemical mechanisms of apoptotic death available to each cell: preprogrammed (constitutive) and programmed (inducible) cell death.
Effect of Thickness of the p-AlGaN Electron Blocking Layer on the Improvement of ESD Characteristics in GaN-Based LEDs (2008)

The following letter presents a study regarding GaN-based light-emitting diodes (LEDs) with p-type AlGaN electron blocking layers (EBLs) of different thicknesses. The study revealed that the LEDs could endure higher electrostatic discharge (ESD) levels as the thickness of the AlGaN EBL increased. The observed improvement in the ESD endurance ability could be attributed to the fact that the thickened p-AlGaN EBL may partly fill the dislocation-related pits that occur on the surface of the InGaN-GaN multiple-quantum well (MQW) and that are due to the strain and the low-temperature-growth process. If these dislocation-related pits are not partly suppressed, they will eventually result in numerous surface pits associated with threading dislocations that intersect the InGaN-GaN (MQW), thereby reducing the ESD endurance ability. The results of the experiment show that the ESD endurance voltages could increase from 1500 to 6000 V when the thickness of the p-AlGaN EBL in the GaN LEDs is increased from 32.5 to 130 nm, while the forward voltages and light output powers remained almost the same.
Stability of cylindrospermopsin, the toxin from the cyanobacterium,Cylindrospermopsis raciborskii: Effect of pH, temperature, and sunlight on decomposition (1999)

Cylindrospermopsin is a powerful hepatotoxin produced by the cyanobacterium Cylindrospermopsis raciborskii. It is considered a potential threat to livestock, wildlife, and humans, and is the suspected cause of an outbreak of hepatoenteritis on Palm Island, Queensland, Australia, and various stock poisoning incidents around Australia. In this study, the stability of cylindrospermopsin was investigated using different parameters, including visible and UV light, sunlight, temperature and pH. Cylindrospermopsin decomposes rapidly (half-life of 1.5 h) when exposed to sunlight in an algal extract solution; however, no decomposition was recorded in pure cylindrospermopsin and Milli-Q water solutions. Cylindrospermopsin decomposes slowly in temperatures ranging from 4 to 50°C at pH 7. After 10 weeks at 50°C, cylindrospermopsin had degraded to 57% of the original concentration. This degradation was accompanied by an increase in another compound which is believed to be structurally related to cylindrospermopsin. Boiling does not cause a significant degradation of cylindrospermopsin within 15 min. Initial investigations indicate that cylindrospermopsin is degraded slowly under artificial light ranging from 42, 29, and 9 μE m−1 s−1 and in darkness. Degradation of cylindrospermopsin was not affected by changes in pH. Experiments were performed in sterile conditions. ©1999 John Wiley & Sons, Inc. Environ Toxicol 14: 155–161, 1999
Applying Deep Learning for Epilepsy Seizure Detection and Brain Mapping Visualization (2019)

Deep Convolutional Neural Network (CNN) has achieved remarkable results in computer vision tasks for end-to-end learning. We evaluate here the power of a deep CNN to learn robust features from raw Electroencephalogram (EEG) data to detect seizures. Seizures are hard to detect, as they vary both inter- and intra-patient. In this article, we use a deep CNN model for seizure detection task on an open-access EEG epilepsy dataset collected at the Boston Children's Hospital. Our deep learning model is able to extract spectral, temporal features from EEG epilepsy data and use them to learn the general structure of a seizure that is less sensitive to variations. For cross-patient EEG data, our method produced an overall sensitivity of 90.00%, specificity of 91.65%, and overall accuracy of 98.05% for the whole dataset of 23 patients. The system can detect seizures with an accuracy of 99.46%. Thus, it can be used as an excellent cross-patient seizure classifier. The results show that our model performs better than the previous state-of-the-art models for patient-specific and cross-patient seizure detection task. The method gave an overall accuracy of 99.65% for patient-specific data. The system can also visualize the special orientation of band power features. We use correlation maps to relate spectral amplitude features to the output in the form of images. By using the results from our deep learning model, this visualization method can be used as an effective multimedia tool for producing quick and relevant brain mapping images that can be used by medical experts for further investigation.
En-face OCT imaging of the anterior chamber (2002)

