gebhart/patrepeval huggingface dataset:
Integrated control of cell proliferation and cell death by the c- myc oncogene (1994)

Regulation of multicellular architecture involves a dynamic equilibrium between cell proliferation, differentiation with consequent growth arrest, and cell death. Apoptosis is one particular form of active cell death that is extremely rapid and characterized by auto-destruction of chromatin, cellular blebbing and condensation, and vesicularization of internal components. The c-myc proto-oncogene encodes an essential component of the cell's proliferative machinery and its deregulated expression is implicated in most neoplasms. Intriguingly, c-myc can also act as a potent inducer of apoptosis. Myc-induced apoptosis occurs only in cells deprived of growth factors or forcibly arrested with cytostatic drugs. Myc-induced apoptosis is dependent upon the level at which it is expressed and deletion mapping shows that regions of c-Myc required for apoptosis overlap with regions necessary for co-transformation, autoregulation, inhibition of differentiation, transcriptional activation and sequence-specific DNA binding. Moreover, induction of apoptosis by c-Myc requires association with c-Myc's heterologous partner, Max. All of this strongly implies that c-Myc drives apoptosis through a transcriptional mechanism: presumably by modulation of target genes. Two simple models can be invoked to explain the induction of apoptosis by c-Myc. One holds that death arises from a conflict in growth signals which is generated by the inappropriate or unscheduled expression of c-Myc under conditions that would normally promote growth arrest. In this 'Conflict' model, induction of apoptosis is not a normal function of c-Myc but a pathological manifestation of its deregulation. It thus has significance only for models of carcinogenic progression in which myc genes are invariably disrupted.(ABSTRACT TRUNCATED AT 250 WORDS)
Optimally designed nanolayered metal-dielectric particles as probes for massively multiplexed and ultrasensitive molecular assays (2010)

An outstanding challenge in biomedical sciences is to devise a palette of molecular probes that can enable simultaneous and quantitative imaging of tens to hundreds of species down to ultralow concentrations. Addressing this need using surface-enhanced Raman scattering-based probes is potentially possible. Here, we theorize a rational design and optimization strategy to obtain reproducible probes using nanospheres with alternating metal and reporter-filled dielectric layers. The isolation of reporter molecules from metal surfaces suppresses chemical enhancement, and consequently signal enhancements are determined by electromagnetic effects alone. This strategy synergistically couples interstitial surface plasmons and permits the use of almost any molecule as a reporter by eliminating the need for surface attachment. Genetic algorithms are employed to optimize the layer dimensions to provide controllable enhancements exceeding 11 orders of magnitude and of single molecule sensitivity for nonresonant and resonant reporters, respectively. The strategy also provides several other opportunities, including a facile route to tuning the response of these structures to be spectrally flat and localization of the enhancement within a specific volume inside or outside the probe. The spectrally uniform enhancement for multiple excitation wavelengths and for different shifts enables generalized probes, whereas enhancement tuning permits a large dynamic range by suppression of enhancements from outside the probe. Combined, these theoretical calculations open the door for a set of reproducible and robust probes with controlled sensitivity for molecular sensing over a concentration range of over 20 orders of magnitude.
FACT facilitates chromatin transcription by RNA polymerases I and III (2009)

Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III and facilitates their transcription in cells. Our findings indicate that, beyond the established role in Pol II transcription, FACT has physiological functions in chromatin transcription by all three nuclear RNA Pols. Our data also imply that local chromatin dynamics influence transcription of the active rRNA genes by Pol I and of Pol III-transcribed genes.
The complete genome sequence ofMycobacterium bovis (2003)

Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette-Guérin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and its comparison with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison with M. leprae reveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host-bacillus interactions or immune evasion. Furthermore, there are no genes unique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis.
Effect of dietary carbohydrates on the in vitro epithelial adhesion of Candida albicans, Candida tropicalis, and Candida krusei. (2000)

