gebhart/patrepeval huggingface dataset:
Lessons learned from the contamination of heparin (2009)

Heparin is unique as one of the oldest drugs currently still in widespread clinical use as an anticoagulant, a natural product, one of the first biopolymeric drugs, and one of the few carbohydrate drugs. Recently, certain batches of heparin have been associated with anaphylactoid-type reactions, some leading to hypotension and death. These reactions were traced to contamination with a semi-synthetic oversulfated chondroitin sulfate (OSCS). This Highlight reviews the heparin contamination crisis, its resolution, and the lessons learned. Pharmaceutical scientists now must consider dozens of natural and synthetic heparinoids as potential heparin contaminants. Effective assays, which can detect both known and unknown contaminants, are required to monitor the quality of heparin. Safer and better-regulated processes are needed for heparin production.
High performance superconducting wire in high applied magnetic fields via nanoscale defect engineering (2008)

High temperature superconducting (HTS) wires capable of carrying large critical currents with low dissipation levels in high applied magnetic fields are needed for a wide range of applications. In particular, for electric power applications involving rotating machinery, such as large-scale motors and generators, a high critical current, Ic, and a high engineering critical current density, JE, in applied magnetic fields in the range of 3–5 Tesla (T) at 65 K are required. In addition, exceeding the minimum performance requirements needed for these applications results in a lower fabrication cost, which is regarded as crucial to realize or enable many large-scale bulk applications of HTS materials. Here we report the fabrication of short segments of a potential superconducting wire comprised of a 4 µm thick YBa2Cu3O7−δ (YBCO) layer on a biaxially textured substrate with a 50% higher Ic and JE than the highest values reported previously. The YBCO film contained columns of self-assembled nanodots of BaZrO3 (BZO) roughly oriented along the c-axis of YBCO. Although the YBCO film was grown at a high deposition rate, three-dimensional self-assembly of the insulating BZO nanodots still occurred. For all magnetic field orientations, minimum Ic and JE at 65 K, 3 T for the wire were 353 A cm−1 and 65.4 kA cm−2, respectively.
Multicenter Phase II and Translational Study of Cetuximab in Metastatic Colorectal Carcinoma Refractory to Irinotecan, Oxaliplatin, and Fluoropyrimidines (2006)

Cetuximab is active and well tolerated in metastatic CRC refractory to irinotecan, oxaliplatin, and fluoropyrimidines. The severity of rash was related to efficacy. Neither EGFR kinase domain mutations nor EGFR gene amplification appear to be essential for response to cetuximab in this setting.
Ribonucleotide reductase from calf thymus. Separation of the enzyme into two nonidentical subunits, proteins M1 and M2. (1980)

Ribonucleotide reductase from calf thymus was separated into two nonidentical subunits (proteins M1 and M2) by chromatography on Blue Sepharose.Each subunit was inactive when assayed alone, but full activity was recovered on recombination.Protein M1 was purified to homogeneity as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, chromatography on Ultrogel AcA 34, and sedimentation equilibrium centrifugation.In solution, protein M l behaves as a monomer (5.7 S) with a molecular weight of 84,000.Addition of dTTP leads to dimer formation (8.8 S, molecular weight 170,000), while addition of dATP induces tetramer formation (15.2 S).In the presence of ATP, the protein exists as a mixture of dimers and tetramers.Oligomerization probably reflects conformational changes induced by the nucleotides.Binding of nucleotides to protein M1 was measured in equilibrium dialysis experiments.A maximum of 1.8 mol of dATP or 0.7 mol of dTl" was bound by 170,000 g of protein.In both cases, cooperativity of binding was observed with final dissociation constants of 3 X 10" M and 2 X M for dATP and dTTP, respectively.These data as well as competition experiments indicated the presence of two classes of effector binding sites, one specific for ATP and dATP, while the second class in addition bound dTTP and dGTP.Protein M2 was not obtained as a homogeneous preparation.It had a molecular weight of about 110,000, did not bind nucleotides, and was not influenced by nucleotides in its sedimentation behavior.
Immune Complex-Loaded Dendritic Cells Are Superior to Soluble Immune Complexes as Antitumor Vaccine (2006)