We report a system capable of collecting pairs of en-face OCT and confocal images from the anterior chamber. Pairs of such images are collected from up to 7 mm deep in the anterior chamber measured from the top of the cornea. The wavelength is 85micrometers and the power 0.3 mW. The system offers: (i) versatility, being capable of displaying both C-scan OCT images (constant depth, oriented perpendicularly on the optic axis) as well as B-scan OCT images (containing the optic axis or longitudinal); (ii) eye alignment using the Purkinje reflections in the confocal channel; (iii) overall eye guidance, on the confocal image; (iv) correction for the en-face movement in the B-scan images generated by en-face imaging using the confocal image. Animations of such pairs of images demonstrate the utility of the system for in vivo imaging of the anterior segment of the eye.
Profiling Core Proteomes of Human Cell Lines by One-dimensional PAGE and Liquid Chromatography-Tandem Mass Spectrometry (2003)

Protein expression profiles vary considerably between human cell lines and tissues, which is in part a reflection of their specialized roles within an organism. It is of considerable practical use to establish which proteins constitute the primary components of the respective proteomes. When compiled into databases, such information can facilitate the assessment of selectivity and specificity of a wide range of proteomic experiments. Here we describe the major constituents of proteomes of six human immortalized cell lines. By employing a combination of one-dimensional SDS-PAGE and nanocapillary liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified up to 1785 non-redundant cytoplasmic and nuclear proteins from a single cell line using 50 and 30 microg of total protein from the corresponding fractions. Up to 38 proteins could be identified from a single band in one liquid chromatography-MS/MS experiment. When combined with systematic gridding of gel lanes into 48 slices, a dynamic range for protein identification of approximately 1:2000 can be envisaged for this approach. Identified proteins range from 4-553 kDa in size, cover the pI range between 3.4 and 12.8, and include 255 proteins with predicted transmembrane domains. Repeated analysis of peptides derived from the same gel band showed that the reproducibility of nanocapillary liquid chromatography-MS/MS of such complex mixtures is about 60-70% suggesting that a particular analytical experiment would need to be repeated about three times to arrive at a representative estimate of the set of highly abundant proteins in a given proteome. Given its technical simplicity, sensitivity, and wealth of generated information, we have adopted this experimental approach to characterize every cell line and tissue that is the subject of experimentation in our laboratory. The combined dataset for the six cell lines consists of 2341 non-redundant human proteins and thus constitutes one of the largest collections of human proteomic data published to date.
Measurement of Agonist-Stimulated [<sup><small>35</small></sup>S]GTPγS Binding to Cell Membranes (2003)

This chapter describes a functional assay which measures the increase in guanine nucleotide exchange at G-proteins in cell membranes, resulting from agonist binding to G-protein-coupled receptors (GPCRs), by monitoring the binding of [35S]GTPγS, a radiolabeled, hydrolysis-resistant analog of GTP (guanosine triphosphate), in the presence of unlabeled GDP (guanosine triphosphate).
Simultaneous reconstruction of electrode contact impedances and internal electrical properties: I. Theory (2002)