Adhesion to epithelial surfaces is considered as a critical step in the pathogenesis of oral candidosis. Therefore, the effects of the most commonly consumed dietary carbohydrates on the adhesion of Candida albicans, Candida tropicalis, and Candida krusei to monolayered HeLa cells were investigated. Adherence of C. albicans and C. tropicalis appeared significantly promoted by incubation in defined medium containing a high concentration (500 mM) of fructose, glucose, maltose, and sucrose (p < 0.001). C. albicans organisms grown in sucrose elicited maximal increase in adhesion, whereas adhesion of C. tropicalis and C. krusei was enhanced to the greatest extent when cultured in glucose. Maltose and fructose also promoted adherence of C. albicans and C. tropicalis (p < 0.001), but to a lesser extent than sucrose and glucose. On the other hand, sorbitol-grown yeasts demonstrated a marginal increase in adhesion (p > 0.01). Xylitol only significantly reduced adherence of C. albicans (p < 0.001). These results suggest that the frequent consumption of carbohydrates, such as sucrose, glucose, maltose, or fructose, might represent a risk factor for oral candidosis. The limitation of their consumption by substituting xylitol or sorbitol could be of value in the control of oral Candida colonization and infection.
The Generation of Multicopy Recombinant Strains (1998)

The extremely high levels of alcohol oxidase produced from the native AOX1 gene in Pichia pastoris (5–30% of cell protein on induction) suggested that single-copy AOX1 -promoter expression vectors would be sufficient for efficient foreign gene expression. Therefore, the first strategy adopted for generating recombinant strains was to replace the AOX1 gene with a single copy of the foreign gene expression cassette (transplacement), since this type of transformant is the most stable. Some of the earliest studies supported this strategy, e.g., expression of β-galactosidase or hepatitis B surface antigen was efficient and was not improved by increasing vector copy number (1,2).
Handbook of Food and Beverage Fermentation Technology (2004)

PART 1. CULTURED PRODUCTS: HISTORY, PRINCIPLES, AND APPLICATIONS Origin and History of Food Fermentations, K.S. Steinkraus Microorganisms, E.B. Hansen Starter Cultures and Fermented Products, J. Josephsen and Lene Jespersen Manufacture of Fermented Products, W-K. Nip Quality and Flavor of Fermented Products, G. Smit, J.T.M. Wouters, and W.C. Meijer PART II. SEMISOLID CULTURED DAIRY PRODUCTS Semisolid Cultured Dairy Products: Principles and Applications, D. Patel and M. Walker Yogurt, K.R. Nauth Sour Cream and Creme Fraiche, L. Meunier-Goddik Yogurt and Sour Cream: Operational Procedures and Processing Equipment, S. Clark and V.C. Plotka Fromage Frais, L. Meunier-Goddik Semisolid Cultured Dairy Products: Packaging, Quality Assurance, and Sanitation, Y. Zhao PART III. SOLID CULTURED DAIRY PRODUCTS Principles of Cheese Production, E.W. Nielsen Traditional Greek Feta, A. Polychroniadou-Alichanidou Cheddar Cheese, J.M. Banks and A.G. Williams Semihard Scandinavian Cheeses Made with Mesophilic DL-Starter, Y. Ardo Cheeses Made with Thermophilic Lactic Starters, S. Lortal Manufacture of Cheese: Operational Procedures and Processing Equipment, J.M.B. Kristensen, E.W. Nielsen, and J. Josephsen Packaging of Cheese, G. Mortensen, G. Bertelsen, and P.V. Nielsen Cheese Production: Quality Control and Sanitation, S. Lillevang PART IV. FERMENTED MEATS Meat Fermentation: Principles and Applications, D. Demeyer Dry-Cured Ham, F. Toldra Semidry Fermented Sausages, J.G. Sebranek Dry-Fermented Sausages, R. Talon, S. Leroy-Setrin, and S. Fadda Mold-Ripened Sausages, K. Incze Meat Products Processing: Operational Procedures and Processing Equipment, P. Bladini Fermented and Dry-Cured Meat: Packaging and Quality Control, F. Toldra, R. Gavara, and J.M. Lagaron Meat Processing Plant Sanitation, N.G. Marriott PART V. FERMENTED SOY PRODUCTS Fermented Soy Products: An Overview, K. Liu Soy Sauce: Manufacturing and Biochemical Changes, T-C. Huang and D-F. Teng Fermented Whole Soybeans and Soybean Paste, D-F. Teng, C-S. Lin, and P-C. Hsieh Fermented Tofu: Sufu and Stinky Tofu, D-F. Teng, C-S. Lin, and P-C. Hsieh Tempeh: The Other White Beancake, S. Tibbott PART IV. FERMENTED VEGETABLES Fermentation: Principles and Microorganisms, K-Y. Li Chinese Pickles: Leaf Mustard and Derived Products, R.Y-Y. Chiou Kimchi, K-Y. Park and H-S. Cheigh Jalapeno Pepper Preservation by Fermentation or Pickling, R.M.G. Cabrera Sauerkraut, Y.D. Hang Pickle Manufacturing in the United States: Quality Assurance and Establishment Inspection, Y.H. Hui PART VII. FERMENTED CEREAL FOODS Baker's Yeast, B. Poitrenaud Fermented Cereal-Based Functional Foods, H. Salovaara and L. Simonson Sourdough Bread, A...S. Hansen Fermented Doughs in Bread Production, F. Meuser and M. Valentin Packaging, Quality Control, and Sanitation of Bakery Products, P.V. Nielsen Kenkey: An African Fermented Maize Product, M. Halm, W.K. Amoa-Awua, and M. Jakobsen PART VIII. BEVERAGES Fermented Liquid Milk Products, V.V. Mistry Partially Fermented Tea, T. Kan, Y, Tsai, R. Chang. and W-K. Nip Whiskey, M. Henderson
Validation of spiral CT and optical surface scanning for lower limb stump volumetry (1995)

