gebhart/patrepeval huggingface dataset:
Effects of carbon dioxide and iron enrichment of a calcareous soil on Fe‐chlorosis, root and shoot development of grain sorghum (1988)

Abstract Changes in atmospheric CO2 have been shown to influence plant growth and maturity of many plants. A greenhouse experiment was conducted to determine the effects of enriched soil CO2 and moisture on Fe utilization and Fe deficiency chlorosis of grain sorghum (Sorghum bicolor L. Moench). Clareville cl (Pachic Argiustoll) was treated with 0, 2, and 4 mg Fe kg‐1 soil. Soil moisture regimes of 0.5 and 5.0 bars were compared at unaltered CO2 levels (control) and with CO2 injected into the potted soil periodically at measured intervals. Shoots and roots dry matter yields increased with increasing Fe rates and higher moisture content. However, soil CO2‐enrichment drastically depressed roots and shoots growth, dry matter yields and suppressed response to applied Fe. Overall analysis of variance for chlorosis and dry matter yields indicated that Fe explained most of the total variation in chlorosis ratings, while CO2 accounted for most of the total variation in dry matter yields. Iron uptakes were slightly lower, while P uptakes were drastically depressed with soil CO2‐enrichment. Tissue manganese concentrations were slightly lower, while Zn tissue contents were depressed as much as 60%. Tissue calcium contents were higher while Mg and K contents were lower with CO2‐enrichment. Soil DTPA extractable Fe at harvest was slightly lower with CO2‐enrichment, and generally ranged in the deficient category. Key words: Sorghum bicolor LFe‐EDDHAcalcareoustissue FeMnZnCuCaK and MgANOVAFe and P uptake
Design and Modeling of High-Impedance Electromagnetic Surfaces for Switching Noise Suppression in Power Planes (2005)

This paper presents a detailed design and modeling approach for power planes with integrated high-impedance electromagnetic surfaces (HIS). These novel power planes, which were introduced recently, have the unique ability of providing effective broadband simultaneous switching noise (SSN) mitigation. Full-wave electromagnetic simulation is used to study the impact of the geometry on the performance of these novel power planes. It is demonstrated that power planes using inductance-enhanced HIS can be designed for broadband mitigation of the SSN from the upper hundred megahertz to the gigahertz frequencies. Physics-based compact models for the unit cell of power planes with integrated HIS are developed and several of them connected in a two-dimensional array to build full models for large and multilayer power planes. The compact model offers fast analysis of power planes. As an example, we show that the full-wave simulation time of a 10/spl times/10 cm power plane with integrated HIS can be dramatically reduced from 24 to 48 h using a commercially available three-dimensional full-wave solver to less than 1 min when using the compact circuit model developed here.
Anemia in Cancer: Some Pathophysiological Aspects (2003)

After completing this course, the reader will be able to: Recognize the causes of anemia in cancer patients. Describe ways in which the action of erythropoietin is regulated. Explain the methods for treating anemia and indications for treatment. Access and take the CME test online and receive one hour of AMA PRA category 1 credit at CME.TheOncologist.com More than 30% of cancer patients experience anemia and its side effect, fatigue. Its causes can be numerous, but anemia is usually secondary to an imbalance of cytokines. Among these, tumor necrosis factor-alpha seems to be the major culprit, creating anemia by blunting the physiological effect of erythropoietin. Pharmacologically increasing the erythropoietin level corrects the anemia in about half the treated patients. Several studies have shown that quality of life is substantially improved through such therapy.
Chick myotendinous antigen. II. A novel extracellular glycoprotein complex consisting of large disulfide-linked subunits. (1984)

This report describes the biochemical characterization of a novel extracellular matrix component, " myotendinous antigen," which appears early in chick limb morphogenesis at sites connecting developing muscle fibers, tendons, and bone ( Chiquet , M., and D. Fambrough , 1984; J. Cell Biol., 98:1926-1936). This extracellular matrix antigen is a major component of the secretory proteins released into the medium by fibroblast and muscle cultures; the soluble form is characterized here. This form of myotendinous antigen is a large glycoprotein complex consisting of several disulfide linked subunits (Mr approximately 150,000-240,000). The differently sized antigen subunits are related, since they yielded very similar proteolytic cleavage patterns. M1 antibody can bind to the denatured subunits. The antigen subunits, as well as a Mr approximately 80,000 pepsin-resistant antigenic domain derived from them, are resistant to bacterial collagenase. Despite possessing subunits similar in size to fibronectin, myotendinous antigen appears to be both structurally and antigenically unrelated to fibronectin or to other known extracellular matrix components. About seven times more M1 antigen per cell nucleus was released into the medium in fibroblast as compared to muscle cultures. In muscle conditioned medium, myotendinous antigen is noncovalently complexed to very high molecular weight material that could be heavily labeled by [3H]glucosamine and [35S]sulfate. This material is sensitive to chondroitinase ABC and hence appears to contain sulfated glycosaminoglycans. We speculate that myotendinous antigen might interact with proteoglycans on the surface of muscle fibers, thereby acting as a link to tendons.
Analysis and Prediction of the Metabolic Stability of Proteins Based on Their Sequential Features, Subcellular Locations and Interaction Networks (2010)