In electrical impedance tomography (EIT) currents are applied through the electrodes attached on the surface of the object and the resulting voltages are measured using the same or additional electrodes. The internal admittivity distribution is estimated based on the current and voltage data. When the voltages are measured on the current carrying electrodes the contact impedance that exists in the electrode–surface interface causes a voltage drop. In some cases this effect of the electrodes is known. However, this is not always the case and the contact impedance has to be taken into account in the image reconstruction. In this paper we propose an approach for estimating the contact impedance of the electrodes simultaneously with the estimation of the admittivity of the object. The complete electrode model (CEM) is used in the estimation procedure. We compare the proposed approach to a simple method which is based on the well known definition of the sample resistivity. The proposed approach is tested with real measurements by estimating the admittivity of isotonic saline solution in a cylindrical test cell and with simulations in a three-dimensional cylindrical domain. The CEM-based approach is shown to produce results that are similar to the results obtained with the simple approach in the test cell case. The advantage of the CEM-based approach over the simple approach is that the complete electrode model does not have any geometrical constraints, which makes it possible to utilize it in EIT studies. The results show that the CEM-based approach works well and can be used in practical contact impedance estimation with real measurements. This will be further studied in part II of this paper.
Tuberculosis Screening in Adults Who Have Received Bacille Calmette-Guérin Vaccine (1995)

The incidence of tuberculosis among immigrants to the United States is 12 times that in the native-born population. Screening immigrants for tuberculosis is complicated by the widespread use of bacille Calmette-Guérin (BCG) vaccination. To determine the utility of tuberculin testing in adults who have been vaccinated with BCG vaccine, we studied the tuberculin reactions of 80 adults who came to us for naturalization physical examinations. No adverse effects were reported from tuberculin testing. Subjects from regions with a low prevalence of tuberculosis who had received BCG vaccine were significantly more likely to have a positive reaction than subjects who had not received BCG vaccine. However, among subjects from regions with a high prevalence of tuberculosis, there was no difference in the prevalence of positive reactions between those who reported having BCG vaccinations and those who said they had not. Interpretation of tuberculin reactions in immigrants who receive BCG vaccinations depends on the prevalence of tuberculosis in the country of origin. Adults receiving BCG vaccination who have a positive reaction and no evidence of active tuberculosis should receive prophylactic therapy or be observed carefully.
Behaviour (2002)

For a parasitic nematode, hosts represent oases of resource where reproduction and/or growth is possible, in an inhospitable desert where they are not. Parasites must cross this desert because their host is not immortal and the death of the host results in the death of the parasites contained within it. Thus, despite the difficulties, parasites have to face the hazards of transmission and infect new hosts to ensure the survival of the species. In this context the survival strategies of parasitic nematodes can be seen as mechanisms which either assist them to locate and infect a new host or to survive the period between hosts.
Tissue factor induction in human monocytes. Two distinct mechanisms displayed by different alloantigen-responsive T cell clones. (1985)

One component of the cellular immune response to antigens is the expression of procoagulant activity (PCA) by monocytes and macrophages. Induction of human monocyte PCA in response to alloantigenic stimulation requires the collaboration of HLA-DR-responsive T cells. In mixed lymphocyte cultures (MLCs), the induction of monocyte tissue factor appears to be mediated exclusively by a T cell-derived lymphokine. We have used a soft agar cloning method to generate alloantigen-responsive T cell clones from MLCs between irradiated Daudi lymphoblastoid cells and human peripheral blood mononuclear cells. Developing clones were screened for the ability to induce PCA in fresh autologous monocytes in response to Daudi stimulator cells. PCA induction was observed with some, but not all, proliferating T cell clones and two modes of induction were apparent. Some T cell clones mediated PCA induction exclusively by lymphokine production, whereas other clones delivered induction signals by direct cellular collaboration with the monocyte effector cells. These two inductive pathways were represented in distinct, non-inclusive functional subsets of T cell clones. Constitutive production of soluble inducer signals was not observed in T inducer clones. The magnitude of the monocyte PCA response increased in response to an increase in the allogeneic stimulator/T clone responder ratio, and third-party allogeneic cells were unable to elicit the PCA-inducing lymphokine signals from T inducer clones. Both modes of induction were shown to generate tissue factor protein activity in monocytes. Collectively, these results suggest that PCA induction can be initiated in response to alloantigens through collaboration with certain OKT3+, OKT4+, OKT8-, OKM1- T inducer clones, and that induction can be mediated by at least two different functional subsets of human T cells. Stimulation with the appropriate alloantigen may elicit both lymphokine and T cell-contact pathways of induction of tissue factor in human monocytes.
Studies on the Separation of Minor Actinides from High-Level Wastes by Extraction Chromatography Using Novel Silica-Based Extraction Resins (2000)

