gebhart/patrepeval huggingface dataset:
A cell culture model system for genetic analyses of the cell cycle by targeted homologous recombination. (1993)

Analysis of how external proliferation signals impinge on the regulation of the cell cycle is ideally performed in cells that are capable of normal physiological withdrawal into the quiescent (G0) phase of the cell cycle as well as resumption of growth following appropriate stimuli. Targeted homologous recombination (gene targeting) provides an important new approach to determine the function of specific genes in these cellular processes. Current gene targeting methodology necessitates the use of immortal and stably diploid cell lines. This report investigates several rodent cell lines, by both genetic and physiological criteria, for use in gene targeting studies of the G0 to G1 transition. All murine cell lines examined were aneuploid. Some rat cell lines were euploid by chromosome number, but three specific genes, c-myc, c-raf-1 and Rb, were not always diploid. Only one cell line, an early-passage subclone of the Rat-1 cell line, was diploid for c-myc, c-raf-1 and Rb. An hprt- derivative of this cell line was isolated (designated TGR-1) and its karyotype was established by G-banding. TGR-1 cells were shown to withdraw into G0 upon serum starvation and to uniformly enter S phase after refeeding. Expression patterns of the c-myc, c-raf-1 and Rb genes and several properties of the gene products were found to be normal. The frequency of targeted homologous recombination of the c-myc and c-raf-1 loci was found to be within values observed with other cell lines. Thus, by both genetic and physiological criteria the TGR-1 cell line is a good model system for the analysis of the roles of c-myc, c-raf-1 and Rb in signal transduction, and will probably prove useful in studies involving other genes.
Two defects contribute to hypothalamic leptin resistance in mice with diet-induced obesity (2000)

Obesity in humans and in rodents is usually associated with high circulating leptin levels and leptin resistance. To examine the molecular basis for leptin resistance, we determined the ability of leptin to induce hypothalamic STAT3 (signal transducer and activator of transcription) signaling in C57BL/6J mice fed either low-fat or high-fat diets. In mice fed the low-fat diet, leptin activated STAT3 signaling when administered via the intraperitoneal (ip) or the intracerebroventricular (icv) route, with the half-maximal dose being 30-fold less when given by the icv route. The high-fat diet increased body-weight gain and plasma leptin levels. After 4 weeks on the diet, hypothalamic STAT3 signaling after ip leptin administration was equivalent in both diet groups. In contrast, peripherally administered leptin was completely unable to activate hypothalamic STAT3 signaling, as measured by gel shift assay after 15 weeks of high-fat diet. Despite the absence of detectable signaling after peripheral leptin at 15 weeks, the mice fed the high-fat diet retained the capacity to respond to icv leptin, although the magnitude of STAT3 activation was substantially reduced. These results suggest that leptin resistance induced by a high-fat diet evolves during the course of the diet and has at least two independent causes: an apparent defect in access to sites of action in the hypothalamus that markedly limits the ability of peripheral leptin to activate hypothalamic STAT signaling, and an intracellular signaling defect in leptin-responsive hypothalamic neurons that lies upstream of STAT3 activation.
Rest-Activity Cycle and Melatonin Rhythm in Blind Free-Runners Have Similar Periods (2010)

In the absence of the entraining light-dark cycle, most totally blind humans free-run, albeit with relative coordination to nonphotic zeitgebers. Such blind free-runners (BFRs) often attempt to maintain a 24-h sleep-wake schedule and consequently suffer from recurrent sleep disruption and daytime somnolence. This study was conducted to determine the periods of the free-running melatonin rhythm and of the rest-activity cycle in 16 BFRs. It was found that the non-24-h component of the rest-activity rhythm correlated with the observed period of the circadian pacemaker.
Thermosensitive Liposomes Modified with Poly(N-isopropylacrylamide-co-propylacrylic acid) Copolymers for Triggered Release of Doxorubicin (2010)

A novel polymer-modified thermosensitive liposome (pTSL) was developed for the delivery of Doxorubicin (DOX) for cancer therapy. Copolymers containing temperature-responsive N-isopropylacrylamide (NIPAAm) and pH-responsive propylacrylic acid (PAA) were synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization, yielding copolymers with dual pH/temperature-dependent phase transition properties. When attached to liposomes, these copolymers were membrane-disruptive in a pH/temperature-dependent manner. pTSL demonstrated enhanced release profile and significantly lower thermal dose threshold when compared to traditional thermosensitive formulations and were stable in serum with minimal drug leakage over time. These liposomes thus have the potential to dramatically reduce the risk of damage to healthy tissues that is normally associated with liposomal cancer therapy.
Effects of Fish Heme Protein Structure and Lipid Substrate Composition on Hemoglobin-Mediated Lipid Oxidation (2007)

