gebhart/patrepeval huggingface dataset:
Separation of factors required for cleavage and polyadenylation of yeast pre-mRNA. (1992)

Cleavage and polyadenylation of yeast precursor RNA require at least four functionally distinct factors (cleavage factor I [CF I], CF II, polyadenylation factor I [PF I], and poly(A) polymerase [PAP]) obtained from yeast whole cell extract. Cleavage of precursor occurs upon combination of the CF I and CF II fractions. The cleavage reaction proceeds in the absence of PAP or PF I. The cleavage factors exhibit low but detectable activity without exogenous ATP but are stimulated when this cofactor is included in the reaction. Cleavage by CF I and CF II is dependent on the presence of a (UA)6 sequence upstream of the GAL7 poly(A) site. The factors will also efficiently cleave precursor with the CYC1 poly(A) site. This RNA does not contain a UA repeat, and processing at this site is thought to be directed by a UAG...UAUGUA-type motif. Specific polyadenylation of a precleaved GAL7 RNA requires CF I, PF I, and a crude fraction containing PAP activity. The PAP fraction can be replaced by recombinant PAP, indicating that this enzyme is the only factor in this fraction needed for the reconstituted reaction. The poly(A) addition step is also dependent on the UA repeat. Since CF I is the only factor necessary for both cleavage and poly(A) addition, it is likely that this fraction contains a component which recognizes processing signals located upstream of the poly(A) site. The initial separation of processing factors in yeast cells suggests both interesting differences from and similarities to the mammalian system.
Autolysins of Bacillus subtilis: multiple enzymes with multiple functions (2000)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Oxidative versus reductive succinic acid production in the yeast saccharomyces cerevisiae (2011)

Bio-based succinic acid is receiving increasing attention, as it could provide a cost-effective, ecologically sustainable alternative to the current petrochemical production process, thus promising a significantly higher market potential. The yeast Saccharomyces cerevisiae is a robust and well-established industrial production organism exhibiting an extraordinarily high acid- and osmotolerance. These features in conjunction with the sophisticated toolbox for genetic engineering make it particularly suitable for succinic acid production. The high tolerance towards acidity is a major advantage over previously established bacterial succinic acid production hosts, since it makes the use of neutralisation salts dispensable and thus enormously facilitates the downstream process. By constructing yeast strains capable of producing significant amounts of succinic acid, we have recently established S. cerevisiae as a promising host for succinic acid production. Our metabolic engineering strategy relied on the implementation of an oxidative production route using the glyoxylate cycle. We here discuss theoretical and practical aspects of oxidative and reductive succinic acid production routes in S. cerevisiae.
Pinholes and spin transfer effect in magnetic tunnel junction heads (2005)

Spin-transfer-induced microwave excitations in magnetic tunnel junction (MTJ) read heads have been investigated via spin-torque-modified micromagnetic modeling. This study focuses on the effect of possible pinholes in the barrier layer for a MTJ read head with permanent magnet stabilization. It is found that the critical current threshold for the spin-transfer-excited microwaves is significantly reduced if small pinholes exist in the tunnel barrier layer. The smaller effective conductive area, the smaller the current threshold. For a single small pinhole in the center of the barrier surface, the resulted spin-transfer-excited microwaves are chaotic in nature, yielding a significant 1∕f noise below 1GHz. The microwave excitation also strongly depends on the exact location of the pinhole(s). The study suggests that by studying the spin-transfer-excited microwaves, one can obtain a good knowledge about the possible existence of pinholes as well as their spatial distributions for the magnetic tunnel junction read heads.
IBM Memory Expansion Technology (MXT) (2001)

Several technologies are leveraged to establish an architecture for a low-cost, high-performance memory controller and memory system that more than double the effective size of the installed main memory without significant added cost. This architecture is the first of its kind to employ real-time main-memory content compression at a performance competitive with the best the market has to offer. A large low-latency shared cache exists between the processor bus and a content-compressed main memory. High-speed, low-latency hardware performs real-time compression and decompression of data traffic between the shared cache and the main memory. Sophisticated memory management hardware dynamically allocates main-memory storage in small sectors to accommodate storing the variable-sized compressed data without the need for “garbage” collection or significant wasted space due to fragmentation. Though the main-memory compression ratio is limited to the range 1:1–64:1, typical ratios range between 2:1 a nd 6:1, as measured in “real-world” system applications.
Characterization of carotenoids in soil bacteria and investigation of their photodegradation by UVA radiation via resonance Raman spectroscopy (2015)