Dendritic cells (DCs) play an important role in the induction of T cell responses. Fc gammaRs, expressed on DCs, facilitate the uptake of complexed Ag, resulting in efficient MHC class I and MHC class II Ag presentation and DC maturation. In the present study, we show that prophylactic immunization with DCs loaded with Ag-IgG immune complexes (ICs) leads to efficient induction of tumor protection in mice. Therapeutic vaccinations strongly delay tumor growth or even prevent tumors from growing out. By depleting CD4+ and CD8+ cell populations before tumor challenge, we identify CD8+ cells as the main effector cells involved in tumor eradication. Importantly, we show that DCs that are preloaded in vitro with ICs are at least 1000-fold more potent than ICs injected directly into mice or DCs loaded with the same amount of noncomplexed protein. The contribution of individual Fc gammaRs to Ag presentation, T cell response induction, and induction of tumor protection was assessed. We show that Fc gammaRI and Fc gammaRIII are capable of enhancing MHC class I-restricted Ag presentation to CD8+ T cells in vitro and that these activating Fc gammaRs on DCs are required for efficient priming of Ag-specific CD8+ cells in vivo and induction of tumor protection. These findings show that targeting ICs via the activating Fc gammaRs to DCs in vitro is superior to direct IC vaccination to induce protective tumor immunity in vivo.
Targeting Therapeutic Oligonucleotides (2017)

Two recent studies test whether oligonucleotide drugs that are tailored to target different cell types — the hepatocyte and the myocyte and cardiomyocyte — actually target those cell types.
Presence of Donor-Derived DNA and Cells in the Urine of Sex-Mismatched Hematopoietic Stem Cell Transplant Recipients: Implication for the Transrenal Hypothesis (2008)

This report is the first to demonstrate the presence of donor-derived DNA in the urine of HSCT recipients; however, we show that much of this DNA originates from donor-derived cells, rather than from the transrenal passage of cell-free plasma DNA. Our discovery of donor-derived cytokeratin-producing epithelial cells raises interesting biological and therapeutic implications, e.g., the capacity of marrow stem cells to serve as an extrarenal source for renal tubule regeneration.
Clinical Significance of C-Reactive Protein Levels in Predicting Responsiveness to Iron Therapy in Patients with Inflammatory Bowel Disease and Iron Deficiency Anemia (2014)

Patients with high baseline CRP achieved a lower Hb response with oral iron therapy. Our results suggest that CRP may be useful to identify IBD patients who can benefit from first-line treatment with i.v. iron to improve their IDA.
Stochastic Spiking Neural Networks Enabled by Magnetic Tunnel Junctions: From Nontelegraphic to Telegraphic Switching Regimes (2017)

Artificial neural networks built around nanoelectronic components are a means to realizing compact, energy-efficient cognitive intelligence. The authors use the inherent device physics of nanomagnets to emulate the computational primitives of a neural network, reducing the energy and area requirements of the underlying hardware. They analyze the performance of stochastic neuromorphic computing platforms with magnets of different barrier heights, and show how the core network architecture must be modified as the magnets scale down to the superparamagnetic regime.
An Optimized Image Data Compression Technique Utilized In The Kodak Sv9600 Still Video Transceiver (1989)

The Kodak still video transceiver system is designed to electronically transmit and receive high quality color video images over standard telephone lines. A detailed description of the algorithm used in compressing the digital image data is provided. The algorithm is based on the discrete cosine transform (DCT) and uses human visual system (HVS) sensitivity models to achieve high compression ratios without visible artifacts.
Stereochemical studies of the 4‐alkyl‐4‐arylpiperidine class of opioid ligand (1989)

Abstract The 1 H (270, 400 MHz) and 13 C (67.5 MHz) NMR spectra of some 4‐methyl‐ (also 4‐ n ‐propyl‐ and ‐isobutyl)‐4‐(3‐hydroxy‐ and 3‐methoxy‐phenyl)piperidines and their 3‐methyl diastereoisomers are reported. Many of the compounds had opioid ligand activities. The data were analysed in terms of preferred conformation and configuration (3‐methyl derivatives). Only compounds with preference for axial 4‐aryl chair conformations displayed marked agonist properties and the one potent antagonist, cis ‐1,3,4‐trimethyl‐4‐(3‐hydroxyphenyl)piperidine, favoured an equatorial 4‐aryl chair.
Rigorous 3D simulation of phase defects in alternating phase-shifting masks (2002)

