gebhart/patrepeval huggingface dataset:
Effects of corticosteroids and cyclophosphamide on a mouse model of Chlamydia trachomatis pneumonitis (1982)

Suppression of the inflammatory reaction with daily doses of cortisone acetate or cyclophosphamide substantially prolonged the pulmonary infection in mice which had been intranasally inoculated with a trachoma biotype of Chlamydia trachomatis. Titration of organisms recovered from the lungs of treated mice revealed a drop in titer after day 2 (postinfection), followed by a prominent increase on day 6. In cyclophosphamide-treated mice the infection was resolved after day 12, whereas in cortisone acetate-treated mice a significant titer remained after day 17. In contrast, no organisms were recoverable after day 6 in control mice treated with saline or in mice treated with hydrocortisone succinate. Histologically, the ability of cortisone acetate and cyclophosphamide to inhibit the inflammatory reaction correlated with the respective course of chlamydial pneumonitis. This study demonstrated that mice were intrinsically capable of sustaining a lung infection induced by a human strain of S. trachomatis.
BMI-1 gene amplification and overexpression in hematological malignancies occur mainly in mantle cell lymphomas. (2001)

The BMI-1 gene is a putative oncogene belonging to the Polycomb group family that cooperates with c-myc in the generation of mouse lymphomas and seems to participate in cell cycle regulation and senescence by acting as a transcriptional repressor of the INK4a/ARF locus. The BMI-1 gene has been located on chromosome 10p13, a region involved in chromosomal translocations in infant leukemias, and amplified in occasional non-Hodgkin's lymphomas (NHLs) and solid tumors. To determine the possible alterations of this gene in human malignancies, we have examined 160 lymphoproliferative disorders, 13 myeloid leukemias, and 89 carcinomas by Southern blot analysis and detected BMI-1 gene amplification (3- to 7-fold) in 4 of 36 (11%) mantle cell lymphomas (MCLs) with no alterations in the INK4a/ARF locus. BMI-1 and p16INK4a mRNA and protein expression were also studied by real-time quantitative reverse transcription-PCR and Western blot, respectively, in a subset of NHLs. BMI-1 expression was significantly higher in chronic lymphocytic leukemia and MCL than in follicular lymphoma and large B cell lymphoma. The four tumors with gene amplification showed significantly higher mRNA levels than other MCLs and NHLs with the BMI-1 gene in germline configuration. Five additional MCLs also showed very high mRNA levels without gene amplification. A good correlation between BMI-1 mRNA levels and protein expression was observed in all types of lymphomas. No relationship was detected between BMI-1 and p16INK4a mRNA levels. These findings suggest that BMI-1 gene alterations in human neoplasms are uncommon, but they may contribute to the pathogenesis in a subset of malignant lymphomas, particularly of mantle cell type.
Noise in homodyne and heterodyne detection (1983)

Quantum-mechanical calculations of the mean-square fluctuation spectra in optical homodyning and heterodyning are made for arbitrary input and local-oscillator quantum states. In addition to the unavoidable quantum fluctuations, it is shown that excess noise from the local oscillator always affects homodyning and, when it is broadband, also heterodyning. Both the quantum and the excess noise of the local oscillator can be eliminated by coherent subtraction of the two outputs of a 50-50 beam splitter. This result also demonstrates the fact that the basic quantum noise in homodyning and heterodyning is signal quantum fluctuation, not local-oscillator shot noise.
A Small Electromagnetic Bandgap Structure (2006)

We present a small electromagnetic bandgap (EBG) cell which is easy to fabricate on standard PCB material and can be used where space is a premium. The EBG structure is an extension of the classical uni-planar structure where the inductance due to the thin transmission line sections is increased by meandering in these microstrip lines within the EBG cell itself. We demonstrate the concept with an EBG surface that was designed and developed at 300 MHz on standard FR4. The size of a 3 times 3 structure is only 7.53 cm times 7.53 cm and provides 10 dB attenuation across the surface
Enriched environment increases neurogenesis in the adult rat dentate gyrus and improves spatial memory (1999)

