gebhart/patrepeval huggingface dataset:
Rapid assessment of Diff-Quik-stained pancreatic aspirates. A retrospective study of 40 intraoperative fine needle aspiration consultations, with measurement of nuclear size of look-alike small tissue fragments by image analysis. (1994)

Pancreatic cytomorphology based on Papanicolaou-stained smears has been studied extensively; however, studies on Diff-Quik-stained pancreatic smears are rather limited. Air-dried, Diff-Quik-stained smears lack crisp nuclear details, the cells are flattened on the slides, and the nuclei appear large and hyperchromatic. Between January 1988 and June 1992, 40 cases of intraoperative pancreatic fine needle aspirates were assessed by Diff-Quik stain. The objective of this study was to find practical clues applicable to the rapid and accurate assessment of Diff-Quik-stained pancreatic aspirates for intraoperative consultations. All cases were reviewed and correlated with histopathology. In particular, three cases that proved to be adenocarcinoma on subsequent frozen section but were not so diagnosed during intraoperative fine needle aspiration evaluation were analyzed. The nuclear sizes of small tissue fragments with overlapping nuclei, including three cases of normal pancreatic acini (mean diameter, 0.98, 1.17 and 1.04 x RBCs; coefficient of variation, 0.53, 0.83 and 0.62 x RBCs), 2 cases of islet cell tumor (mean diameter, 1.19 and 1.32 x RBCs; coefficient of variation, 1.88 and 1.4 x RBCs) and 3 cases of adenocarcinoma (mean diameter, 1.55, 1.86 and 1.72 x RBCs; coefficient of variation, 1.5, 1.7 and 1.9 x RBCs) were obtained with an image analyzer. The adjacent RBCs served as internal size controls. In Diff-Quik-stained, air-dried smears we relied on the accurate identification of pancreatic acini, which had the same size as the adjacent RBCs. Islet cell tumors had slightly larger nuclei, which were much more variable in size. The nuclei of adenocarcinoma were much larger than the surrounding RBCs and also showed marked variation in size. The composition of the pancreatic aspirate is important: ductal epithelium predominates in ductal carcinoma, and acini predominate in pancreatitis.
Analysis of the integrant in MyK-103 transgenic mice in which males fail to transmit the integrant. (1987)

Males in the transgenic mouse pedigree MyK-103, although fertile, do not transmit the integrant to offspring. The integrant is on chromosome 6 near the T-cell receptor beta-chain locus. It contains four fragments of the plasmid pMK (a metallothionein-thymidine kinase fusion gene) and a 532-base-pair fragment of displaced mouse DNA originating from a previously uncharacterized repetitive DNA family. The integration complex is flanked on either side by a 5-kilobase duplication of mouse DNA normally found in a single copy at this locus. Sequence analysis of the six novel junctions and their donor sequences shows that plasmid-plasmid junctions occurred at patches of limited homology, whereas chromosome-plasmid junctions were nonhomologous.
Rabbit aorta and human atherosclerotic lesions hydrolyze the sphingomyelin of retained low-density lipoprotein. Proposed role for arterial-wall sphingomyelinase in subendothelial retention and aggregation of atherogenic lipoproteins. (1996)

Aggregation and retention of LDL in the arterial wall are key events in atherogenesis, but the mechanisms in vivo are not known. Previous work from our laboratories has shown that exposure of LDL to bacterial sphingomyelinase (SMase) in vitro leads to the formation of LDL aggregates that can be retained by extracellular matrix and that are able to stimulate macrophage foam cell formation. We now provide evidence that retained LDL is hydrolyzed by an arterial-wall SMase activity. First, we demonstrated that SMase-induced aggregation is caused by an increase in particle ceramide content, even in the presence of excess sphingomyelin (SM). This finding is compatible with previous data showing that lesional LDL is enriched in SM, though its ceramide content has not previously been reported. To address this critical compositional issue, the ceramide content of lesional LDL was assayed and, remarkably, found to be 10-50-fold enriched compared with plasma LDL ceramide. Furthermore, the ceramide was found exclusively in lesional LDL that was aggregated; unaggregated lesional LDL, which accounted for 20-25% of the lesional material, remained ceramide poor. When [3H]SM-LDL was incubated with strips of rabbit aorta ex vivo, a portion of the LDL was retained, and the [3H]SM of this portion, but not that of unretained LDL, was hydrolyzed to [3H]ceramide by a nonlysosomal arterial hydrolase. In summary, LDL retained in atherosclerotic lesions is acted upon by an arterial-wall SMase, which may participate in LDL aggregation and possibly other SMase-mediated processes during atherogenesis.
System and Interface Framework for SCAPE as a Collaborative Infrastructure (2004)