Hemoglobin (Hb) promoted lipid oxidation more effectively in washed tilapia as compared to washed cod in spite of a 2.8-fold higher polyenoic index in the washed cod. This suggested that increasing the fatty acid unsaturation of the substrate did not accelerate the onset of lipid oxidation. Substantial phospholipid hydrolysis in the washed cod was observed, which has the potential to inhibit lipid oxidation. MetHb formation and lipid oxidation occurred more rapidly at pH 6.3 as compared to pH 7.4. Trout Hb autoxidized faster and was a better promoter of lipid oxidation as compared to tilapia Hb. The greater ability of trout Hb to promote lipid oxidation was attributed in part to its lower conformational and structural stability based on secondary and tertiary structure, acid-induced unfolding, and thermal aggregation measurements. It is suggested that the structural instability and lipid oxidation capacity of trout Hb were at least partly due to low hemin affinity. Trout and tilapia Hb were equivalent in their ability to cause lipid oxidation in washed cod muscle heated to 80 degrees C. Apparently, these high temperatures denature both trout and tilapia Hb to such an extent that any differences in conformational stability observed at lower temperatures were negated.
Jordan Fantosme's Chronicle. A Postscript (1981)

Journal Article JORDAN FANTOSME'S CHRONICLE A POSTSCRIPT Get access R. C. JOHNSTON R. C. JOHNSTON Freeland, Oxford Search for other works by this author on: Oxford Academic Google Scholar Forum for Modern Language Studies, Volume XVII, Issue 4, October 1981, Pages 373–374, https://doi.org/10.1093/fmls/XVII.4.373 Published: 01 October 1981
Scalable Liquid Shear‐Driven Fabrication of Polymer Nanofibers (2015)

A simple process for batch or continuous formation of polymer nanofibers and other nanomaterials in the bulk of a sheared fluid medium is introduced. The process may be of high value to commercial nanotechnology, as it can be easily scaled up to the fabrication of staple nanofibers at rates that may exceed tens of kilograms per hour.
Short-term SSRI treatment normalises amygdala hyperactivity in depressed patients (2012)

Our results suggest that short-term SSRI treatment in depressed patients remediates amygdala hyperactivity in response to negative emotional stimuli prior to clinical improvement in depressed mood. This supports the hypothesis that the clinical effects of antidepressant treatment may be mediated in part through early changes in emotional processing. Further studies will be needed to show if these early effects of antidepressant medication predict eventual clinical outcome.
CMOS-Compatible Integrated Spectrometer Based on Echelle Diffraction Grating and MSM Photodetector Array (2013)

We demonstrate an integrated spectrometer-on-a-chip composed of an echelle diffraction grating (EDG) and metal-semiconductor-metal (MSM) waveguide photodetector array based on silicon-on-insulator (SOI). In the passive section, silicon oxynitride (SiON) is chosen as the material for the waveguide core and is deposited after selectively removing the top silicon layer of the SOI wafer. The buried silicon dioxide layer of the SOI wafer functions as the lower cladding for the SiON core waveguide. In the active section, the MSM photodetector array is fabricated on the top silicon layer of the SOI waveguide with a pitch width of 7.5 μm. With the butt-coupling structure, a responsivity of 0.41 A/W is obtained at 850 nm. Based on the CMOS-compatible fabrication process, we have fabricated a 60-channel spectrometer with a chip size of 9 mm × 6 mm operating around 850 nm. The measured channel spacing is 0.494 nm, with an adjacent channel crosstalk around 18 dB. The channel nonuniformity is less than 1.5 dB. The CMOS-compatible spectrometer with integrated silicon photodetector array can provide a low-cost solution for high-resolution on-chip spectral analysis for visible and near-infrared light with the wavelength below 1100 nm.
Engineering promoter regulation (2006)