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein's metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein's metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: "short", "medium", "long", and "extra-long" half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age.
Therapeutic hypothermia and controlled normothermia in the intensive care unit: Practical considerations, side effects, and cooling methods* (2009)

Temperature management and hypothermia induction are gaining importance in critical care medicine. Intensive care unit physicians, critical care nurses, and others (emergency physicians, neurologists, and cardiologists) should be familiar with the physiologic effects, current indications, techniques, complications and practical issues of temperature management, and induced hypothermia. In experienced hands the technique is safe and highly effective.
Endocrine Therapy Resistance in Breast Cancer: Current Status, Possible Mechanisms and Overcoming Strategies (2015)

Endocrine therapy has become one of most effective forms of targeted adjuvant therapy for hormone-sensitive breast cancer and may be given after surgery or radiotherapy, and also prior, or subsequent to chemotherapy. Current commonly used drugs for adjuvant endocrine therapy can be divided into following three classes: selective estrogen receptor modulators, aromatase inhibitors and selective estrogen receptor downregulators. Tumor cells can develop resistance to endocrine therapy, a major obstacle limiting the success of breast cancer treatment. The complicated crosstalk, both genomic and nongenomic, between estrogen receptors and growth factors was considered to be a crucial factor contributing to endocrine resistance. However, resistance to this therapy is thought to be a progressive, step-wise process, and the underlying mechanism remains unclear. In this review, we summarize the possible biological and molecular mechanisms that underlie endocrine resistance, and discuss some novel strategies to overcoming these issues.
Role of IL-10 for Induction of Anemia During Inflammation (2002)

Anemia is frequently observed in patients suffering from chronic inflammatory disorders. Recent in vitro data suggest that Th2 cytokines, such as IL-10, could be involved in its pathogenesis. We analyzed 1) changes in hemoglobin values in 329 patients with chronic active Crohn's disease receiving the anti-inflammatory cytokine IL-10 as part of a randomized, double-blind, placebo-controlled study, 2) serum iron parameters in a subgroup of these patients (n = 54), and 3) the in vitro effects of IL-10 on ferritin transcription and translation in human monocytic cells (THP-1) by means of Northern blot and immunoprecipitation after metabolic labeling. Patients receiving higher doses of IL-10 developed anemia and presented with a dose-dependent increase of ferritin and soluble transferrin receptor levels, an indicator of iron restriction to erythroid progenitor cells. According to our in vitro data, hyperferritinemia may result from direct stimulation of ferritin translation by IL-10 in activated monocytic cells, most likely by cytokine-mediated reduction of the binding affinity of translational repressors, iron-regulatory proteins, to the 5'-untranslated region of ferritin mRNA. In patients, all observed changes were most pronounced at the end of therapy (day +29), and thereafter hemoglobin levels and serum iron parameters returned to baseline levels within 4 wk of follow-up. Our data demonstrate that IL-10 causes anemia in patients with inflammatory bowel disease which may be referred to the induction of imbalances in iron homeostasis by the cytokine, leading to hyperferritinemia and limited iron availability to erythroid progenitor cells, a condition typically seen in the anemia of chronic inflammation.
Binding of 125I-fasciculin to rat brain acetylcholinesterase. The complex still binds diisopropyl fluorophosphate (1993)