We have developed a multi-user collaborative infrastructure, SCAPE (an acronym for Stereoscopic Collaboration in Augmented and Projective Environments), which is based on recent advancement in head-mounted projective display (HMPD) technology. SCAPE combines the functionalities of an interactive workbench and a room-sized immersive display to concurrently create both exocentric and egocentric perspectives. SCAPE intuitively provides a shared space in which multiple users can simultaneously interact with a 3D synthetic environment from their individual viewpoints, and each user has concurrent access to the environment from multiple perspectives at multiple scales. SCAPE also creates a platform to merge the traditionally separate paradigms of virtual and augmented realities. In this paper, we discuss the design principles we have followed to conceptualize the SCAPE system and briefly summarize SCAPE's hardware implementation. Furthermore, we discuss in detail the high-level design and implementation of the SCAPE architecture, and present a set of unique widget interfaces currently available in our implementation that enable and facilitate interaction and cooperation. Finally, we demonstrate SCAPE's unique visualization and interface capabilities via a testbed application— Aztec Explorer.
Low, but not high, doses of melatonin entrained a free-running blind person with a long circadian period (2002)

In a previous report, we were unable to entrain one out of seven totally blind people with free-running endogenous melatonin rhythms to 10 mg of exogenous melatonin. This person had the longest circadian period (24.9 h) of the group. We now find that this person can be entrained to 0.5 mg of melatonin, but not to 20 mg. These results are consistent with the idea that too much melatonin may spill over onto the wrong zone of the melatonin phase-response curve.
Sequence of the Cloned Escherichia coli K1 CMP-N-acetylneuraminic Acid Synthetase Gene (1989)

The Escherichia coli CMP-N-acetylneuraminic acid (CMP-NeuAc) synthetase gene is located on a 3.3-kilobase (kb) HindIII fragment of the plasmid pSR23 which contains the genes for K1 capsule production (Vann, W. F., Silver, R. P., Abeijon, C., Chang, K., Aaronson, W., Sutton, A., Finn, C. W., Lindner, W., and Kotsatos, M. (1987) J. Biol. Chem. 262, 17556-17562). The CMP-NeuAc synthetase gene expression was increased 10-30-fold by cloning of a 2.7-kb EcoRI-HindIII fragment onto the vector pKK223-3 containing the tac promoter. The complete nucleotide sequence of the gene encoding CMP-NeuAc synthetase was determined from progressive deletions generated by selective digestion of M13 clones containing the 2.7-kb fragment. CMP-NeuAc synthetase is located near the EcoRI site on this fragment as indicated by the detection of an open reading frame encoding a 49,000-dalton polypeptide. The amino- and carboxyl-terminal sequences of the encoded protein were confirmed by sequencing of peptides cleaved from both ends of the purified enzyme. The nucleotide deduced amino acid sequence was confirmed by sequencing several tryptic peptides of purified enzyme. The molecular weight is consistent with that determined from sodium dodecyl sulfate-gel electrophoresis. Gel filtration and ultracentrifugation experiments under nondenaturing conditions suggest that the enzyme is active as a 49,000-dalton monomer but may form aggregates.
The fibroblast growth factor 2 gene is associated with embryonic mortality in cattle1 (2008)