A study of both the printability and inspectability of phase defects in alternating phase-shifting masks is made using rigorous FDTD simulation of mask topography and vector-based models for optical imaging that account for the angular dependence of the mask scattering coefficients and high numerical aperture effects. Aerial images inside the photoresist are calculated through focus under typical 193nm stepper imaging conditions in order to assess the effects of size, phase, location and shape on the printability of phase bump defects. Defects located adjacent to the vertical sidewalls of the phase shifter are found to affect CD more than defects located in the center of the phase shifter. Defect shape does not appear to be a strong factor in printability. Aerial images and difference signals for various defects under mask transmission-imaging inspection conditions are calculated. A study of illumination pupil effects in mask inspection is presented. Defect visibility when varying defect size and position is investigated. Defects close to the phase shifter vertical sidewall are less visible. Defects are observed to be more visible when the mask is defocused. An investigation of illumination effects show that coherent systems can see defects better than incoherent systems, while certain incident plane waves are found to 'see' a particular defect better than others.
Subspace Analysis Using Random Mixture Models (2005)

In a work by Wang and Tang (2004), three popular subspace face recognition methods, PCA, Bayes, and LDA were analyzed under the same framework and an unified subspace analysis was proposed. However, since they are all based on a single Gaussian model, a global linear subspace often fails to deliver good performance on the data set with complex intrapersonal variation. They also have to face the problem caused by high dimensional face feature vector and the difficulty in finding optimal parameters for subspace analysis. In this paper, we develop a random mixture model to improve Bayes and LDA subspace analysis. By clustering the intrapersonal difference, the complex intrapersonal variation manifold is learned by a set of local linear intrapersonal subspaces. To boost the system performance, we construct multiple low dimensional subspaces by randomly sampling on the high dimensional feature vector and randomly selecting the parameters for subspace analysis. The effectiveness of our method is demonstrated by experiments on the AR face database containing 2340 face images.
Hybrid Rice Production Costs and Returns: Comparisons with Conventional & Clearfield Varieties (2010)

Rice producers in Louisiana have several rice varieties to choose from when deciding to diversify their farm acreage. Recommended rice varieties can differ in many aspects which ultimately influence costs and returns, such as seedling vigor, disease resistance, milling quality and yield potential. A good farm management practice would be to have a mix of rice varieties planted in a given season to mitigate yield risk across all planted rice acreage on the farm. According to the 2009 Louisiana rice acreage summary, compiled by the LSU AgCenter, of the approximate 456,000 acres of rice in planted in the state in 2009, long grain varieties were produced on roughly 89 percent of the total rice acreage, with the remaining 11 percent of acreage in medium grain varieties. Leading conventional rice varieties in production included the long grain varieties Cocodrie (8.9%) and Cheniere (7.9%) as well as the medium grain variety Jupiter (8.9%). Approximately 47% of the state’s total rice acreage was planted in Clearfield varieties, with CL151 accounting for 25.6% of all rice acreage and smaller acreages planted to CL131, CL161 and CL171. Acreage planted in hybrid rice varieties represented about 15% of the total rice acreage planted in the state in 2009. The largest hybrid acreages were in the varieties CLXL729 and CLXL745, each accounting for about 6% of total state rice acreage, with smaller acreages planted in the varieties CLXL730, XP746 and XL723,
Complement Component C3 Mediates Inflammatory Injury Following Focal Cerebral Ischemia (2006)

