gebhart/patrepeval huggingface dataset:
Development of novel chimeric transmembrane proteins for multimodality imaging of cancer cells (2007)

Tracking the migration of cancer cells is essential to understanding the metastatic process. In order to facilitate the tracking of metastatic progression, we have generated transgenic cancer cell lines that express novel chimeric proteins composed of truncated human type II transmembrane proteins fused in-frame to a red fluorescence protein. These chimeric proteins have been engineered to display the fluorescence domain on the surface of cells. The three novel chimeric proteins exhibited high transient expression in several cancer cell lines. Membrane expression was well characterized in MCF-7 cell lines that stably express the chimeric proteins. Indirect immunocytochemistry of non-premeablized cells demonstrated co-localization of endogenous red and green fluorescence labeled secondary antibody bound on the cell surfaces. Immunoblots of total protein prepared from membrane, cytosolic and nuclear fractions indicated that the chimeric proteins were mainly associated with the membrane fraction. Further evidence of the membrane expression of these proteins was confirmed by confocal microscopy. Moreover, the chimeric protein was detected on the cell surface by T2-weighted magnetic resonance imaging using anti-red fluorescence protein antibody and superparamagnetic iron oxide particles in vitro and by optical imaging in vivo. The development of this non-mammalian cell surface marker, that can be detected by multi-modality imaging, will find utility in non-invasive longitudinal tracking of biological processes including metastatic progression, solid tumor treatment regimes and the fate of cells used in cell therapies such as islet or stem cells.
Switched prediction and quantization of LSP frequencies (2002)

We present new results on switched prediction and quantization of the line spectral frequencies applicable to high-quality coding of speech at rates below 8 kb/s. The predictor-quantizer exploits both the temporal inter-frame correlations among the line-spectral frequency vectors of successive frames as well as the spatial within-frame correlations. Best results are obtained by separately training two split vector quantizers, one on predictable frames and one on non-predictable frames. Line-frequency differences are found to yield the lowest quantization error for both the high and low order quantizers for the non-predictable condition, as well as the low order quantizer of the predictable condition. With 10 ms frame separation, 18 bit split VQs, one for each mode, with 1-bit mode indication yield a mean spectral distortion near 1 dB. With 20 ms frame separation, 20 bit quantizers are required.
Sperm‐mediated gene transfer in mice (1998)

Sperm-mediated DNA transfer to offspring has the potential to markedly simplify the generation of transgenic animals, but the efficiency in mice has been controversial. To determine the basis of the variability of the procedure in mice, we undertook a large, collaborative study of sperm-mediated DNA transfer to mouse eggs in well-established laboratory conditions for in vitro fertilization and offspring development following embryo transfer. Sperm were incubated with plasmid DNA during the capacitation period and then added to freshly ovulated mouse oocytes for fertilization; cleaved embryos were then transferred to the oviducts of pseudopregnant recipients for gestation. From a total of 75 experiments, 13 produced 130 transgenic offspring, amounting to 7.4% of total fetuses. In five experiments, more than 85% of offspring were transgenic, but the factors leading to this high success rate were not discovered. Clustering of such a low frequency event could account for the disparate reports of transgenic success with sperm-mediated DNA transfer to mouse offspring. Discovering the factors important to success would not only allow this simplified approach to become an important tool in the generation of transgenic mice, but could also lead to important insights into natural protective mechanisms against sperm-mediated transfer of foreign DNA. Mol. Reprod. Dev. 50:406–409, 1998. © 1998 Wiley-Liss, Inc.
Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration (2007)