The objective of this study was to investigate the association of the fibroblast growth factor 2 (FGF2) gene with embryonic survival and fertilization rate in cattle. This gene was chosen because of its role in regulating trophectoderm expression of interferon-tau, the maternal pregnancy recognition factor in ruminants. To evaluate the effect of FGF2 on fertility traits, we produced in vitro-fertilized embryos from 281 Holstein cows and from 7 sires. A total of 4,542 in vitro fertilizations were performed, from which a total of 3,171 embryos were produced. Survival and fertilization rates were assessed at d 7 of embryonic development. Using the pooled DNA sequencing approach, we identified 2 SNP in FGF2, SNP11646 and SNP23. All sires and cows were genotyped for these SNP. For fertilization rate, no significant differences between genotypes were found for either SNP, whereas the effect on survival rate was significant for SNP11646. The survival rate of embryos produced from GG cows for this SNP was 37%, compared with 28 and 29% for embryos produced from AG and AA cows, respectively. Although the molecular mechanisms that cause embryonic mortality have not yet been identified, this study provides the first evidence of association between FGF2 and embryonic mortality in cattle. Thus, we propose that FGF2 can be used in animal breeding strategies to test for improved reproductive performance.
Nasal administration of amyloid-beta peptide decreases cerebral amyloid burden in a mouse model of Alzheimer's disease. (2000)

Progressive cerebral deposition of amyloid-beta (Abeta) peptide, an early and essential feature of Alzheimer's disease (AD), is accompanied by an inflammatory reaction marked by microgliosis, astrocytosis, and the release of proinflammatory cytokines. Mucosal administration of disease-implicated proteins can induce antigen-specific anti-inflammatory immune responses in mucosal lymphoid tissue which then act systemically. We hypothesized that chronic mucosal administration of Abeta peptide might induce an anti-inflammatory process in AD brain tissue that could beneficially affect the neuropathological findings. To test this hypothesis, we treated PDAPP mice, a transgenic line displaying numerous neuropathological features of AD, between the ages of approximately 5 and approximately 12 months with human Abeta synthetic peptide mucosally each week. We found significant decreases in the cerebral Abeta plaque burden and Abeta42 levels in mice treated intranasally with Abeta peptide versus controls treated with myelin basic protein or left untreated. This lower Abeta burden was associated with decreased local microglial and astrocytic activation, decreased neuritic dystrophy, serum anti-Abeta antibodies of the IgG1 and IgG2b classes, and mononuclear cells in the brain expressing the anti-inflammatory cytokines interleukin-4, interleukin-10, and tumor growth factor-beta. Our results demonstrate that chronic nasal administration of Abeta peptide can induce an immune response to Abeta that decreases cerebral Abeta deposition, suggesting a novel mucosal immunological approach for the treatment and prevention of AD.
Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision (2004)

The aim of this study was to determine the impact of ischemia on gene and protein expression profiles of healthy and malignant colon tissue and, thus, on screening studies for identification of molecular targets and diagnostic molecular patterns. Healthy and malignant colon tissue were snap-frozen at various time points (3-30 min) after colon resection. Gene and protein expression were determined by microarray (HG-U133A chips) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) technology (CM10 chips, SAX2 chips, and IMAC3Ni chips), respectively. Real-time reverse transcription PCR (RT-PCR) was used for comparative measurement of expression of particular genes. Initial changes of gene and protein expression profiles were already observed 5-8 min after colon resection. Fifteen minutes after surgery, 10%-15% of molecules, and after 30 min, 20% of all detectable genes and proteins, respectively, differed significantly from the baseline values. Significant changes of expression were found in most functional groups. As confirmed by real-time RT-PCR, this included not only known hypoxia-related molecules (HIF-1 alpha, c-fos, HO-1) but also cytoskeletal genes (e.g., CK20) and tumor-associated antigens (e.g., CEA). In conclusion, preanalytical factors, such as tissue ischemia time, dramatically affect molecular data. Control of these variables is mandatory to obtain reliable data in screening programs for molecular targets and diagnostic molecular patterns.
Thermotoga maritima 3-Deoxy-D-arabino-heptulosonate 7-Phosphate (DAHP) Synthase (2003)

