gebhart/patrepeval huggingface dataset:
Micro CT and Micro MR imaging of 3D architecture of animal skeleton. (2000)

Quantitative assessment of three-dimensional (3D) trabecular structural characteristics may improve our ability to understand the pathophysiology of osteoporosis, to test the efficacy of pharmaceutical intervention, and to estimate bone biomechanical properties. Considerable progress has been made in advanced imaging techniques for noninvasive and/or nondestructive assessment of 3D trabecular structure and connectivity. Micro computed tomography (microCT) has been used to measure 3D trabecular bone structure in rats, both in vivo and in vitro. It can directly quantify 3D trabecular bone structure such as trabecular volume, trabecular thickness, number, separation, structure model index, degree of anisotropy, and connectivity, in a model-independent manner. We have used microCT to study ovariectomy (OVX) induced osteopenia in rats and its treatment with agents such as estrogen, and sodium fluoride. We have demonstrated that 3D microCT can quantify mouse trabecular and cortical bone structure with an isotropic resolution of 9 microm(3). It is also useful for studying osteoporosis in mice and in phenotypes of transgenic mice or gene knockout mice. MicroCT can be used to quantify osteogenesis in mouse Ilizarov leg lengthening procedures, to quantify osteoconduction in a rat cranial defect model, and to quantify cortical bone porosity. Recently, microCT using high intensity and tight collimation synchrotron radiation to achieve spatial resolution of 1-2 microm has provided the capability to assess additional features such as resorption cavities. Unlike microCT, micro magnetic resonance imaging (IMRI) is nonionizing. Recently, the ability of microMRI to assess osteoporosis in animal models has been explored. Using a small, high-efficiency coil in a high-field imager, microMRI can give resolutions sufficient to discriminate individual trabeculae. We have shown that, with appropriate settings, it is possible to image trabecular bone in rats in vivo and in vitro. In our study of OVX rats, analysis of microMR images can demonstrate differences in rat trabecular bone that are not detected by DXA measurements. In a rabbit OA model, with the OA induced by meniscectomy or anterior cruciate ligament transection, MRI shows decreased cartilage thickness, subchondral osteosclerosis and osteophytes, while radiographs can only show subchondral osteosclerosis and osteophytes could not be found. Advanced imaging methods are able to measure 3D trabecular structure and connectivity in arbitrary orientations in a highly automated, objective, non-user-specific manner, allowing greater numbers of samples for unbiased comparisons between controls and the disordered or treated. They can be utilized on a large sample leading to fewer sampling errors. They are non-destructive allowing multiple tests such as biomechanical testing and chemical analysis on the same sample; and non-invasive permitting longitudinal studies and reducing the number of animals needed.
Uptake, Degradation, and Release of Fibrillar and Soluble Forms of Alzheimer's Amyloid β-Peptide by Microglial Cells (1999)

Microglia are phagocytic cells that are the main inflammatory response cells of the central nervous system. In Alzheimer's disease brain, activated microglia are concentrated in regions of compact amyloid deposits that contain the 39-43-amino acid Abeta peptide. We examined the uptake, degradation, and release of small aggregates of fibrillar Abeta (fAbeta) or soluble Abeta (sAbeta) by microglia. We found that although some degradation of fAbeta was observed over 3 days, no further degradation was observed over the next 9 days. Instead, there was a slow release of intact Abeta. The poor degradation was not due to inhibition of lysosomal function, since the rate of alpha2-macroglobulin degradation was not affected by the presence of fAbeta in the late endosomes/lysosomes. In contrast to fAbeta, internalization of sAbeta was not saturable. After internalization, sAbeta was released rapidly from microglia, and very little was degraded. These data show that fAbeta and sAbeta interact differently with microglia but that after internalization a large fraction of both are released without degradation.
A novel nuclear receptor superfamily member inXenopusthat associates with RXR, and shares extensive sequence similarity to the mammalian vitamin D3 receptor (1994)

We report the isolation of xONR1, a novel member of the nuclear receptor superfamily from Xenopus laevis. xONR1 shares a high degree of amino acid sequence identity with the mammalian receptor for 1 alpha, 25-dihydroxy vitamin D3, particularly within the DNA-binding domain, although it does not bind this ligand. xONR1 DNA binding is stimulated by association with retinoid X receptor gamma (RXR gamma).
Synthesis and Characterization of Phosphorescent Cyclometalated Iridium Complexes (2001)