Pseudomonas aeruginosa in the lungs of cystic fibrosis patients grows to high densities in mucopurulent material that is depleted in oxygen. Some have concluded that growth in these circumstances is dependent on anaerobic nitrate respiration. Here we present data in favour of the alternative hypothesis that microaerobic respiration is the predominant mode of P. aeruginosa growth in the cystic fibrosis lung. We found that P. aeruginosa strain PAO1 and a mucoid derivative of strain PAO1 each grew at dissolved oxygen concentrations of less than 3 microM. This is lower than the concentration of oxygen that has been measured in hypoxic cystic fibrosis mucous. A transcriptome analysis comparing cells grown under aerobic conditions (185 microM dissolved oxygen) with cells grown with 20 microM or 3 microM dissolved oxygen, or anaerobically with nitrate, revealed that overlapping sets of genes are expressed depending on oxygen availability. This suggests that P. aeruginosa responds to changes in oxygen concentration along a continuum rather than having a discrete low oxygen regulon. Any one of three high affinity terminal oxidases that P. aeruginosa encodes supported microaerobic growth. A triple mutant lacking all three of these oxidases failed to grow at low oxygen and formed abnormal biofilms.
Tetracycline‐aptamer‐mediated translational regulation in yeast (2003)

We describe post-transcriptional gene regulation in yeast based on direct RNA-ligand interaction. Tetracycline-dependent translational regulation could be imposed via specific aptamers inserted at two different positions in the 5' untranslated region (5'UTR). Translation in vivo was suppressed up to ninefold upon addition of tetracycline. Repression via an aptamer located near the start codon (cap-distal) in the 5'UTR was more effective than repression via a cap-proximal position. On the other hand, suppression in a cell-free system reached maximally 50-fold and was most effective via a cap-proximal aptamer. Examination of the kinetics of tetracycline-dependent translational inhibition in vitro revealed that preincubation of tetracycline and mRNA before starting translation led not only to the fastest onset of inhibition but also the most effective repression. The differences between the behaviour of the regulatory system in vivo and in vitro are likely to be related to distinct properties of mRNP structure and mRNA accessibility in intact cells as opposed to cell-extracts. Tetracycline-dependent regulation was also observed after insertion of an uORF sequence upstream of the aptamer, indicating that our system also targets reinitiating ribosomes. Polysomal gradient analyses provided insight into the mechanism of regulation. Cap-proximal insertion inhibits binding of the 43S complex to the cap structure whereas start-codon-proximal aptamers interfere with formation of the 80S ribosome, probably by blocking the scanning preinitiation complex.
Limitations and requirements of diffusion tensor fiber tracking: An assessment using simulations (2002)

Diffusion tensor fiber tracking potentially can give information about in vivo brain connectivity. However, this technique is difficult to validate due to the lack of a gold standard. Fiber tracking reliability will depend on the quality of the data and on the robustness of the algorithms used. Information about the effects of various anatomical and image acquisition parameters on fiber tracking reliability may be used in the design of imaging sequences and of tracking algorithms. In this study, tracking was performed on two different simulated models to study the effects on tracking quality of SNR, anisotropy, curvature, fiber cross-section, background anisotropy, step size, and interpolation. Tracking was also performed on volunteer data to assess the relevance of the simulations to real data. Our results show that, in general, tracking with high SNR and high anisotropy using interpolation and a low step size gives the most reliable results. Partial volume effects are shown to have a detrimental effect when the background is anisotropic and when tracking narrow fibers. The results derived from real data show similar trends and thus support the findings of the simulations. These simulations may therefore help to determine which structures can be tracked for a given image quality.
Light-Dependent Sequestration of TIMELESS by CRYPTOCHROME (1999)

Most organisms have circadian clocks consisting of negative feedback loops of gene regulation that facilitate adaptation to cycles of light and darkness. In this study, CRYPTOCHROME (CRY), a protein involved in circadian photoperception in Drosophila, is shown to block the function of PERIOD/TIMELESS (PER/TIM) heterodimeric complexes in a light-dependent fashion. TIM degradation does not occur under these conditions; thus, TIM degradation is uncoupled from abrogation of its function by light. CRY and TIM are part of the same complex and directly interact in yeast in a light-dependent fashion. PER/TIM and CRY influence the subcellular distribution of these protein complexes, which reside primarily in the nucleus after the perception of a light signal. Thus, CRY acts as a circadian photoreceptor by directly interacting with core components of the circadian clock.
Novel Approaches to the Treatment of Hepatitis C Virus Infection (2000)