Systems for easily controlled, conditional induction or repression of gene expression are indispensable tools in fundamental research and industrial-scale biotechnological applications. Both native and rationally designed inducible promoters have been widely used for this purpose. However, inherent regulation modalities or toxic, expensive or inconvenient inducers can impose limitations on their use. Tailored promoters with user-specified regulatory properties would permit sophisticated manipulations of gene expression. Here, we report a generally applicable strategy for the directed evolution of promoter regulation. Specifically, we applied random mutagenesis and a multi-stage flow cytometry screen to isolate mutants of the oxygen-responsive Saccharomyces cerevisiae DAN1 promoter. Two mutants were isolated which were induced under less-stringent anaerobiosis than the wild-type promoter enabling induction of gene expression in yeast fermentations simply by oxygen depletion during cell growth. Moreover, the engineered promoters showed a markedly higher maximal expression than the unmutated DAN1 promoter, under both fastidious anaerobiosis and microaerobisois.
Artifact-free High Dynamic Range imaging (2009)

The contrast in real world scenes is often beyond what consumer cameras can capture. For these situations, High Dynamic Range (HDR) images can be generated by taking multiple exposures of the same scene. When fusing information from different images, however, the slightest change in the scene can generate artifacts which dramatically limit the potential of this solution. We present a technique capable of dealing with a large amount of movement in the scene: we find, in all the available exposures, patches consistent with a reference image previously selected from the stack. We generate the HDR image by averaging the radiance estimates of all such regions and we compensate for camera calibration errors by removing potential seams. We show that our method works even in cases when many moving objects cover large regions of the scene.
U.S. Economic Growth at the Industry Level (2000)

The U.S. economy has expanded rapidly in recent years, with total factor productivity (the source of growth most closely identified with technological gains) rising sharply since the mid-1990’s (see e.g., Bureau of Labor Statistics, 1999; William Gullickson and Michael J. Harper, 1999; Mun S. Ho et al., 1999; Daniel E. Sichel, 1999). This strong aggregate performance and the well-documented explosion of investment in computers and other high-tech equipment have led many to believe that the United States has experienced a permanent, technology-led growth revival. It is essential, however, to disaggregate estimates of economic growth to the industry level to understand the new trends in the U.S. economy. Productivity growth, the ability to produce more outputs from the same inputs, differs widely among industries. For the economy as a whole, negative productivity growth in one industry can offset positive productivity growth in another, and Jorgenson (1990) shows that a measure of productivity based solely on aggregate data is valid only under very stringent conditions. We avoid the limitations of an aggregate measure of productivity by decomposing U.S. growth across industries for the period 1958–1996. By breaking down the U.S. economy into 37 industries (35 private industries, private households, and general government), we identify the contribution of each industry to aggregate productivity growth. This enables us to isolate the underlying sources of gains in productivity and provides a better understanding of the forces driving the U.S. economy. Economy-wide productivity from an aggregate production function increased 0.45 percent per year during 1958–1996, while methodology developed by Evsey Domar (1961) for aggregating over industries yields an aggregate estimate of 0.48 percent. Over the same period, however, industry productivity growth ranged from 1.98 percent in Electronic and Electric Equipment to 20.52 percent in Government Enterprises, highlighting fundamental differences in technology and productivity growth across industries. These results show that the aggregate production function provides a reasonable estimate of productivity trends over long periods but also masks important differences among industries.
Pop-Cola Acids and Tooth Erosion: AnIn Vitro,In Vivo, Electron-Microscopic, and Clinical Report (2010)

Introduction. Manufactured Colas are consumed universally as soft drinks. Evidence about the acid contents of Cola-beverages and its effects on teeth is rare. Aim. To assess (i) cola acidity and buffering capacity in vitro, (ii) tooth erosion after swishing with colas in vivo (iii) scanning electron microscopic effects on teeth of colas, and tooth-brush abrasion, and (iv) report a clinical case of erosion from cola consumption. Materials and Methods. (i) We measured six commercially available pop "Cola beverages", pH, and buffering capacities using a pH-Mettler Automatic Titrator, with weak solution of Sodium Hydroxide (ii) two cohorts, one with teeth, the second without teeth rinsed with aliquots of Cola for 60 seconds. Swished cola samples tested for calcium and phosphorus contents using standardized chemical analytical methods (iii) enamel, dentine, and the enamel-cemental junction from unerupted extracted wisdom teeth were examined with a scanning electron microscope after exposure to colas, and tested for tooth-brush abrasion; (iv) a clinical case of pop cola erosion presentation, are all described. Results. Comparisons among pop colas tested in vitro reveal high acidity with very low pH. Buffering capacities in millilitres of 0.5 M NaOH needed to increase one pH unit, to pH 5.5 and pH 7 are reported. Rinsing in vivo with pop cola causes leeching of calcium from teeth; SEM shows dental erosion, and pop-cola consumption induces advanced dental erosion and facilitates abrasion. Conclusions. (i) Pop-Cola acid activity is below the critical pH 5.5 for tooth dissolution, with high buffering capacities countering neutralization effects of saliva; (ii) calcium is leeched out of teeth after rinsing with pop colas; (iii) SEM evidence explains why chronic exposure to acid pop colas causes dental frangibles; (iv) a clinical case of pop-cola erosion confirms this.
A Population-Based Clinical Trial Comparing Endocervical High-Risk HPV Testing Using Hybrid Capture 2 and Cervista From the SHENCCAST II Study (2011)