The complement cascade has been implicated in ischemia/reperfusion injury, and recent studies have shown that complement inhibition is a promising treatment option for acute stroke. The development of clinically useful therapies has been hindered, however, by insufficient understanding of which complement subcomponents contribute to post-ischemic injury. To address this issue, we subjected mice deficient in selected complement proteins (C1q, C3, C5) to transient focal cerebral ischemia. Of the strains investigated, only C3-/- mice were protected, as demonstrated by 34% reductions in both infarct volume (P<0.01) and neurological deficit score (P<0.05). C3-deficient mice also manifested decreased granulocyte infiltration (P<0.02) and reduced oxidative stress (P<0.05). Finally, administration of a C3a-receptor antagonist resulted in commensurate neurological improvement and stroke volume reduction (P<0.05). Together, these results establish C3 activation as the key constituent in complement-related inflammatory tissue injury following stroke and suggest a C3a anaphylatoxin-mediated mechanism.
Molecular analysis of evolutionary patterns in U genome wild wheats (1995)

The theory of pivotal-differential evolution states that one genome of polyploid wheats remains stable (i.e., pivotal) during evolution, while the other genome or genomes may become modified (i.e., differential). A proposed mechanism for apparent modification of the differential genome is that different polyploid species with only one genome in common may exchange genetic material. In this study, we analyzed a set of sympatric and allopatric accessions of tetraploid wheats with the genomic constitutions UM and UC. The U genome of these species is from Triticum umbellulatum and is considered to be the pivotal genome. The M and C genomes, from T. comosum and T. dichasians, respectively, are considered to be the differential genomes. Low copy DNA was analyzed using "sequence tagged site" primer sets in the polymerase chain reaction, followed by digestion with restriction enzymes. Genetic similarity matrices based on shared restriction fragments showed that sympatric accessions of different U genome tetraploid species did not tend to share more restriction fragments than did allopatric accessions. Thus, no evidence for introgression was found. Analysis of the diploid progenitor species showed that the U genome was less variable than the M and C genomes. Additionally, comparison of diploid and polyploid species using genome-specific primer sets suggests a possible polyphyletic origin for T. triunciale and T. machrochaetum. Thus, our results suggest that the differential nature of the M and C genomes may be the result of variability introduced by the diploid progenitors and not the result of frequent introgression events after formation of the polyploid.
Neutrophil and monocyte adherence to and migration across monolayers of cytokine-activated endothelial cells: the contribution of CD18, ELAM-1, and VLA-4 (1991)

Pretreatment of endothelial cells with cytokines enhances the adherence of leukocytes, a process that is mediated by surface proteins expressed on both cell types. A three-dimensional model system for the simultaneous determination of leukocyte adherence and migration was used to study the contribution of CD11/CD18, endothelial leukocyte-adhesion molecule-1 (ELAM-1) and VLA-4 in neutrophil and monocyte adherence to and migration through cytokine-activated endothelial cells. Pretreatment of endothelial cells for 4 hours with recombinant interleukin-1 beta (rIL-1 beta) was found to enhance neutrophil adherence and migration to a much greater extent than monocyte adherence and migration. Neutrophil adherence was almost completely prevented by the combined use of monoclonal antibodies (MoAbs) against ELAM-1 and CD18. Although ELAM-1 has been designated an endothelial cell-specific cytokine-inducible receptor for neutrophils, we observed that ENA2, an anti-ELAM-1 MoAb, significantly reduced monocyte adherence about 30%. MoAbs against VLA-4, the ligand of the cytokine-inducible receptor VCAM-1, did not affect monocyte adherence. However, the combined use of the MoAbs against CD18, ELAM-1, and VLA-4 had a very strong and additive inhibitory effect on rIL-1 beta-induced monocyte adherence. The anti-CD18 MoAb reduced both rIL-1 beta-induced neutrophil and monocyte migration far below the level of the unstimulated controls, whereas neither the anti-ELAM-1 nor the anti-VLA-4 MoAb significantly affected the process of migration. Our results indicate that neutrophils and monocytes initially adhere to cytokine-activated endothelial cells by CD18-independent and (to a lesser extent) by CD18-dependent mechanisms and subsequently change gears to a completely CD18-dependent migratory mechanism.
Association of the transmembrane 4 superfamily molecule CD53 with a tyrosine phosphatase activity (1995)