The gene encoding the 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase from the thermophilic microorganism Thermotoga maritima was cloned, and the enzyme was overexpressed in Escherichia coli. The purified DAHP synthase displays a homotetrameric structure and exhibits maximal activity at 90 degrees C. The enzyme is extremely thermostable, with 50% of its initial activity retained after incubation for approximately 5 h at 80 degrees C, 21 h at 70 degrees C, and 86 h at 60 degrees C. The enzyme appears to follow Michaelis-Menten kinetics with Km for phosphoenolpyruvate = 9.5-13 microm, Km for d-erythrose 4-phosphate = 57.3-350.1 microm, and kcat = 2.3-7.6 s-1 between 50 degrees C and 70 degrees C. Metal analysis indicates that DAHP synthase as isolated contains Zn2+, and the enzyme is inactivated by treatment with EDTA. The apo-enzyme is partially reactivated by a variety of divalent metals including Zn2+, Cd2+, Mn2+, Cu2+, Co2+, and Ni2+. These observations suggest that T. maritima DAHP synthase is a metalloenzyme. The activity of T. maritima DAHP synthase is inhibited by two of the three aromatic amino acids (l-Phe and l-Tyr) formed in the Shikimate pathway. This report is the first description of a thermophilic eubacterial DAHP synthase.
Protection against mammary tumor growth by vaccination with full-length, modified humanErbB-2 DNA (1999)

ErbB-2 is overexpressed in several human cancers and conveys a transforming activity that is dependent on tyrosine kinase activity. Antibodies and T cells to ErbB-2 have been isolated from cancer patients, indicating ErbB-2 as a potential target of active vaccination. In this study, 3 mutant ErbB-2 DNA constructs encoding full-length, ErbB-2 proteins were tested as tumor vaccines. To eliminate tyrosine kinase activity, the ATP binding lysine residue 753 was substituted with alanine by replacing codon AAA with GCA in mutant ErbB-2A. To direct recombinant ErbB-2 to the cytoplasm where major histocompatibility complex (MHC) I peptide processing takes place, the endoplasmic reticulum (ER) signal sequence was deleted in cyt ErbB-2. The third construct cyt ErbB-2A contained cytoplasmic ErbB-2 with the K to A mutation. Expression of recombinant proteins was measured by flow cytometry in transfected murine mammary tumor cell line D2F2. Transmembrane ErbB-2 and ErbB-2A were readily detected. Cytoplasmic ErbB-2 and ErbB-2A were detected only after the transfected cells were incubated overnight with a proteasome inhibitor, indicating prompt degradation upon synthesis. ErbB-2 autophosphorylation was eliminated by the K to A mutation as demonstrated by Western blot analysis. Growth of ErbB-2-positive tumor in BALB/c mice was inhibited after vaccination with ErbB-2 or ErbB-2A, but not with cyt ErbB-2 or cyt ErbB-2A. ErbB-2A that is free of tyrosine kinase activity is a potential candidate for anticancer vaccination. The 3 mutant constructs should be useful tools to delineate the role of individual immune effector cell in ErbB-2-specific antitumor immunity and to develop strategies for enhancing such immunity.
Treatment of Carbamyl Phosphate Synthetase Deficiency with Keto Analogues of Essential Amino Acids (1975)

Congenital carbamyl phosphate synthetase deficiency was diagnosed by liver biopsy in a 13-year-old girl, alpha-Keto analogues of essential amino acids have been shown to spare nitrogen by reducing urea formation; hence, they were given to this patient in the hope of reducing hyperammonemia and improving protein tolerance. After intravenous infusion of the keto analogues of valine, leucine, isoleucine, methionine and phenylalanine, the corresponding plasma amino acids, including alloisoleucine and tyrosine, rose sharply. Twenty-four hours later, fasting plasma ammonia had fallen from the preinfusion value of 0.050 to 0.028 mM. Protein intake was kept at 0.5 g per kilogram for two weeks. Addition of keto acids by mouth reduced plasma ammonia and alanine to normal or near normal levels. Seizures and episodes of vomiting and lethargy decreased in frequency. Urinary nitrogen decreased, suggesting that nitrogen balance improved. These data indicate that keto acids may be useful in the treatment of congenital hyperammonemia.
Kinetic properties of human AMPA‐type glutamate receptors expressed in HEK293 cells (2003)