The preparation, photophysics, and solid state structures of octahedral organometallic Ir complexes with several different cyclometalated ligands are reported. IrCl3.nH2O cleanly cyclometalates a number of different compounds (i.e., 2-phenylpyridine, 2-(p-tolyl)pyridine, benzoquinoline, 2-phenylbenzothiazole, 2-(1-naphthyl)benzothiazole, and 2-phenylquinoline), forming the corresponding chloride-bridged dimers, CwedgeN2Ir(mu-Cl)2IrCwedgeN2 (CwedgeNis a cyclometalated ligand) in good yield. These chloride-bridged dimers react with acetyl acetone (acacH) and other bidentate, monoanionic ligands such as picolinic acid (picH) and N-methylsalicylimine (salH), to give monomeric CwedgeN2Ir(LX) complexes (LX = acac, pic, sal). The emission spectra of these complexes are largely governed by the nature of the cyclometalating ligand, leading to lambda(max) values from 510 to 606 nm for the complexes reported here. The strong spin-orbit coupling of iridium mixes the formally forbidden 3MLCT and 3pi-pi* transitions with the allowed 1MLCT, leading to a strong phosphorescence with good quantum efficiencies (0.1-0.4) and room temperature lifetimes in the microsecond regime. The emission spectra of the CwedgeN2Ir(LX) complexes are surprisingly similar to the fac-IrCwedgeN3 complex of the same ligand, even though the structures of the two complexes are markedly different. The crystal structures of two of the CwedgeN2Ir(acac) complexes (i.e., CwedgeN = ppy and tpy) have been determined. Both complexes show cis-C,C', trans-N,N' disposition of the two cyclometalated ligands, similar to the structures reported for other complexes with a "CwedgeN2Ir" fragment. NMR data (1H and 13C) support a similar structure for all of the CwedgeN2Ir(LX) complexes. Close intermolecular contacts in both (ppy)2Ir(acac) and (tpy)2Ir(acac) lead to significantly red shifted emission spectra for crystalline samples of the ppy and tpy complexes relative to their solution spectra.
Dielectric Constant Studies. III. Aqueous Gelatin Solutions (1934)

Measurements have been made of the dielectric constant of gelatin solutions. A test of the Bjerrum ``Zwitter-ionen'' theory was furnished by a study of the effect of pH on the dielectric constant as measured by the Drude method; the data obtained support the theory. Through the application of an equation suggested by Marinesco, an attempt was made to determine the amount of water fixed by gelatin; if this equation is valid for gelatin the results obtained for absorbed water must be interpreted as indicating that the water bound by the gelatin is still free to show its dielectric properties. By means of another equation given by Marinesco relating dielectric absorption with molecular weight, values were calculated for the molecular weight of gelatin; the results obtained are consistent with those given by other methods.
Identification of genes that are associated with DNA repeats in prokaryotes (2002)

Using in silico analysis we studied a novel family of repetitive DNA sequences that is present among both domains of the prokaryotes (Archaea and Bacteria), but absent from eukaryotes or viruses. This family is characterized by direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non-repetitive sequences. To appreciate their characteri-stic structure, we will refer to this family as the clustered regularly interspaced short palindromic repeats (CRISPR). In most species with two or more CRISPR loci, these loci were flanked on one side by a common leader sequence of 300-500 b. The direct repeats and the leader sequences were conserved within a species, but dissimilar between species. The presence of multiple chromosomal CRISPR loci suggests that CRISPRs are mobile elements. Four CRISPR-associated (cas) genes were identified in CRISPR-containing prokaryotes that were absent from CRISPR-negative prokaryotes. The cas genes were invariably located adjacent to a CRISPR locus, indicating that the cas genes and CRISPR loci have a functional relationship. The cas3 gene showed motifs characteristic for helicases of the superfamily 2, and the cas4 gene showed motifs of the RecB family of exonucleases, suggesting that these genes are involved in DNA metabolism or gene expression. The spatial coherence of CRISPR and cas genes may stimulate new research on the genesis and biological role of these repeats and genes.
A Detailed Heat and Fluid Flow Analysis of an Internal Permanent Magnet Synchronous Machine by Means of Computational Fluid Dynamics (2011)