Hepatitis C virus (HCV) has infected millions of people worldwide and emerged as a global health crisis. This review reports approaches currently being taken to combat the virus. Viral targets have received the most attention, particularly the NS3 serine protease where potent inhibitors have been described. Crystal structures of key replicative enzymes, NS3 protease, NS3 helicase, NS5B polymerase and now full-length NS3 protease-helicase, are available. More recently, targeting the host system has become of interest, particularly inhibitors of inosine monophosphate dehydrogenase. Research aimed at novel treatments for HCV disease is gathering pace and very recent developments in cell-based assay systems can only hasten the discovery of improved therapies.
Biochemical and Molecular Mechanisms in the Development of Diabetic Vascular Complications (1996)

Hyperglycemia is the major causal factor in the development of diabetic vascular complications. The mechanism by which hyperglycemia causes the complications is not clear; however, it is very likely that hyperglycemia is mediating its adverse effects through multiple mechanisms. We have summarized some of these mechanisms in this review, with particular attention to the effect of hyperglycemia on the activation of diacylglycerol (DAG)-protein kinase C (PKC) pathway. We have reviewed existing information regarding various vascular tissues that show increased DAG and PKC levels. In addition, the mechanism by which hyperglycemia increases DAG as well as the cellular physiological consequences on the activation of PKC have been reviewed.
Microbubble Contrast Agent with Focused Ultrasound to Create Brain Lesions at Low Power Levels: MR Imaging and Histologic Study in Rabbits (2006)

MR imaging-based temperature measurements appeared to correlate with focused ultrasound-induced lesions in the brain when microbubbles were present, even though the temperature appeared to be below the threshold for thermal damage.
Initial experience with non-invasive prenatal testing of cell-free DNA for major chromosomal anomalies in a clinical setting (2014)

NIPT has the potential to be a highly effective screening method for major CA in a clinical setting.
Separation of chemotherapy plus G-CSF-mobilized peripheral blood mononuclear cells by counterflow centrifugal elutriation: in vitro characterization of two different CD34+ cell populations. (1996)

Counterflow centrifugal elutriation (CCE) has been extensively employed in T cell depletion of bone marrow cells for allografting. Nevertheless very little is known about CCE properties of mobilized hematopoietic progenitors. In this study five leukapheresis products collected after chemotherapy and G-CSF from patients with non-Hodgkin's lymphoma were elutriated. Two mononuclear cell fractions were obtained containing smaller and less dense cells (lymphocyte fraction) and larger and denser cells (monocyte fraction), respectively. The presence of immature CD34+ progenitor cells, not co-expressing CD33, CD38 and HLA-DR antigens, was demonstrated in both cell fractions. CD34+ cells were isolated from each fraction and grown in various culture conditions (CFU-GM and BFU-E assay, blast cell colony assay, cytokine supplemented liquid culture). CD34+ cells isolated from the monocyte fraction showed a longer lasting expansion in liquid culture and a higher number of blast cell colonies than CD34+ cells selected from the lymphocyte fraction. Moreover a significant reduction of T cell number was obtained in the monocyte fraction. These data suggest that chemotherapy plus G-CSF-mobilized progenitor cells show a characteristic behavior when subjected to CCE, allowing an efficient T cell depletion without losing more immature progenitors.
Population analysis of cellular responses to synthetic peptides of Der p II, a major allerg molecule of Dermatophagoides pteronyssinus, in allergic and nonallergic subjects (1994)

Responses of peripheral blood mononuclear cells to synthetic oligopeptides of Der p II, one of the major allergen molecules of Dermatophagoides pteronyssinus, were compared between allergic and nonallergic subjects. Healthy subjects showed positive responses to crude extracts of D. pteronyssinus, but only allergic subjects showed elevated cellular responses to Der p II. We synthesized three oligopeptides of Der p II in which motifs of a possible T-cell epitope were included. Of 14 subjects with positive response to Der p II, three responded to all three peptides, while five did not respond to any peptide tested. In 11 allergic patients who showed positive response to Der p II, responsiveness to the peptide K33-T47 was significantly higher than that to other peptides (P < 0.05). All the responding patients were also positive for scratch test to Der p II, suggesting that those epitopes induced IgE-promoting helper T-cell response in allergic persons. On the other hand, the in vitro cellular responses were not necessarily correlated to IgE production against Der p II in healthy subjects.
Course Notes on the Interpretation of Infrared and Raman Spectra (2004)