Iodination of fasciculin 3 (FAS3) from Dendroaspis viridis venom provided us with a fully active specific probe of fasciculin binding sites on rat brain acetylcholinesterase (AChE). Binding and inhibition are concomitant, as association and inhibition rate constants k1 and ki are identical. The 125I-FAS3.AChE complex dissociates very slowly (t 1/2 = 48 h) and is characterized by a dissociation constant, Kd, of 0.4 pM. All the specific binding of 125I-FAS3 to AChE is prevented by FAS3 as from D. angusticeps venom (Kd = 0.4, 14, and 25 pM, respectively). It is also prevented by propidium iodide, BW284C51, and d-tubocurarine, which bind to peripheral anionic sites of AChE, by Ca2+ and Mg2+, known to enhance AChE activity through an allosteric phenomenon and by acetylthiocholine concentrations which lead to excess substrate inhibition of the enzyme. Diisopropyl fluorphosphate and paroxon, which inhibit AChE by phosphorylating the catalytic serine, have no effect on either the binding rate or the number of binding sites of 125I-FAS3. O-Ethyl-S2-diisopropylaminoethyl methylphosphonothionate, however, which binds irreversibly to the AChE catalytic site but reversibly to a peripheral site, induces a 130% increase in the binding rate of 125I-FAS3, without changing the total number of 125I-FAS3 binding sites. Our results demonstrate that fasciculins bind on a peripheral site of AChE, distinct from the catalytic site and, at least partly, common with the sites on which some cationic inhibitors and the substrate in excess bind. Since phosphorylation of the catalytic serine (esteratic subsite) by [1,3-3H]diisopropyl fluorophosphate can still occur on the FAS3.AChE complex, the structural modification induced by fasciculins may affect the anionic subsite of AChE catalytic site.
True Color Correction of Autonomous Underwater Vehicle Imagery (2015)

This paper presents an automated approach to recovering the true color of objects on the seafloor in images collected from multiple perspectives by an autonomous underwater vehicle (AUV) during the construction of three‐dimensional (3D) seafloor models and image mosaics. When capturing images underwater, the water column induces several effects on light that are typically negligible in air, such as color‐dependent attenuation and backscatter. AUVs must typically carry artificial lighting when operating at depths below 20‐30 m; the lighting pattern generated is usually not spatially consistent. These effects cause problems for human interpretation of images, limit the ability of using color to identify benthic biota or quantify changes over multiple dives, and confound computer‐based techniques for clustering and classification. Our approach exploits the 3D structure of the scene generated using structure‐from‐motion and photogrammetry techniques to provide basic spatial data to an underwater image formation model. Parameters that are dependent on the properties of the water column are estimated from the image data itself, rather than using fixed in situ infrastructure, such as reflectance panels or detailed data on water constitutes. The model accounts for distance‐based attenuation and backscatter, camera vignetting and the artificial lighting pattern, recovering measurements of the true color (reflectance) and thus allows us to approximate the appearance of the scene as if imaged in air and illuminated from above. Our method is validated against known color targets using imagery collected in different underwater environments by two AUVs that are routinely used as part of a benthic habitat monitoring program.
NICE: Non-linear Independent Components Estimation (2014)

We propose a deep learning framework for modeling complex high-dimensional densities called Non-linear Independent Component Estimation (NICE). It is based on the idea that a good representation is one in which the data has a distribution that is easy to model. For this purpose, a non-linear deterministic transformation of the data is learned that maps it to a latent space so as to make the transformed data conform to a factorized distribution, i.e., resulting in independent latent variables. We parametrize this transformation so that computing the Jacobian determinant and inverse transform is trivial, yet we maintain the ability to learn complex non-linear transformations, via a composition of simple building blocks, each based on a deep neural network. The training criterion is simply the exact log-likelihood, which is tractable. Unbiased ancestral sampling is also easy. We show that this approach yields good generative models on four image datasets and can be used for inpainting.
Moving cast shadow elimination for robust vehicle extraction based on 2D joint vehicle/shadow models (2004)

A new algorithm to eliminate moving cast shadow for robust vehicle detection and extraction in a vision-based highway monitoring system is investigated. The proposed algorithm is based on a simplified 2D vehicle/shadow model of six types projected on to a 2D image plane. Parameters of the joint 2D vehicle/shadow models can be estimated from the input video without light source and camera calibration information. Simulations are performed to verify that the proposed technique is effective for vision-based highway surveillance systems.
Fluorescence probes for monitoring polymerization processes (1996)

Several intramolecular charge transfer fluorescence probes, such as the dansyl amides (1a-d), 4-dimethylamino-4′-nitrobiphenyl (2) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (3), have been developed and evaluated. The fluorescence emission of the probes is sensitive to both the solvent polarity and medium microviscosity. A spectral blue shift, attributed to an increase in microviscosity, was observed as polymerization proceeded. Therefore, these fluorescence probes can be used for monitoring polymerization processes. The correlation between the fluorescence emission intensity ratio and degree of cure is linear in various formulations, which may be cured either photochemically or thermally. The selectivity and sensitivity of the fluorescence probes have been investigated. 4-Dimethylamino-4′-nitrobiphenyl (2) was found to be the most sensitive probe to both solvent polarity and medium microviscosity. © 1996 John Wiley & Sons, Inc.
Assessing sample and miRNA profile quality in serum and plasma or other biofluids (2012)