AMPA-type glutamate receptors (AMPAR) display a high variability in functional properties, which determine the time course of excitatory postsynaptic potentials. They are assembled as tetramers of GluR subunits 1-4 of different splice variants and nuclear edited isoforms. Presently, the kinetics of activation, desensitization and recovery from desensitization of human AMPARs (GluR1, 3 and 4 flip and flop, and GluR2 flip and flop in R and G edited forms, respectively) transiently expressed in HEK293 cells were studied with patch-clamp techniques and ultra fast agonist application. Activation time constants were identical for all receptors (0.13 ms). The GluR2 flip G variant showed the slowest desensitization (10.8 ms), GluR4 flip the fastest (1.6 ms). Recovery from desensitization varied between 3.1 ms (GluR4 flip) and 178 ms (GluR1 flip). To determine functional interactions between subunits in heteromeric receptors the GluR1 flip and the GluR2 flip R were coexpressed. The time constant of desensitization increased linearly from 2.5 ms (GluR1 flip homomers) to 6.8 ms (GluR2 flip R homomers) with the amount of GluR2 flip R cDNA transfected. Recovery followed a monoexponential time course and had a time constant of 178 ms in GluR1 flip homomeric expression. In all GluR1 flip/GluR2 flip heteromers and in GluR2 flip R homomers desensitization recovered with a time constant of approximately 50 ms. Thus, subunit interaction seems likely during recovery but not desensitization. Both parameters might influence the ability of AMPA receptors to mediate glutamate induced chronic excitotoxicity in neurodegenerative diseases.
Design of a two‐step pulsed pressure‐swing adsorption‐based oxygen concentrator (2009)

Abstract A two‐step pulsed pressure‐swing adsorption (PPSA) process has been modeled to assess the extent to which an oxygen concentrator might be miniaturized for medical applications. The process consists of a single bed of packed adsorbent particles that is alternately pressurized and depressurized at the feed end. An enriched oxygen product is withdrawn at ambient pressure from the product end when the bed is pressurized at the feed end. The product end remains closed during depressurization. The model development addresses the manner in which axial dispersion enters into the describing equations and the formulation of proper boundary conditions, both of which have not been handled rigorously in some prior modeling studies. The describing equations are solved using COMSOL® Multiphysics software. The effect on the performance of the adsorption time, desorption time, bed length, particle diameter, and imposed pressure drop across the bed have been investigated. An interesting novel result is that for a chosen particle size, bed length, and applied pressure drop, there is an optimum combination of adsorption and desorption times that maximizes the product purity. The results suggest that there are operating windows for both 5A and partially Ag‐exchanged Li‐substituted 13X zeolite adsorbents wherein the product oxygen purity is greater than 90%. At a given product flow rate within this operating window, the extent of miniaturization is limited by the (maximum) cycling frequency that is practically achievable. Sizing of an oxygen concentrator for personal medical applications is also discussed. A principal conclusion is that a compact oxygen concentrator capable of producing a highly oxygen‐enriched product is possible using commercially available adsorbents and implementable operating conditions. © 2009 American Institute of Chemical Engineers AIChE J, 2010
On the nature of the 5‐HT receptor subtype inhibiting acetylcholine release in the guinea‐pig ileum (1994)

1. The nature of the 5-hydroxytryptamine (5-HT) receptor subtype controlling acetylcholine release and contraction induced by stimulation of the neurokinin NK3 receptor has been studied in the longitudinal muscle-myenteric plexus preparation from guinea-pig ileum. 2. In preparations preloaded with [3H]-choline, the selective NK3 agonist, senktide, produced a concentration-dependent increase in tritium overflow, an index of [3H]-acetylcholine release. Low concentrations of neurokinin B, also markedly increased tritium efflux. 3. The senktide-induced acetylcholine release was markedly increased by the same concentration of methysergide and mesulergine. The 5-HT2A/2C agonist DOI (1 microM) inhibited the tritium overflow while 8-OH-DPAT, sumatriptan and ketanserin (1 microM each) were without effect on the senktide-induced tritium efflux. 4. The contractile response to senktide in the guinea-pig ileum was attenuated by atropine, 0.1 microM. Methysergide, a 5-HT1/2 receptor antagonist, and mesulergine, a 5-HT2A/2B/2C receptor antagonist, (1 microM each), enhanced the contractile effect of the NK3 receptor agonist. 5. It is concluded that the acetylcholine release induced by a NK3 receptor agonist is inhibited by stimulation of a 5-HT receptor, possibly of the 5-HT2C or 5-HT2C subtype.
Soluble Methane Monooxygenase (2019)

Aerobic life is possible because the molecular structure of oxygen (O<sub>2</sub>) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O<sub>2</sub> activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O<sub>2</sub> activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.