Interpretation of IR and Raman Spectra provides the fundamentals of interpreting IR and Raman spectra of complex molecules primarily organic molecules. Examinations of theory provide a basis for predicting functional group frequency location in new molecular structures. Generously enriched with sample exercises to help rapidly develop powerful interpretive skills. Includes appendices with fourteen bibliographies by subject area.
Cloning, sequencing, and expression of a gene encoding a 100-kilodalton mosquitocidal toxin from Bacillus sphaericus SSII-1 (1991)

A cosmid library was prepared from a partial BamHI digest of total DNA from Bacillus sphaericus SSII-1. Two hundred fifty Escherichia coli clones were screened for toxicity against larvae of the mosquito Culex quinquefasciatus. One toxic clone, designated pKF2, was chosen for further study. Two toxic subclones, designated pXP33 and pXP34, obtained by ligating PstI-derived fragments of pKF2 into pUC18, contained the same 3.8-kb fragment, but in opposite orientations. Sequence analysis revealed the presence of an open reading frame corresponding to a 100-kDa protein and the 3' end of a further open reading frame having significant homology to open reading frames of transposons Tn501 and Tn21. The sequence of the SSII-1 toxin was compared with those of known toxins and was found to show regional homology to those of ADP-ribosyltransferase toxins. The distribution of the toxin gene among other B. sphaericus strains was examined.
Enhancement of transdermal delivery of progesterone using medium-chain mono and diglycerides as skin penetration enhancers (2009)

We evaluated whether medium-chain mono and diglycerides (MCG) can be utilized to optimize the transdermal delivery of progesterone (PGT). MCG was studied at 10-70% (w/w) in propylene glycol (a polar solvent) or Myvacet oil (nonpolar solvent); PGT was used at 1% (w/w). The topical (to the skin) and transdermal (across the skin) delivery of PGT were evaluated in vitro using porcine ear skin. When incorporated in propylene glycol, MCG at 10% enhanced the topical and transdermal delivery of PGT by 2.5- and 7-fold, respectively. At 20-50%, topical delivery was further enhanced while transdermal delivery gradually returned towards baseline. At 70%, MCG enhanced neither the delivery to viable skin nor the transdermal delivery of PGT. Similar concentration-dependent effects were observed when MCG was incorporated in Myvacet oil, but their magnitudes were 2- to 3-fold smaller. The relative safety of MCG was assessed in cultured fibroblasts and compared to propylene glycol (regarded as safe) and sodium lauryl sulfate (moderate-to-severe irritant). Both MCG and propylene glycol were substantially less cytotoxic than sodium lauryl sulfate. We conclude that formulations containing 10% MCG in propylene glycol may be a simple and safe method to improve the transdermal delivery of progesterone and promote its use in hormone replacement therapy.
Ultrasensitive Chemiresistors Based on Electrospun TiO2 Nanofibers (2006)

Nanostructured semiconducting metal oxides and particularly single nanowire devices offer exceptional gas sensitivity but at the expense of statistical variations and excessive noise levels. In this study TiO2/poly(vinyl acetate) composite nanofiber mats were directly electrospun onto interdigitated Pt electrode arrays, hot pressed at 120 degrees C, and calcined at 450 degrees C. This resulted in a novel multiple nanowire network composed of sheaths of 200-500 nm diameter cores filled with readily gas accessible approximately 10 nm thick single-crystal anatase fibrils. TiO2 nanofiber sensors tested for NO2, in dry air, exhibited exceptional sensitivity showing with, for example, a 833% increase in sensor resistance when exposed to 500 ppb NO2 at 300 degrees C, consistent with a detection limit estimated to be well below 1 ppb. Unusual response patterns were observed at high NO2 concentrations (> 12.5 ppm), consistent with n to p inversion of the surface-trap limited conduction facilitated by the high surface-to-volume ratio of this material.
Differential effects between amphoterin and advanced glycation end products on colon cancer cells (2003)