A soil habitat consists of an enormous number of pigmented bacteria with the pigments mainly composed of diverse carotenoids. Most of the pigmented bacteria in the top layer of the soil are photoprotected from exposure to huge amounts of UVA radiation on a daily basis by these carotenoids. The photostability of these carotenoids depends heavily on the presence of specific features like a carbonyl group or an ionone ring system on its overall structure. Resonance Raman spectroscopy is one of the most sensitive and powerful techniques to detect and characterize these carotenoids and also monitor processes associated with them in their native system at a single cell resolution. However, most of the resonance Raman profiles of carotenoids have very minute differences, thereby making it extremely difficult to confirm if these differences are attributed to the presence of different carotenoids or if it is a consequence of their interaction with other cellular components. In this study, we devised a method to overcome this problem by monitoring also the photodegradation of the carotenoids in question by UVA radiation wherein a differential photodegradation response will confirm the presence of different carotenoids irrespective of the proximities in their resonance Raman profiles. Using this method, the detection and characterization of carotenoids in pure cultures of five species of pigmented coccoid soil bacteria is achieved. We also shed light on the influence of the structure of the carotenoid on its photodegradation which can be exploited for use in the characterization of carotenoids via resonance Raman spectroscopy.
In Vivo Expression of Natural Killer Cell Inhibitory Receptors by Human Melanoma–Specific Cytolytic T Lymphocytes (1999)

Natural killer (NK) receptor signaling can lead to reduced cytotoxicity by NK cells and cytolytic T lymphocytes (CTLs) in vitro. Whether T cells are inhibited in vivo remains unknown, since peptide antigen-specific CD8(+) T cells have so far not been found to express NK receptors in vivo. Here we demonstrate that melanoma patients may bear tumor-specific CTLs expressing NK receptors. The lysis of melanoma cells by patient-derived CTLs was inhibited by the NK receptor CD94/NKG2A. Thus, tumor-specific CTL activity may be decreased through NK receptor triggering in vivo.
Endostatin Blocks Vascular Endothelial Growth Factor-mediated Signaling via Direct Interaction with KDR/Flk-1 (2002)

Endostatin, a fragment of collagen XVIII, is a potent anti-angiogenic protein, but the molecular mechanism of its action is not yet clear. We examined the effects of endostatin on the biological and biochemical activities of vascular endothelial growth factor (VEGF). Endostatin blocked VEGF-induced tyrosine phosphorylation of KDR/Flk-1 and activation of ERK, p38 MAPK, and p125(FAK) in human umbilical vein endothelial cells. Endostatin also inhibited the binding of VEGF(165) to both endothelial cells and purified extracellular domain of KDR/Flk-1. Moreover, the binding of VEGF(121) to KDR/Flk-1 and VEGF(121)-stimulated ERK activation were blocked by endostatin. The direct interaction between endostatin and KDR/Flk-1 was confirmed by affinity chromatography. However, endostatin did not bind to VEGF. Our findings suggest that a direct interaction of endostatin with KDR/Flk-1 may be involved in the inhibitory function of endostatin toward VEGF actions and responsible for its potent anti-angiogenic and anti-tumor activities in vivo.
High and Low Annealing Temperatures Increase Both Specificity and Yield in Touchdown and Stepdown PCR (1996)

Touchdown (TD) PCR represents a versatile one-step procedure for optimizing PCRs even if the degree of primer-template complementarity is not fully known. The protocol relies on incremental annealing temperature decreases in progressive cycles designed to bracket the melting temperature (Tm) of the reaction. Here we investigate the characteristics of TD PCR that serve to minimize the need to optimize annealing temperature or buffer conditions and yet produce single strong target amplicons. We demonstrate that priming initiates above the optimum annealing temperature; this helps to ensure a competitive advantage for the target amplicon. On the other hand, as the cycling program progresses, annealing temperatures well below the Tm can serve to significantly increase yields in reactions that would otherwise be marginal due to suboptimal buffer composition and yet do not promote spurious amplification. Modified forms of TD PCR, termed stepdown PCR, consisting of fewer but steeper incremental declines in annealing temperature, are also shown to be effective and can simplify thermal cycler programming.
The james ewing lecture. The relationship between tumor mass and resistance to chemotherapy. Implications for surgical adjuvant treatment of cancer (1983)