This paper presents a comprehensive computational fluid dynamics (CFD) model of a radial flux permanent magnet synchronous machine with interior magnets. In the CFD model, the water jacket cooling and a simplified model of the topology of the distributed stator winding are considered. The heat sources of the CFD model are determined from a finite-element analysis of the machine. The numerically determined temperature distributions of the machine are compared with measurement results from sensors located both in the stator and rotor. The particular focus of this paper is the analysis of the temperatures and the heat flow in the air gap and from the stator winding heads and the rotor to the inner air. Different operating conditions and two particular rotor designs with different inner air flow configurations are investigated. The potential of improving the thermal utilization of a rotor design with fan blades attached to the mounting plates of the rotor is shown.
CEP-701 and CEP-751 inhibit constitutively activated RET tyrosine kinase activity and block medullary thyroid carcinoma cell growth. (2003)

All of the cases of medullary thyroid carcinoma (MTC) express the RET receptor tyrosine kinase. In essentially all of the hereditary cases and approximately 40% of the sporadic cases of MTC, the RET kinase is constitutively activated by mutation. This suggests that RET may be an effective therapeutic target for treatment of MTC. We show that the indolocarbazole derivatives, CEP-701 and CEP-751, inhibit RET in MTC cells. These compounds effectively inhibit RET phosphorylation in a dose-dependent manner at concentrations <100 nM in 0.5% serum and at somewhat higher concentrations in the presence of 16% serum. They also blocked the growth of these MTC cells in culture. CEP-751 and its prodrug, CEP-2563, also inhibited tumor growth in MTC cell xenografts. These results show that inhibiting RET can block the growth of MTC cells and may have a therapeutic benefit in MTC.
Total parenteral nutrition: a histopathologic analysis of the liver changes in 20 children. (1994)

The histologic features of liver biopsies from 20 children treated with total parenteral nutrition (TPN) are presented. All the children received TPN for no less than 2 wk. Conditions that led clinicians to use this form of treatment included prematurity, sepsis, and gastrointestinal surgical procedures. Fourteen children had a history of prematurity; in nine the birth weight was between 640 and 1300 g. Gestational age and birth weight were not available in five and 11 children, respectively. Ten of the 20 children died. Our findings suggest that the morphologic features observed in the liver can be correlated with the duration of TPN. Thus, we propose a time table of hepatic histologic findings beginning with cholestasis and culminating in cirrhosis.
A systematic review of reboxetine for treating patients with attention deficit hyperactivity disorder (2014)

Non-controlled studies and controlled trials support the promising effect of reboxetine for treating ADHD in a sub-sample of patients that are without co-morbid psychiatric disorder and mental retardation. Reboxetine is tolerated well. However, more controlled trials are needed to reach any firm conclusion.
Characterization of the Plesiomonas shigelloides Genes Encoding the Heme Iron Utilization System (2001)

Plesiomonas shigelloides is a gram-negative pathogen which can utilize heme as an iron source. In previous work, P. shigelloides genes which permitted heme iron utilization in a laboratory strain of Escherichia coli were isolated. In the present study, the cloned P. shigelloides sequences were found to encode ten potential heme utilization proteins: HugA, the putative heme receptor; TonB and ExbBD; HugB, the putative periplasmic binding protein; HugCD, the putative inner membrane permease; and the proteins HugW, HugX, and HugZ. Three of the genes, hugA, hugZ, and tonB, contain a Fur box in their putative promoters, indicating that the genes may be iron regulated. When the P. shigelloides genes were tested in E. coli K-12 or in a heme iron utilization mutant of P. shigelloides, hugA, the TonB system genes, and hugW, hugX, or hugZ were required for heme iron utilization. When the genes were tested in a hemA entB mutant of E. coli, hugWXZ were not required for utilization of heme as a porphyrin source, but their absence resulted in heme toxicity when the strains were grown in media containing heme as an iron source. hugA could replace the Vibrio cholerae hutA in a heme iron utilization assay, and V. cholerae hutA could complement a P. shigelloides heme utilization mutant, suggesting that HugA is the heme receptor. Our analyses of the TonB system of P. shigelloides indicated that it could function in tonB mutants of both E. coli and V. cholerae and that it was similar to the V. cholerae TonB1 system in the amino acid sequence of the proteins and in the ability of the system to function in high-salt medium.
Chemical Mechanical Polishing of Gallium Nitride with Colloidal Silica (2011)