The fetal and even the young brain possesses a considerable degree of plasticity. The plasticity and rate of neurogenesis in the adult brain is much less pronounced. The present study was conducted to investigate whether housing conditions affect neurogenesis, learning, and memory in adult rats. Three-month-old rats housed either in isolation or in an enriched environment were injected intraperitoneally with bromodeoxyuridine (BrdU) to detect proliferation among progenitor cells and to follow their fate in the dentate gyrus. The rats were sacrificed either 1 day or 4 weeks after BrdU injections. This experimental paradigm allows for discrimination between proliferative effects and survival effects on the newborn progenitors elicited by different housing conditions. The number of newborn cells in the dentate gyrus was not altered 1 day after BrdU injections. In contrast, the number of surviving progenitors 1 month after BrdU injections was markedly increased in animals housed in an enriched environment. The relative ratio of neurogenesis and gliogenesis was not affected by environmental conditions, as estimated by double-labeling immunofluorescence staining with antibodies against BrdU and either the neuronal marker calbindin D28k or the glial marker GFAp, resulting in a net increase in neurogenesis in animals housed in an enriched environment. Furthermore, we show that adult rats housed in an enriched environment show improved performance in a spatial learning test. The results suggest that environmental cues can enhance neurogenesis in the adult hippocampal region, which is associated with improved spatial memory.
Definitions of terms relating to the structure and processing of sols, gels, networks, and inorganic-organic hybrid materials (IUPAC Recommendations 2007) (2007)

Abstract This document defines terms related to the structure and processing of inorganic, polymeric, and inorganic-organic hybrid materials from precursors, through gels to solid products. It is divided into four sections - precursors, gels, solids, and processes - and the terms have been restricted to those most commonly encountered. For the sake of completeness and where they are already satisfactorily defined for the scope of this document, terms from other IUPAC publications have been used. Otherwise, the terms and their definitions have been assembled in consultation with experts in the relevant fields. The definitions are intended to assist the reader who is unfamiliar with sol-gel processing, ceramization, and related technologies and materials, and to serve as a guide to the use of standard terminology by those researching in these areas.
Improved Biochemical Control and Clinical Disease-Free Survival with Intraoperative Versus Preoperative Preplanning for Transperineal Interstitial Permanent Prostate Brachytherapy (2006)

Intraoperative preplanning yielded superior disease control outcomes in this analysis, likely due at least in part to improved dosimetric prostate coverage with this method. Although not mandatory for obtaining high prostate brachytherapy efficacy, intraoperative preplanning nevertheless may offer an excellent means of improving dosimetric prostate coverage and therefore disease control outcomes.
Effect of phorbol 12-myristate 13-acetate and its analogue 4 alpha-phorbol 12,13-didecanoate on protein phosphorylation and lysosomal enzyme release in rabbit neutrophils. (1984)

The co-carcinogenic compound phorbol 12-myristate 13-acetate but not its inactive analogue 4 alpha-phorbol 12,13-didecanoate causes the phosphorylation of several rabbit neutrophil polypeptides whose molecular weights and isoelectric points (pI) are as follows: Mr = 40,000, pI = 6.4; Mr = 50,000, pI = 4.9; Mr = 55,000, pI = 6.3; Mr = 64,000, pI = 6.0; Mr = 70,000, pI = 5.6; Mr = 90,000, pI = 6.0. Most of these phosphorylated proteins are located exclusively in the cytosol; the 64,000 molecular weight protein is found both in the cytosol and the cytoskeleton, and the 40,000 molecular weight protein is found in the nuclear pellet. The 50,000 molecular weight protein is also phosphorylated in whole cells by the chemotactic peptide fMet-Leu-Phe and in cell-free systems by protein kinase C. Using limited proteolysis, one phosphopeptide fragment was phosphorylated by the three stimuli. In addition, phorbol 12-myristate 13-acetate but not 4 alpha-phorbol 12,13-didecanoate causes cell aggregation and the exocytotic release of the specific granules of rabbit neutrophils. In contrast, both compounds increase the amount of actin associated with the cytoskeleton. The divalent cation ionophore A23187 at low concentration and the compound phorbol 12-myristate 13-acetate act synergistically in causing neutrophil degranulation. Lysosomal enzyme release and the phosphorylation of the 50,000 molecular weight polypeptide produced by phorbl 12-myristate 13-acetate are inhibited by trifluoperazine, and these two responses seem to be causally related. These results are discussed in terms of the role of 1,2-diacylglycerol and activation of protein kinase C in specific granule release from rabbit neutrophils.
Oxygenation of Monounsaturated Fatty Acids by Soybean Lipoxygenase-1:  Evidence for Transient Hydroperoxide Formation (2006)