Spiral X-ray Computed Tomography (SXCT), Optical Surface Scanning (OSS), and hydrostatic weighing methods were used to measure stump volume of trans-tibial amputees. The precision and accuracy of these methods were assessed in a validation study. A repeated measures analysis of variance statistical design was employed that required each participant to be measured (scanned) twice at each of two separate measurement sessions. For OSS and SXCT, each scan was segmented twice to determine intra-observer error. Plaster cast replicas of subject stumps were formed by certified prosthetists to serve as a reference standard. Accuracy (bias) of SXCT and OSS was determined by comparison to volumetry by hydrostatic weighing. Ten trans-tibial amputees were recruited for this study and nine completed both sessions. Plaster replica measurement precision error relative to the mean was found to be less than 1% for all modalities. The precision was slightly inferior on subjects, 1.1% and 2.2% error for hydrostatic weighting and OSS respectively, due to patient instability during measurement, but was better with SXCT where the subjects' stumps were stabilized during scan acquisition. The OSS and SXCT methods offer advantages over hydrostatic weighing and other volumetry methods since the volume data are represented digitally and can be analyzed in multiple ways. SXCT enables study of the stump and its internal tissues with the prosthesis in place. It was found that SXCT is comparable to hydrostatic weighing in both precision and accuracy. While OSS had a high precision and reproducibility, it was found to have an associated bias.
The Interferon-γ-inducible 11 S Regulator (PA28) and the LMP2/LMP7 Subunits Govern the Peptide Production by the 20 S Proteasome in Vitro (1995)

Antigenic peptides presented on major histocompatibility complex (MHC) class I molecules to cytotoxic T cells are generated in the cytosol by the 20 S proteasome. Upon stimulation of antigen presenting cells with interferon-gamma, two constitutive subunits of the 20 S proteasome are replaced by the MHC-encoded subunits low molecular mass polypeptide (LMP) 2 and LMP 7. In addition the expression of the two subunits of the 11 S regulator of the 20 S proteasome (PA28) are increased. As the function of LMP2 and LMP7 in antigen presentation is still controversial, we tested whether these subunits might operate by modifying proteasome activation through the 11 S regulator. We strongly overexpressed the two LMP subunits separately or together by transfection in murine fibroblasts. Isolated 20 S proteasomes from LMP transfectants were applied in digests of a 25-mer peptide in the presence or absence of a purified preparation of 11 S regulator from rabbit erythrocytes. Analysis of the cleavage products by high performance liquid chromatography and electrospray mass spectroscopy revealed marked differences in the peptide product profile in dependence on the LMP2 and LMP7 content. While the 11 S regulator did not preferentially activate LMP2 or 7 containing proteasomes, the binding of the 11 S regulator to any of the proteasome preparations markedly changed both the quality and quantity of peptides produced. These results suggest that the 11 S regulator increases the spectrum of peptides which can be generated in antigen presenting cells.
Electronmicroscopy of Dental Calculus (1960)