In this report, chemical mechanical polishing (CMP) of gallium nitride (GaN) with colloidal silica was studied. It was confirmed that colloidal silica based slurry could be used for gallium face of GaN. Removal rate of GaN was 17 nm/h under typical polishing conditions. An atomically flat surface with Ra = 0.1 nm was achieved after CMP. Detailed observation of the scratch density was done during the CMP process. Cathode luminescence (CL) imaging was used to understand the sub-surface damage induced by mechanical polishing process and its removal by CMP with colloidal silica based slurry. Combining the optical microscope, atomic force microscope (AFM), CL imaging, and reflection high energy electron diffraction (RHEED) observations before, after and at intermediate stages of the CMP process, the schematic model of the removal of scratch and damage layer from Ga-faced GaN substrate by CMP process was proposed.
Imperative program optimization by partial evaluation (2004)

We implement strength reduction and loop-invariant code motion by specializing instrumented interpreters; we define a novel program transformation that uses bisimulation to identify and remove code duplication in residual programs; and we discover that some simple classical optimizations, notably constant-propagation, seemingly do not lend themselves to implementation by specialization of instrumented interpreters.
Ectopic neural expression of a floor plate marker in frog embryos injected with the midline transcription factor Pintallavis. (1993)

The floor plate, a cell group that develops at the midline of the neural plate in response to inductive signals from the notochord, has been implicated in the control of dorsoventral neural pattern. The frog Pintallavis gene, encoding a member of the HNF-3/fork head transcription factor family, is expressed in the notochord and in midline neural plate cells that give rise to the floor plate. To examine whether Pintallavis might be involved in regulating the differentiation of the floor plate, we ectopically expressed Pintallavis by injection of synthetic mRNA into two-cell frog embryos. Injection of Pintallavis mRNA resulted in the ectopic expression of F-spondin, a gene encoding a floor plate-specific adhesion molecule, at the dorsal midline of the neural tube. The expression of Pintallavis in midline cells may therefore contribute to the establishment of the floor plate fate.
Evaluation of a cold-adapted influenza B/Texas/84 reassortant virus (CRB-87) vaccine in young children (1992)

A cold-adapted (ca) influenza B reassortant virus vaccine that contained the six internal RNA segments from influenza B/Ann Arbor/1/66 ca virus and the neuraminidase and hemagglutinin genes from wild-type influenza B/Texas/1/84 virus was evaluated in children ranging in age from 8 months to 14 years. The children were vaccinated intranasally with doses ranging from 10(3.2) to 10(6.2) 50% tissue culture infective doses (TCID50). Thirty children were seropositive, and 26 were seronegative. Thirty-three children participated as unvaccinated controls. The vaccine was well tolerated by both seronegative and seropositive children. The amount of virus required to infect 50% of seronegative children was approximately 10(4.5) TCID50. Vaccine viruses recovered from airway secretions retained temperature-sensitive and cold-adapted characteristics. The results of this study indicate that the vaccine virus, influenza B/Texas/84 ca reassortant virus, is attenuated, immunogenic, and phenotypically stable when given to young seronegative children.
Cellular immune response to hepatitis B virus-encoded antigens in acute and chronic hepatitis B virus infection. (1990)