To develop an advanced partitioning process by extraction chromatography using a minimal organic solvent and compact equipment to separate minor actinides such as Am and Cm from nitrate acidic high-level waste (HLW) solution, several novel silica-based extraction resins have been prepared by impregnating organic extractants into the styrene-divinylbenzene copolymer, which is immobilized in porous silica particles (SiO2-P). The extractants include octyl(phenyl)-N, N-diisobutylcarbamoylmethylphosphine oxide (CMPO), di(2-ethylhexyl)-phosphoric acid (HDEHP), and bis(2,4,4-trimethylpentyl)dithiophosphinic acid (Cyanex 301). Compared to conventional polymer-matrix resins, these new types of extraction resin are characterized by rapid kinetics and significantly low pressure loss in a packed column.The results of separation experiments revealed that trivalent actinides and lanthanides can be separated from other fission products, such as Cs, Sr, and Ru in simulated HLW solution containing concentrated nitric acid by extraction chromatography using a CMPO/SiO2-P resin-packed column. Satisfactory separation between Am(III) and a macro amount of lanthanides from simulated HLW solution with pH 4 was achieved by using a newly purified Cyanex 301/SiO2-P resin. However, the Am(III) separation was very sensitive to the purity of Cyanex 301, and the improvement of its stability is an important task for practical utilization.
An Expert Ground Truth Set For Audio Chord Recognition And Music Analysis. (2011)

[TODO] Add abstract here.
Experimental Nude Mouse Model of Human Colorectal Cancer Liver Metastases<xref ref-type="fn" rid="FN2">2</xref> (1986)

A nude mouse model (BALB/c) was established for investigating the production of hepatic metastases by human colorectal carcinoma (HCC) cells. The malignant potentials of 3 different HCCs derived from a primary tumor (HCC-P4733), a lymph node metastasis (HCC-M14328), and a hepatic metastasis (HCC-M1410) were investigated following implantation into the spleens of athymic nude mice. Cells of the HCC-M1410 line produced extensive liver tumors in all mice by 30 days after injection. Cells of the HCC-M14328 and HCC-P4733 lines produced few liver tumors in the inoculated mice and then only after a 90-day period. Isozyme and karyotype analyses ascertained the human origin of all the tumors. Studies with [125I]IdUrd-labeled HT-29 carcinoma cells suggested that tumor cells reached the liver shortly after injection into the spleen. Thus the production of HCC tumors in livers of nude mice was determined by the ability of HCC cells to proliferate in the liver parenchyma rather than by the ability of the cells to reach the liver. The results suggest that the intrasplenic injection of HCC cells can provide a valuable model for the study of the biology and therapy of the liver metastases.
Email networks and the spread of computer viruses (2002)

Many computer viruses spread via electronic mail, making use of computer users' email address books as a source for email addresses of new victims. These address books form a directed social network of connections between individuals over which the virus spreads. Here we investigate empirically the structure of this network using data drawn from a large computer installation, and discuss the implications of this structure for the understanding and prevention of computer virus epidemics.
Insights into the chemical logic and enzymatic machinery of NRPS assembly lines (2015)

Appreciation that some cyclic peptide antibiotics such as gramicidin S and tyrocidine were nonribosomally synthesized has been known for 50 years. The past two decades of research including advances in bacterial genetics, genomics, protein biochemistry and mass spectrometry have codified the principles of assembly line enzymology for hundreds of nonribosomal peptides and in parallel for thousands of polyketides. The advances in understanding the strategies used for chain initiation, elongation and termination from these assembly lines have revitalized natural product biosynthetic communities.