Our objective was to directly compare the accuracy of the high-risk human papillomavirus (HPV) assays, Hybrid Capture 2 (hc2; Qiagen, Gaithersburg, MD) and Cervista (Hologic, Bedford, MA), in diagnosing cervical intraepithelial neoplasia (CIN) 3 or worse (cancer). A population-based, cross-sectional study (The Shenzhen Cervical Cancer Screening Trial II) was conducted in Guangdong Province in China. Three high-risk HPV assays, self and direct cervical sampling and cytology, were studied. Abnormal results on any of 6 study tests (33%) resulted in referral to colposcopy. At colposcopy, every patient had at least 5 cervical biopsy specimens obtained. For 8,556 women between the ages of 25 and 59 years (mean, 38.9 years), the rate for CIN 3 or worse was 1.6% (141/8,556). The sensitivity (confidence interval) values for CIN 3 or worse were 97.9% (94.0%-99.6%) and 95.1% (90.0%-98.0%) for hc2 and Cervista, respectively (P > .05). The specificity (confidence interval) values were 87.8% (87.1%-88.5%) and 90.3% (89.6%-90.9%), respectively (P < .05). Differences in accuracy in diagnosing CIN 3 or worse with the hc2 and Cervista tests are minor and result from the decisions made in selecting the cut points.
Comparison of the Transactivation Domains of Stat5 and Stat6 in Lymphoid Cells and Mammary Epithelial Cells (1997)

Stat (signal transducers and activators of transcription) and Jak (Janus kinases) proteins are central components in the signal transduction events in hematopoietic and epithelial cells. They are rapidly activated by various cytokines, hormones, and growth factors. Upon ligand binding and cytokine receptor dimerization, Stat proteins are phosphorylated on tyrosine residues by Jak kinases. Activated Stat proteins form homo- or heterodimers, translocate to the nucleus, and induce transcription from responsive genes. Stat5 and Stat6 are transcription factors active in mammary epithelial cells and immune cells. Prolactin activates Stat5, and interleukin-4 (IL-4) activates Stat6. Both cytokines are able to stimulate cell proliferation, differentiation, and survival. We investigated the transactivation potential of Stat6 and found that it is not restricted to lymphocytes. IL-4-dependent activation of Stat6 was also observed in HC11 mammary epithelial cells. In these cells, Stat6 activation led to the induction of the beta-casein gene promoter. The induction of this promoter was confirmed in COS7 cells. The glucocorticoid receptor was able to further enhance IL-4-induced gene transcription through the action of Stat6. Deletion analysis of the carboxyl-terminal region of Stat6 and recombination of this region with a heterologous DNA binding domain allowed the delimitation and characterization of the transactivation domain of Stat6. The potencies of the transactivation domains of Stat5, Stat6, and viral protein VP16 were compared. Stat6 had a transactivation domain which was about 10-fold stronger than that of Stat5. In pre-B cells (Ba/F3), the transactivation domain of Stat6 was IL-4 regulated, independently from its DNA binding function.
Formation of Pyroglutamic Acid from N-Terminal Glutamic Acid in Immunoglobulin Gamma Antibodies (2006)