The proliferative response of PBMC to hepatitis B virus (HBV) envelope, core, and e Ag was analyzed prospectively in 21 patients with acute self-limited HBV infection and compared with the response of patients with chronic HBV infection and different levels of HBV replication (i.e., hepatitis e Ag (HBeAg)- or anti-HBe-positive) and liver damage (i.e., chronic active hepatitis or chronic asymptomatic carriers). Our results indicate that: 1) HBV-infected subjects who develop a self-limited acute hepatitis show a vigorous PBMC response to hepatitis B core Ag and HBeAg, as expression of T cell activation; 2) appearance of a detectable lymphocyte response to HBV nucleocapsid Ag is temporally associated with the clearance of HBV envelope Ag; 3) in patients with chronic HBV infection the level of T cell responsiveness to hepatitis B core Ag and to HBeAg is significantly lower than that observed during acute infection; 4) T cell sensitization to HBV envelope Ag in acute and chronic HBV infection is usually undetectable and when measurable is expressed transiently and at low levels. These results may reflect immune events of pathogenetic relevance with respect to evolution of disease and viral clearance.
Nonimmobilizers and Transitional Compounds May Produce Convulsions by Two Mechanisms (1999)

Some inhaled compounds cause convulsions.To better appreciate the physical basis for this property, we correlated the partial pressures that produced convulsions in rats with the lipophilicity (nonpolarity) and hydrophilicity (polarity) of 45 compounds: 3 n-alkanes, 18 n-haloalkanes, 3 halogenated aromatic compounds, 3 cycloalkanes and 3 halocycloalkanes, 13 halogenated ethers, and 2 noble gases (He and Ne). In most cases, convulsions were quantified by averaging the alveolar partial pressures just below the pressures that caused and slightly higher pressures that did cause clonic convulsions (ED50). The ED50 did not correlate with hydrophilicity (the saline/gas partition coefficient), nor was there an obvious correlation with molecular structure. For 80% of compounds (36 of 45), the ED50 correlated closely (r2 = 0.99) with lipophilicity (the olive oil/gas partition coefficient). Perhaps because they block the effect of GABA on GABAA receptors, five compounds were more potent than would be predicted from their lipophilicity. Conversely, four compounds may have been less potent than would be predicted because they (like conventional inhaled anesthetics) enhance the effect of GABA on GABAA receptors. Implications: Nonimmobilizers and transitional compounds may produce convulsions by two mechanisms. One correlates with lipophilicity (nonpolarity), and the other correlates with an action on GABAA receptors. (Anesth Analg 1999;88:884-92)
Cultures of Chlamydia trachomatis in Mouse Peritoneal Macrophages: Factors Affecting Organism Growth (1978)

Growth of Chlamydia trachomatis B/TW-5/OT and L(2)/434/Bu strains in cultures of thioglycolate-activated mouse peritoneal macrophages was studied. Both strains grew to a limited extent in the macrophages, but lymphogranuloma venereum (LGV) grew better than trachoma. Growth was enhanced by centrifugation of the inoculum onto the macrophage cell layer and inhibited by pretreatment of macrophages for 2 h with 100 mug of concanavalin A per ml. No significant effect was observed by pretreatment of macrophages with diethylaminoethyl-dextran (30 mug/ml, 30 min), cytochalasin B (20 mug/ml, 1 h), and cyclophosphamide (200 mug/ml, overnight) or by treatment with hydrocortisone (1 and 10 mug/ml, overnight before inoculation and during a 2-day incubation after inoculation). Resistance to intracellular growth of the two organisms was not increased in macrophages obtained from mice immunized with the organisms compared with macrophages from nonimmunized mice unless they were pretreated in vitro with penicillin (100 U/ml, overnight). The yields of LGV organisms from the penicillin-pretreated macrophages of LGV-immunized mice were 100-fold less than from the pretreated macrophages of nonimmunized control mice. At the same time, the yields of LGV organisms from penicillin-pretreated macrophages of mice immunized with trachoma, gonococcus, and HeLa cells were not different from those obtained in pretreated macrophages of nonimmunized control mice.
Peptide nucleic acid (PNA). A DNA mimic with a pseudopeptide backbone (1997)

PNA (peptide nucleic acid) is a DNA mimic with a pseudopeptide backbone composed of N-(2-aminoethyl)glycine units with the nucleobases attached to the glycine nitrogen via carbonyl methylene linkers. PNA was first described in 1991 and has since then attracted broad attention within the fields of bioorganic chemistry, medicinal chemistry, physical chemistry and molecular biology due to its chemical and physical properties, in particular with regard to efficient and sequence specific binding to both single stranded RNA and DNA as well as to double stranded DNA. The present review discusses the structural features that provide the DNA mimicking properties of PNA and gives an overview of structural backbone modifications of PNA.