Cell surface proteins of the transmembrane 4 superfamily (TM4SF) are a newly characterized family of proteins which are presumed to span the plasma membrane four times. The function of this family of molecules is poorly understood, but based on monoclonal antibody studies there is some evidence that they may be involved in transmembrane signal transduction and regulation of cell proliferation, differentiation, or both, in a number of different cell types. CD53 is a member of this family that is expressed on leukocytes, and transduces activation signals through unknown mechanisms that may involve phosphorylation events. However, CD53 has never been shown to associate directly with kinases. Here, we show by immunoprecipitation from cell lysates of lymph nodes and a thymoma cell line, that immune complexes of rat CD53 contain tyrosine phosphatase activity. The CD53-associated phosphatase was able to dephosphorylate in vitro the phosphorylated tyrosine kinase Lck, as well as a synthetic substrate, and its activity was abrogated by a tyrosine phosphatase inhibitor. Although its identity has not been established, it is clear from depletion experiments that it is not CD45. CD63, a second member of the TM4SF, also co-precipitates a phosphatase activity from rat basophilic leukemia cells. These results demonstrate that the TM4SF members associate with tyrosine phosphatases. It seems possible that such associated phosphatases may contribute to the signal transduction capacity of TM4SF molecules.
Animal Fats (2005)

Abstract The depot lipids of land animals have long been used by humans in edible and industrial applications and as ingredients for animal feeds. They differ from the lipids of temperate region plants in that they are solid at room temperature (and are therefore termed fats). This solidity is largely a result of their relatively higher content of saturated fatty acids and reduced content of polyunsaturated fatty acids. The fatty acid contents and the arrangement of these constituent fatty acids within the acylglycerols of animal fats confer distinctive properties that lend these lipids to various applications. The major industrial animal fats are tallow, which is obtained from cattle ( Bos taurus ) and sheep ( Ovis aries ), and lard, which is produced by pigs ( Sus scrofa ). In some countries, poultry fat, obtained primarily from chickens ( Gallus gallus ), is also produced in substantial quantities. Finally, greases, which can be a lard product, consist of spent deep fat fryer lipids, or be derived from other types of waste lipids, are another major class of fats with industrial applications. Annual global production of tallow, grease, and lard was estimated at about 15 million metric tons at the turn of the millennium, with an annual rate of increase in production of approximately 1.5%. This constituted about 14% of the global total lipid production of 105 million metric tons. This chapter provides an overview of the structures, properties, types and classes, and industrial processing technologies of animal fats. Contemporary issues relating to and impacting animal fat usage include (1) concerns for their contribution to coronary disease when consumed as a dietary lipid, (2) their use as feedstocks for the production of diesel engine fuels (biodiesel), (3) the recent appearance of bovine spongifiorm encephalopathy (BSE) in cattle and its spread to humans, and (4) the discovery of the beneficial effects of the consumption of conjugated linoleic acid.
Biological activities of novel lipid mediator sphingosine 1-phosphate in rat hepatic stellate cells (2000)

Sphingosine 1-phosphate (S-1-P), a lipid mediator shown to be a ligand for aortic G protein-coupled receptor [corrected] (AGRs), endothelial differentiation gene (EDG)1, EDG3, and AGR16/EDG5, is stored in platelets and released on their activation. Platelet consumption occurs in acute liver injury. Hepatic stellate cells (HSCs) play an important role in wound healing. Effects of S-1-P on HSCs were investigated. S-1-P enhanced proliferation of culture-activated HSCs. The mitogenic effect was pertussis toxin sensitive, mitogen-activated protein kinase dependent, and more prominent at lower cell density. S-1-P increased contraction of collagen lattices containing HSCs, irrespective of activation state, in a C3 exotoxin-sensitive manner. mRNAs of EDG1 and AGR16, but not of EDG3, were detected in HSCs. In HSC activation, EDG1 mRNA levels were downregulated, whereas AGR16 mRNA levels were unchanged. Considering that HSCs are capable of production of extracellular matrices and modulation of blood flow in sinusoids, our results suggest that S-1-P may play a role in wound healing process in the liver.
Occurrence and effects of octreotide antibodies during nasal, subcutaneous and slow release intramuscular treatment (2000)

Antibody formation against octreotide is much more frequent than previously believed. It depends primarily on drug exposure time and route of administration. It does not alter the GH/IGF-I status in treated acromegalic patients and induces only mild local reactions in some patients.