MicroRNAs (miRNAs) constitute a class of small cellular RNAs (typically 21-23nt) that function as post-transcriptional regulators of gene expression. Current estimates indicate that more than one third of the cellular transcriptome is regulated by miRNAs, although they are relatively few in number (less than 2000 human miRNAs). The high relative stability of miRNA in common clinical tissues and biofluids (e.g. plasma, serum, urine, saliva, etc.) and the ability of miRNA expression profiles to accurately classify discrete tissue types and disease states have positioned miRNA quantification as a promising new tool for a wide range of diagnostic applications. Furthermore miRNAs have been shown to be rapidly released from tissues into the circulation with the development of pathology. To facilitate discovery and clinical development of miRNA-based biomarkers, we developed a genome-wide Locked Nucleic Acid (LNA™)-based miRNA qPCR platform with unparalleled sensitivity and robustness. The platform allows high-throughput profiling of miRNAs from important clinical sources without the need for pre-amplification. Using this system, we have profiled thousands of biofluid samples including blood derived plasma and serum. An extensive quality control (QC) system has been implemented in order to secure technical excellence and reveal any unwanted bias coming from pre-analytical or analytical variables. We present our approaches to sample and RNA QC as well as data QC and normalization. Specifically we have developed normal reference ranges for circulating miRNAs in serum and plasma as well as a hemolysis indicator based on microRNA expression.
In vitro analysis of aminoglycoside therapy for the Arg120stop nonsense mutation in RP2 patients (2002)

X linked retinitis pigmentosa (XLRP) is a heterogeneous disease causing a severe form of retinal degeneration. Patients typically present with night blindness and constricted visual fields within the first two decades of life owing to peripheral photoreceptor degeneration. As the disease progresses, impairment of central vision occurs resulting in loss of visual acuity and complete functional blindness often by the age of 40-50 years.1 The gene that causes one form of this disease, RP2 , has recently been positionally cloned and has been shown to account for between 15-20% of XLRP.2 The RP2 gene consists of five exons encoding a polypeptide of 350 amino acids and is ubiquitously expressed. There are currently few functional data available about this protein. One functional clue is a similarity to cofactor C with the predicted RP2 amino acid sequence having 30.4% identity over 151 amino acids.2 Cofactor C was initially thought to play a role in the folding of β-tubulin,3,4 suggesting that RP2 could also be involved in tubulin biogenesis. A recent study has shown, however, that RP2 undergoes N-terminal acyl modification and thus has a predominantly plasma membrane localisation in cultured cells.5 For this reason it seems unlikely that RP2 functions exclusively in tubulin folding and its precise function and any specific role in the retina are at present unknown. Mutation screening in XLRP patients has identified over 20 different pathogenic mutations in the RP2 gene, including missense, frameshift, insertion, and deletion changes.2,6–11 There are also three different identified nonsense mutations causing a premature stop within the first two exons of the gene.2,6–8

In this study, we have investigated a potential drug mediated therapy to restore RP2 function in patients with nonsense mutations, in particular the opal nonsense mutation converting CGA …
Extensive β -Glucuronidase Activity in Murine Central Nervous System after Adenovirus-Mediated Gene Transfer to Brain (1998)

Mucopolysaccharidosis type VII (MPS VII), caused by beta-glucuronidase deficiency, is a classic lysosomal storage disease. In the central nervous system (CNS), there is widespread pathology with distention of vacuoles in neurons and glia. An approach to therapy for MPS VII would require extensive delivery of enzyme to the CNS and subsequent uptake by the affected cells. In this study we show that intrastriatal injection of recombinant adenovirus encoding beta-glucuronidase (Ad betagluc) to MPS VII or wild-type mice results in focal, intense beta-glucuronidase mRNA expression near the injection site. Further, histochemical staining for enzyme activity showed that beta-glucuronidase activity extended well beyond transduced cells. Activity was detected throughout the ipsilateral striatum as well as in the corpus callosum, ventricles, and bilateral neocortex. Similarly, after injection into the right lateral ventricle or cisterna magna, enzyme activity was present in the ependymal cells of the ventricles, in the subarachnoid spaces, and also in the underlying cortex (150-500 microm from ependyma). The distribution of enzyme was most extensive 21 days after gene transfer to normal mouse brain, with more than 50% of the hemisphere positive for beta-glucuronidase activity. Eighty-four days after adenovirus injection a substantial level of enzyme expression remained (>40% of hemisphere positive for beta-glucuronidase activity). Histological sections from striatum of beta-glucuronidase-deficient mice injected with Ad betagluc showed a marked reduction in the number of distended vacuoles in both neurons and glia, as compared with uninjected striatum. Importantly, correction was noted in both hemispheres. Our finding that a relatively small number of transduced cells produce enzyme that reaches a large proportion of the CNS has favorable implications in developing direct gene transfer therapies for lysosomal storage disorders.