Electron microscopy of ultrathin osmium-fixed sections of dental calculus, cut with a diamond knife without prior decalcification, revealed densely mineralized areas entrapping many degenerating microorganisms, within which were deposited similarly electron-dense crystals. Two principal forms of crystals were found, the predominant type being of the same order of magnitude and shape as those found in bone, and showing the typical characteristics of apatite in selected area electron diffraction patterns.
Rovelizumab (ICOS Corp). (2000)

Rovelizumab is a humanized monoclonal leukointegrin antibody under development by ICOS as a potential treatment for multiple sclerosis (MS), hemorrhagic shock, myocardial infarction (MI) and stroke. ICOS announced the commencement of phase II studies in MS patients experiencing acute exacerbations in January 1997; a randomized, double-blind, placebo-controlled phase III trial for acute ischemic stroke, to involve 800 patients, was initiated in January 1999 [312467,313014]. The compound is also undergoing preclinical investigation for cerebral vasospasm, head trauma, kidney transplantation and restenosis [346437]. In September 1999, results from a phase II clinical trial in 45 patients suffering from acute exacerbations of MS were presented at the Warburg Dillion Read Global Life Sciences Conference (New York). The study was designed to evaluate the safety and efficacy of four weekly doses of rovelizumab, as compared to placebo. Rovelizumab was shown to be safe, but demonstrated no clinical benefit for the recovery of neurological functioning [341638]. In February 1997, ICOS announced the initiation of a phase II trial in MI. The placebo-controlled trial is being coordinated by the Mayo Physician Alliance for Cardiovascular Trials and will evaluate safety, pharmacokinetics and infarct size in 60 patients [234046,264363]. Patient enrollment for this, and an open label phase II trial in trauma-induced hemorrhagic shock, was completed in September 1997 [264363]. An expanded shock trial in 150 trauma patients, is expected to complete enrollment by the end of 1998 [296831]. An expanded trial for MI was also planned [264363]. The company is to evaluate rovelizumab in patients with ischemic stroke, and a double-blind, dose-escalating, placebo-controlled phase II trial has been initiated at several centers in the US [264363]. A patient population of 48 was tested, with patient dosing occurring within 12 h of stroke onset symptoms. There was no significant difference in SAEs between rovelizumab and placebo treatment, and no immunogenicity was observed [315799]. Neuroprotection was observed in a rabbit model of focal ischemia, with greatest reduction in infarct noted in the cortical areas of the brain. Neutrophil infiltration to ischemic brain parenchyma was reduced by 90% [315799]. Rovelizumab is a monoclonal antibody directed against the CD11/CD18 cell adhesion proteins. By binding to these receptors, rovelizumab prevents the migration and adhesion of neutrophils in the central nervous system, which may cause brain inflammation and neuronal loss [167725]. Rovelizumab binds to all four known leukointegrin receptors, blocking neutrophil adhesion and binding to ICAMs [307344]. ICOS collaborated with the University of Washington on the preclinical development of this compound [175193].
Effects of pyruvate and glucose on the development of human preimplantation embryos in vitro (1993)

Although human embryos will develop in vitro for six days or more, little is known about the effects of the primary nutrients, pyruvate and glucose, on development. Because the nutrient requirements of embryos change throughout preimplantation development, the effects of altering substrate concentrations in the culture medium were examined, using 'surplus' human preimplantation embryos cultured from the two-four-cell stage to the blastocyst stage in medium containing various concentrations of pyruvate and glucose. Between the one-cell stage and the two-four-cell stage all of the embryos were exposed to 0.47 mmol pyruvate l-1 and 5.5 mmol glucose l-1. Pyruvate as sole substrate in the medium could support blastocyst development to an extent of 59% (10 of 17). Conversely, culture of embryos in pyruvate-free medium resulted in the developmental arrest of 84% (21 of 25) of embryos, and for the 16% (4 of 25) that did reach the blastocyst stage there was a significant decrease in metabolic activity on day 4-5, during the morula to blastocyst stage transition. Embryos could not use glucose to compensate for the lack of pyruvate in the medium. Pyruvate uptake was related to exogenous concentration and optimal development occurred at the highest concentration tested, 0.47 mmol l-1. Embryo development to the eight-cell stage was slightly enhanced 82% (14 of 17) versus 60% (24 of 40) when no glucose was added to the medium, and the resulting blastocysts had significantly more cells (99.1 +/- 13.5 versus 58.4 +/- 8.2; P < 0.02) than did embryos grown in the presence of 1 mmol glucose l-1.(ABSTRACT TRUNCATED AT 250 WORDS)
Distance-based-decoding of block turbo codes (2005)