Tumor mass negatively influences the outcome of surgery and radiotherapy by its influence on invasiveness and the propensity to metastasize before local treatment is applied. Tumor mass negatively affects the outcome of cancer chemotherapy in a manner quite different from the way in which it does surgery or radiotherapy. Cancer chemotherapy fails because cells develop resistance to anticancer drugs. Conceptually, there are two types of resistance both of which are mass related: temporary resistance (due to pharmacologic sanctuaries or altered cell kinetics) or permanent resistance (mutant lines developing specific and permanent resistance to one or more cancer drugs). Based on somatic mutation theory, it now appears that resistant mutants arise spontaneously early in the natural history of cancers, and the likelihood of a resistant line developing appears closely related to cell number, such that one or more resistant lines are likely present before most human malignancies become clinically evident. The development of permanent resistance more precisely accounts for the invariable inverse relationship between cell number and curability by drugs and the greater effectiveness of combination chemotherapy over single agents. New information on common pathways of drug resistance appear exploitable using tools available today or on the horizon. Treatment of bacterial infections, particularly tuberculosis, now truly appears to be a paradigm for cancer chemotherapy.
Inference networks for document retrieval (1989)

The use of inference networks to support document retrieval is introduced. A network-based retrieval model is described and compared to conventional probabilistic and Boolean models.
The Cell Adhesion Domain in Plasma Vitronectin Is Cryptic (1997)

Vitronectin (Vn) is a major adhesive glycoprotein in blood. However, many of the functions of Vn are regulated by its conformational state and degree of multimerization. Here, the ability of native and denatured Vn to bind to integrin adhesion receptors was compared. Three lines of evidence suggest that the native, plasma form of Vn is not an adhesive glycoprotein. (i) Antibodies that bind in close proximity to the cell adhesion domain of Vn fail to bind to native Vn present in unfractionated plasma. (ii) Denatured Vn binds to both glycoprotein IIb/IIIa and alphavbeta3 in a dose-dependent manner. In contrast, native Vn is unable to bind either integrin. (iii) Thermal denaturation of native Vn, or its complexation with type 1 plasminogen activator inhibitor, exposed the cell adhesion domain of Vn. Thus, while plasma Vn is unable to bind integrins and is not an adhesive glycoprotein, the conformationally altered from of the protein binds avidly to both alphavbeta3 and glycoprotein IIb/IIIa. The data presented here indicate that such conformational changes in Vn are likely to occur in areas of tissue injury and thrombosis.
Morphology and temperature responsiveness–swelling relationship of poly(N‐isopropylamide–chitosan) copolymers and their application to drug release (2004)

Abstract Poly [ N ‐isopropylacrylamide (NIPAAm)–chitosan] crosslinked copolymer particles were synthesized by soapless emulsion copolymerization of NIPAAm and chitosan. An anionic initiator [ammonium persulfate (APS)] and a cationic initiator [2,2′‐azobis(2‐methylpropionamidine)dihydrochloride (AIBA)] were used to initiate the reaction of copolymerization. The chitosan–NIPAAm copolymer synthesized by using APS as the initiator showed a homogeneous morphology and exhibited the characteristic of a lower critical solution temperature (LCST). The copolymer synthesized by using AIBA as an initiator showed a core–shell morphology, and the characteristic of LCST was insignificant. The LCST of the chitosan–NIPAAm copolymer depended on the morphology of the copolymer particles. In addition, the chitosan–NIPAAm copolymer particles were processed to form copolymer disks. Then, the effect of various variables such as the chitosan/NIPAAm weight ratio, the concentration of crosslinking agent, and the pH values on the swelling ratio of chitosan–NIPAAm copolymer disks were investigated. Furthermore, caffeine was used as the model drug to study the characteristics of drug loading of the chitosan–NIPAAm copolymer disks. Variables such as the chitosan/NIPAAm weight ratio and the concentration of the crosslinking agent significantly influenced the behavior of caffeine loading. Two factors (pore size and swelling ratio) affected the behavior of caffeine release from the chitosan–NIPAAm copolymer disks. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3029–3037, 2004
Surface, Pore Morphology, and Optical Properties of Porous 4H-SiC (2001)