The status of the N-terminus of proteins is important for amino acid sequencing by Edman degradation, protein identification by shotgun and top-down techniques, and to uncover biological functions, which may be associated with modifications. In this study, we investigated the pyroglutamic acid formation from N-terminal glutamic acid residues in recombinant monoclonal antibodies. Almost half the antibodies reported in the literature contain a glutamic acid residue at the N-terminus of the light or the heavy chain. Our reversed-phase high-performance liquid chromatography-mass spectrometry method could separate the pyroglutamic acid-containing light chains from the native light chains of reduced and alkylated recombinant monoclonal antibodies. Tryptic peptide mapping and tandem mass spectrometry of the reduced and alkylated proteins was used for the identification of the pyroglutamic acid. We identified the formation of pyroglutamic acid from N-terminal glutamic acid in the heavy chains and light chains of several antibodies, indicating that this nonenzymatic reaction does occur very commonly and can be detected after a few weeks of incubation at 37 and 45 degrees C. The rate of this reaction was measured in several aqueous buffers with different pH values, showing minimal formation of pyroglutamic acid at pH 6.2 and increased formation of pyroglutamic acid at pH 4 and pH 8. The half-life of the N-terminal glutamic acid was approximately 9 months in a pH 4.1 buffer at 45 degrees C. To our knowledge, we showed for the first time that glutamic acid residues located at the N-terminus of proteins undergo pyroglutamic acid formation in vitro.
Mechanisms of action of antimalarials in inflammation: induction of apoptosis in human endothelial cells (1997)

Antimalarials are beneficial therapeutic agents in systemic lupus and rheumatoid arthritis. These autoimmune diseases have abnormally low apoptosis of inflammatory cells. Both disorders have an abnormal angiogenesis. In the present report, antimalarials were demonstrated to selectively increase apoptosis of HUVECs in vitro. A 24-h exposure to 50 or 150 microM of the drugs was associated with a significant loss of substrate-adherent cells. Chloroquine exhibited an inhibitory effect on HUVEC proliferation over 7 days. Programmed cell death in HUVECs rendered nonadherent by chloroquine was confirmed by the induction of DNA fragmentation in floating cells. Northern blot analysis revealed a rapidly increased expression of the bcl-x(s) gene without any change in the expression of the bcl-2 gene, indicating that HUVECs under chloroquine were undergoing apoptosis. The onset of the apoptotic cascade in HUVECs appeared shortly after the addition of chloroquine. The effect of chloroquine on apoptosis was distinct from acute cell lysis and was restricted to HUVECs. Antimalarials also induced IL-1alpha production. In parallel, chloroquine alone did not increase the expression of IL-6. Anti-IL-1alpha Ab or IL-1Ra only marginally reversed chloroquine-induced depression of proliferation for the low drug concentration, but not the massive cell death effect at and above 50 microM. Taken together, these data may indicate that antimalarials repress angiogenesis. The autocrine mechanism involving IL-1alpha accounts only for a minor fraction of the full antiendothelial effect of chloroquine, which is mainly dependent on apoptosis.
Real‐time detection of 13C NMR labeling kinetics in perfused EMT6 mouse mammary tumor cells and βHC9 mouse insulinomas (2004)

A method was developed for obtaining high signal-to-noise 13C NMR spectra of intracellular compounds in metabolically active cultured cells. The method allows TCA cycle labeling kinetics to be determined in real time without significant oxygen transport limitations. Cells were immobilized on the surface of nonporous microcarriers that were either uncoated or coated with polypeptides and used in a 12-cm3 packed bed. The methods were tested with two EMT6 mouse mammary tumor cell lines, one strongly adherent and the other moderately adherent, and a weakly adherent mouse insulinoma line (betaHC9). For both EMT6 lines, NTP and oxygen consumption measurements indicated that the number of cells in the spectrometer ranged from 6 x 10(8) to 1 x 10(9). During infusion of [1-13C]glucose, labeling in C-4 glutamate (indicative of flux into the first half of the TCA cycle) could be detected with 15-min resolution. However, labeling for C-3 and C-2 glutamate (indicative of complete TCA cycle activity) was fivefold lower and difficult to quantify. To increase TCA cycle labeling, cells were infused with medium containing [1,6-13C2]glucose. A 2.5-fold increase was observed in C-4 glutamate labeling and C-3 and C-2 glutamate labeling could be monitored with 30-min resolution. Citrate synthase activity was indirectly detected in real time, as [3,4-13C2]glutamate was formed from [2-13C]oxaloacetate and [2-13C]acetate (of acetyl-CoA). Cell mass levels observed with betaHC9 cells were somewhat lower. However, the 13C S/N was sufficient to allow real-time monitoring of the response of intracellular metabolite labeling to a step change in glucose and a combined glutamine/serum pulse.