Amphoterin is 1 ligand of the receptor for advanced glycation end products (RAGE). We studied expression of amphoterin and RAGE mRNA and proteins in colorectal carcinoma cells and investigated their associations with the invasive activities of cells exposed to advanced glycation end products (AGE). Expression of RAGE and amphoterin was examined in 4 colorectal carcinoma cell lines. All cell lines expressed both RAGE and amphoterin. The effects of RAGE and amphoterin on cell growth (MTT assay), migration (wound healing assay) and invasion (in vitro invasion assay) were tested by treatment of cells with RAGE and amphoterin antisense S-oligodeoxynucleotides (ODNs). Cell growth, migration and invasion were inhibited significantly in Colo320 and WiDr carcinoma cells treated with RAGE and amphoterin antisense S-ODNs compared with sense-treated cells. Differences in ligand activity between amphoterin and AGE were examined with AGE-bovine serum albumin (BSA). AGE-BSA decreased cell growth, migration and invasion of amphoterin antisense S-ODN-treated Colo320 and WiDr cells compared with those of cells treated with Colo320 conditioned medium. Phosphorylation of extracellular signal-regulated kinase-1/2, Rac1 and AKT and production of matrix metalloproteinase 9 were increased to a greater degree by amphoterin than by AGE-BSA. In contrast, production of inducible nitric oxide synthase and nuclear factor-kappaBp65 were increased to a greater degree by AGE-BSA than by amphoterin.
A Double-Blind Placebo-Controlled Trial with Loperamide in Irritable Bowel Syndrome (1996)

This trial lends support to a multifactorial aetiology in IBS. Treatment must be individualized with regard to both the effect and the risk of constipation and abdominal pain. The trial shows a benefit of loperamide in an unselected cohort of IBS patients with regard to stool frequency, stool consistency, and the overall pain intensity, but with increased abdominal pain during the night. It should be recommended that the patients take the medication in divided daily doses.
N/P Ratio Significantly Influences the Transfection Efficiency and Cytotoxicity of a Polyethylenimine/Chitosan/DNA Complex (2009)

For designing a complex vector that has the advantages of both polyethylenimine (PEI) and chitosan for gene delivery, a PEI/chitosan/DNA complex was constructed at various N/P ratios (the ratios of moles of the amine groups of cationic polymers to those of the phosphate ones of DNA) and both the cytotoxicity and the transfection efficiency of the vector were evaluated. The results demonstrated that the chitosan/DNA binding degree was depended on the N/P ratio. The mean size of the complex vector was between 100 nm and 150 nm. Compared with PEI/DNA, the complex vector (PEI/chitosan/DNA with chitosan/DNA N/P=4, PEI/DNA N/P=10) appeared to have low cytotoxicity, which maintained the cell survival rate at greater than 80%, and showed higher transfection efficiency of nearly 1000 fold compared with that using chitosan/DNA alone. Furthermore, the expression efficiency of the complex vector carrying enhanced green fluorescent protein was not inhibited in the presence of serum in both HeLa cells and A549 cells. The PEI/chitosan complex may be a promising gene carrier that has high transfection efficiency as well as low cytotoxicity.
Printed antenna suitable for mobile communicationhandsets (1997)

A printed antenna consisting of an annular ring coupled to a shorted patch is presented. The size of the antenna is compatible with typical mobile communications handset terminals and its impedance bandwidth satisfies the requirements for such systems as broadband personal communications systems (PCS).
[Clinical experiences using modified Schwarz double plates]. (1991)

The efficiency of supported double plates according to A.M. Schwarz in the treatment of patients with distocclusion is well-known. When using these appliances we prefer the following procedure: First maxillary and mandibular dentition are treated separately with biomechanically active plates. Then the mandible is adjusted to the normal occlusion but not before the eruption of the first premolars. We attach great importance to the motivation of parents as well as patients for a 12-week intensive co-operation. During this period the patient is expected to wear the appliance 16 to 17 hours per day. It is not necessary for the patient to wear the double-plates at school. The modification of our double plates consists in a U-shaped "Vorbissbügel" (a guidance for protrusive occlusion) with an adequate frontal inclined plan at the mandibular plate.