Soybean lipoxygenase-1 (SBLO-1) catalyzes the oxygenation of polyunsaturated fatty acids to produce conjugated diene hydroperoxides. Previous work from our laboratories has demonstrated that SBLO-1 will also catalyze the oxygenation of monounsaturated acids (Clapp, C. H., Senchak, S. E., Stover, T. J., Potter, T. C., Findeis, P. M., and Novak, M. J. (2001) Soybean Lipoxygenase-Mediated Oxygenation of Monounsaturated Fatty Acids to Enones, J. Am. Chem. Soc. 123, 747-748). Interestingly, the products are alpha,beta-unsaturated ketones rather than the expected allylic hydroperoxides. In the present work, we provide evidence that the monoolefin substrates are initially converted to allylic hydroperoxides, which are subsequently converted to the enone products. The hydroperoxide intermediates can be trapped by reduction to the corresponding allylic alcohols with glutathione peroxidase plus glutathione or with SnCl2. Under some conditions, the hydroperoxide intermediates accumulate and can be detected by HPLC and peroxide assays. Kinetics measurements at low concentrations of [1-14C]-9(Z)-octadecenoic acid indicate that oxygenation of this substrate at 25 degrees C, pH 9.0 occurs with kcat/Km = 1.6 (+/-0.1) x 10(2) M-1 s-1, which is about 105 lower than kcat/Km for oxygenation of 9(Z),12(Z)-octadecadienoic acid (linoleic acid). Comparison of the activities of 9(Z)-octadecenoic acid and 12(Z)-octadecenoic acid implies that the two double bonds of linoleic acid contribute almost equally to the C-H bond-breaking step in the normal lipoxygenase reaction. The results are consistent with the notion that SBLO-1 functionalizes substrates by a radical mechanism.
An evoked indirect response in the cervical vagal nerve (2009)

The response of fibers in the vagal nerve, evoked by electrical stimulation, has been studied in both animals and humans. These compound action potentials (CAPs) consist of components coming from thick, myelinated fibers to thin, unmyelinated fibers. In our study, the possibility is addressed of an indirect component in the CAP which is involved in reflexive control. By using multiple, consecutive electrode sites along the cervical vagal nerve, both the direction and the velocity along the nerve of the CAPs can be analyzed. This information can be used to distinguish direct from indirect components. In this way an indirect component was revealed.
A method for hexahedral mesh shape optimization (2003)

Abstract Methods for improving the quality of all‐hexahedral unstructured meshes by node‐movement strategies have, until recently, been lacking. Laplacian smoothing, while easily implemented and well‐known, fails to guarantee improvement of mesh quality and may result in inverted elements where none existed before. A method for improving unstructured hexahedral mesh shape‐quality that guarantees untangled elements is proposed. The method is based on optimization of an objective function built from the quality of individual hexahedral elements. The shape‐quality measure for hexahedral elements is based on the condition number of a set of Jacobian metrics associated with the element. The theory of the condition number quality metric and of the objective function are reviewed. A numerical optimization procedure to find the improved‐quality mesh is described. The purpose of this paper is to demonstrate the robustness of the method. We do so by giving a realistic example. The method has also been successfully applied to dozens of meshes on complex geometries. Published in 2003 by John Wiley &amp; Sons, Ltd.
Bubble-based acoustic radiation force for monitoring intraocular lens elasticity (2005)