Partial transmit sequence (PTS) is a promising technique for peak-to-average-power ratio (PAPR) reduction in orthogonal frequency division multiplexing (OFDM) systems. Computation of optimal PTS weight factors via exhaustive search requires exponential complexity in the number of subblocks; consequently, many suboptimal strategies have been developed to date. In this letter, we introduce an efficient algorithm for computing the optimal PTS weights that has lower complexity than exhaustive search.
Endogenous Surfactant Turnover in Preterm Infants Measured with Stable Isotopes (1998)

We studied surfactant synthesis and turnover in vivo in preterm infants using the stable isotope [U-13C]glucose, as a precursor for the synthesis of palmitic acid in surfactant phosphatidylcholine (PC). Six preterm infants (birth weight, 916 +/- 244 g; gestational age, 27.7 +/- 1.7 wk) received a 24-h [U-13C]glucose infusion on the first day of life. The 13C-enrichment of palmitic acid in surfactant PC, obtained from tracheal aspirates, was measured by gas chromatography-combustion interface-isotope ratio mass spectrometry. We observed a significant incorporation of carbon-13 from glucose into surfactant PC palmitate. PC palmitate became enriched after 19.4 +/- 2.3 (16.5 to 22.3) h and reached maximum enrichment at 70 +/- 18 (48 to 96) h after the start of the label infusion. The fractional synthesis rate (FSR) of surfactant PC palmitate from glucose was 2.7 +/- 1.3%/d. We calculated the absolute production rate of surfactant PC to be 4.2 mg/kg/d, and the half-life to be 113 +/- 25 (87 to 144) h. Data on endogenous surfactant production and turnover were obtained for the first time in human infants with the use of stable isotopes. This novel and safe method could be applied to address many important issues concerning surfactant metabolism in preterm infants, children, and adults.
Rice dwarf mutant d1 , which is defective in the α subunit of the heterotrimeric G protein, affects gibberellin signal transduction (2000)

Previously, we reported that the rice dwarf mutant, d1, is defective in the alpha subunit of the heterotrimeric G protein (Galpha). In the present study, gibberellin (GA) signaling in d1 and the role of the Galpha protein in the GA-signaling pathway were investigated. Compared with the wild type, GA induction of alpha-amylase activity in aleurone cells of d1 was greatly reduced. Relative to the wild type, the GA(3)-treated aleurone layer of d1 had lower expression of Ramy1A, which encodes alpha-amylase, and OsGAMYB, which encodes a GA-inducible transcriptional factor, and no increase in expression of Ca(2 +)-ATPase. However, in the presence of high GA concentrations, alpha-amylase induction occurred even in d1. The GA sensitivity of second leaf sheath elongation in d1 was similar to that of the wild type in terms of dose responsiveness, but the response of internode elongation to GA was much lower in d1. Furthermore, Os20ox expression was up-regulated, and the GA content was elevated in the stunted internodes of d1. All these results suggest that d1 affects a part of the GA-signaling pathway, namely the induction of alpha-amylase in the aleurone layer and internode elongation. In addition, a double mutant between d1 and another GA-signaling mutant, slr, revealed that SLR is epistatic to the D1, supporting that the Galpha protein is involved in GA signaling. However, the data also provide evidence for the presence of an alternative GA-signaling pathway that does not involve the Galpha protein. It is proposed that GA signaling via the Galpha protein may be more sensitive than that of the alternative pathway, as indicated by the low GA responsiveness of this Galpha-independent pathway.