We test the hypothesis that local viscoelastic properties of the intraocular lens can be measured by applying acoustic radiation force to laser-generated bubbles. Presbyopia is an age-related condition resulting from increased stiffness of the lens, reducing its ability to accommodate. A technique to measure local lens viscoelastic properties is needed to better understand the onset of presbyopia and guide potential correction procedures. Laser-induced optical breakdown (LIOB) is used to create bubbles within porcine intraocular lenses. Optical breakdown occurs when sufficiently high threshold fluence is attained at the focus of femtosecond pulsed lasers, inducing plasma formation and bubble generation. The small transient gas bubbles can be used as targets for acoustic radiation force measurements prior to their ultimate collapse. While ultrasonic speckle is extremely limited within the lens, LIOB bubbles provide strong ultrasonic backscatter to measure lens viscoelastic properties. In this investigation, explanted porcine lenses are embedded within a gelatin phantom (5 w/w%) prior to laser treatment. An integrated optical-acoustical system has been constructed enabling simultaneous bubble creation and radiation force experiments. A two-element confocal ultrasonic transducer generates acoustic radiation force with the 1.5 MHz outer element while monitoring the bubble displacement within the lens using the 7.44 MHz inner element. Preliminary experiments have demonstrated the ability to create LIOB bubbles within explanted porcine lenses with lifetimes on the order of a few minutes and at any depth within the lens. Acoustic radiation force experiments with LIOB bubbles in porcine lenses exhibit exponential responses with time constants near 2 ms and maximum displacements on the order of 100 /spl mu/m. These results advance the development of an in vivo technique to measure local lens viscoelastic properties.
Early postoperative adherence of matrix‐induced autologous chondrocyte implantation for the treatment of full‐thickness cartilage defects of the femoral condyle (2004)

Matrix-induced autologous chondrocyte implantation (MACI) is a tissue-engineering technique for the treatment of full-thickness articular cartilage defects and requires the use of a three-dimensional collagen type I-III membrane seeded with cultured autologous chondrocytes. The cell-scaffold construct is implanted in the debrided cartilage defect and fixed only with fibrin glue, with no periosteal cover or further surgical fixation. In a clinical pilot study, the MACI technique was used for the treatment of full-thickness, weight-bearing chondral defects of the femoral condyle in 16 patients. All patients were followed prospectively and the early postoperative attachment rate, 34.7 days (range: 22-47) after the scaffold implantation, was determined. With the use of high-resolution magnetic resonance imaging (MRI), the transplant was graded as completely attached, partially attached, or detached. In 14 of 16 patients (87.5%), a completely-attached graft was found, and the cartilage defect site was totally covered by the implanted scaffold and repair tissue. In one patient (6.25%), a partial attachment occurred with partial filling of the chondral defect. A complete detachment of the graft was found in one patient (6.25%), which resulted in an empty defect site with exposure of the subchondral bone. Interobserver variability for the MRI grading of the transplants showed substantial agreement (kappa=0.775) and perfect agreement (kappa(w)=0.99). In conclusion, the implantation and fixation of a cell-scaffold construct in a deep cartilage defect of the femoral condyle with fibrin glue and with no further surgical fixation leads to a high attachment rate 34.7 days after the implantation, as determined with high resolution MRI.
Progression of human cutaneous melanoma is associated with loss of expression of c‐kit proto‐oncogene receptor (1992)

Mutations at the white spotting (w) locus in mice have deleterious effects on germ cells, melanocytes and hematopoietic stem cells. The w locus encodes the c-kit tyrosine-kinase receptor whose ligand is the product of the SI locus. Using monoclonal antibodies (MAb(s)) to the extracellular domain, we have evaluated the expression of c-kit in normal and transformed melanocytes. This cell lineage synthesizes a receptor with a mw of 145 kDa. The gene product is expressed in epidermal melanocytes and in a fraction of nevocytic and blue nevi. In primary melanomas, loss of the receptor is observed in more invasive lesions. Only 30% of the metastatic lesions express detectable levels of the receptor. These findings demonstrate that the c-kit product is down-regulated in melanocytes following malignant transformation. The functional relevance of this modulation remains to be evaluated.
A placebo controlled, dose-ranging, safety study of allogenic mesenchymal stem cells injected by endomyocardial delivery after an acute myocardial infarction (2007)

Although mesenchymal stem cells (MSCs) show promising signs in reducing myocardial infarct (MI) size, the safety of endomyocardial delivery and the most efficacious dose is unknown.Three days after MI, female Yorkshire swine (25-32 kg, age 2 months, n = 32) were randomized to endomyocardial delivery of one of three MSC doses (2.4 x 10(7), 2.4 x 10(8), 4.4 x 10(8) cells) or vehicle control. Animals were sacrificed at 12 weeks. There were no safety issues related to cell delivery and all animals tolerated the procedure. By magnetic resonance imaging infarct size (g) was decreased in the experimental groups and increased in the control group; 2.4 x 10(7): Delta -2.5 +/- 2.5 g, 2.4 x 10(8): -0.9 +/- 2.71 g, 4.4 x 10(8): -1.6 +/- 5.8 g, and control +3.6 +/- 3.4 g (P = 0.002, P = 0.016, and P = 0.055 compared with control, respectively). There was no effect on ejection fraction or left ventricular volumes. By histology there were no toxic effects of MSC delivery, however, few engrafted MSCs were observed.Direct MSC delivery into infarcted myocardium was safe and produced a local but not a functional effect. There was no dose-dependent effect. The effect of MSCs on infarct reduction may result from transient residence and subsequent paracrine effects.
Quantification of Human Immunodeficiency Virus Type 1 Proviral Load by a TaqMan Real-Time PCR Assay (2001)

Proviral human immunodeficiency virus type 1 (HIV-1) DNA could be a useful marker for exploring viral reservoirs and monitoring antiretroviral treatment, particularly when HIV-1 RNA is undetectable in plasma. A new technique was developed to quantify proviral HIV-1 using a TaqMan real-time PCR assay. One copy of proviral HIV-1 DNA could be detected with 100% sensitivity for five copies and the assay had a range of 6 log(10). Reproducibility was evaluated in intra- and interassays using independent extractions of the 8E5 cell line harboring the HIV-1 proviral genome (coefficients of variation [CV], 13 and 27%, respectively) and peripheral blood mononuclear cells (PBMC) from a patient with a mean proviral load of 26 copies per 10(6) PBMC (CV, 46 and 56%, respectively). The median PBMC proviral load of 21 patients, measured in a cross-sectional study, was determined to be 215 copies per 10(6) PBMC (range, <10 to 8,381). In a longitudinal study, the proviral load of 15 out of 16 patients with primary infection fell significantly during 1 year of antiretroviral therapy (P = 0.004). In the remaining patient, proviral HIV-1 DNA was detectable but not quantifiable due to a point mutation at the 5' end of the TaqMan probe. No correlation was observed between proviral load and levels of CD4(+) cells or HIV-1 RNA in plasma. TaqMan PCR is sensitive and adaptable to a large series of samples. The full interest of monitoring proviral HIV-1 DNA can now be ascertained by its application to the routine monitoring of patients.
Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer (2005)

Quantitative expression of ER-related genes, proliferation genes, and immune-related genes are strong predictors of pCR in women with locally advanced breast cancer receiving neoadjuvant anthracyclines and paclitaxel.
Expression of the Wilms' tumor gene (WT1) in normal hemopoiesis. (1997)

The Wilms tumor suppressor gene (WT1) is mutated in a number of cases of Wilms' tumor as well as in mesothelioma and leukemia. It encodes a transcription factor derived from any one of four alternate transcripts. WT1 has a restricted pattern of expression within the body and within the hemopoietic system its expression is limited to primitive leukemias and a number of leukemic cell lines. Given the overexpression of WT1 in leukemias, we have addressed the question of whether this gene is expressed within the normal hemopoietic system. Mononuclear bone marrow (BM) cells obtained from normal donors were separated by fluorescence-activated cell sorting (FACS) into "primitive" (CD34+) and "mature" (CD34-) cell populations. Total RNA extracted from these cells was subjected to reverse transcriptase polymerase chain reaction (RT-PCR) using primers based on the WT1 sequence, to examine the expression of this gene within the hemopoietic system. Phenotypic purity of cells was guaranteed by performing single-cell sorting followed by RT-PCR to define the precise cellular phenotypes that express WT1. Expression of WT1 was detected in cells bearing the CD34+ phenotype but not in those cells lacking expression of CD34. In addition, single-cell analysis revealed that expression of WT1 occurred in the candidate stem cell-containing population of hemopoietic cells which have the phenotype CD34+ CD38-. Moreover, the single-cell RT-PCR analysis also demonstrated that differential expression of alternate transcripts of WT1 occurs between hemopoietic progenitor cells with the same phenotype. In conclusion, expression of WT1 is limited to early progenitors of the blood system, which suggests that this gene plays a critical role in hemopoietic development.