Electron microscopy and spectroscopic ellipsometry are used to investigate the microstructural and optical properties of porous SiC. It is discussed that 1c dislocations are likely to play a role in the initial phases of the anodization process in terms of formation of nanometer sized holes. Pores are found to initially propagate nearly parallel with the sample surface and gradually change direction toward the c axis. Pore sizes are found to increase with depth toward the interface between the porous SiC and the substrate. A different pore morphology is found along the internal surfaces of micropipes, where structures are relatively large in size and appear spherical in shape. The anisotropy in pore propagation influences the etch rate, which varies in a nonlinear manner with the anodization time. The etching rate is also influenced by the larger absorptivity of the porous layers caused by formation of a disordered phase at the interface between the crystalline SiC and the pores. Ellipsometric analysis of porous SiC layers yields thicknesses and porosities in good agreement with the electron microscopy observations. Optical properties of the solid content of the porous layers are significantly different from those of bulk crystalline SiC, and depend on the etching time and sample thickness. © 2001 The Electrochemical Society. All rights reserved.
Optimal quantization of LSP parameters (speech coding) (2003)

Two nonuniform aspects of the line spectrum pair (LSP) linear predictive coding parameters are investigated, including nonuniform statistical distributions and spectral sensitivities of adjacent LSP frequency differences. Based on these two nonuniform properties, a novel, globally optimal, scalar quantizer is designed for each differential LSP frequency. The design algorithm is based on dynamic programming, and minimization of a nontrivial data dependent spectral distortion is adopted as the optimality criterion. The LSP quantizer can achieve a 1-dB average log spectral distortion, which is the experimental difference limen (DL) for producing perceptually transparent spectral information at 32 bits/frame. The quantization performance is shown to be fairly robust across different speakers and databases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intracavitary radiotherapy boosting for nasopharynx cancer. (1997)

Intracavitary radiotherapy is conceptually an attractive method of boosting dose to nasopharynx cancer whilst sparing sensitive normal tissues. A high dose rate (HDR) microselectron can be used to deliver a brachytherapy boost conveniently, safely, comfortably and effectively. Following external radiotherapy a single outpatient treatment has been given to patients using the remote afterloading system of sources placed in modified paediatric endotracheal tubes. This has been associated with good primary control and no evidence of serious morbidity in eight patients. The main limitation of this method is restriction of its utilization to small volume primary disease.
Renaturation of citrate synthase: Influence of denaturant and folding assistants (1992)

Citrate synthase (CS), which has been denatured in either guanidine hydrochloride (GdnHCl) or urea can be assisted in its renaturation in a variety of ways. The addition of each of the assistants--bovine serum albumin (BSA), oxaloacetate (OAA), and glycerol--promotes renaturation. In combination, the effect of these substances is additive with respect to the yield of folded CS. The report of Buchner et al. (Buchner, J., Schmidt, M., Fuchs, M., Jaenicke, R., Rudolph, R., Schmid, F.X., & Kiefhaber, T., 1991, Biochemistry 30, 1586-1591) that refolding of CS is facilitated by the GroE system (an Escherichia coli chaperonin [cpn] that is composed of GroEL [cpn60] and GroES [cpn10]) has been confirmed. However, we observed substantially higher yield of reactivated CS, 82%, and almost no reactivation in the absence of GroES, < 5%, whereas Buchner et al. reported 28% and 16%, respectively. In addition, we find that GroE-assisted refolding is more efficient for CS denatured in GdnHCl than for CS denatured in urea. This result is discussed in light of the known difference in the denatured states generated in GdnHCl and urea. Because GroEL inhibits the BSA/glycerol/OAA-assisted refolding, this system will be useful in future studies on the mechanism of GroE-facilitated refolding.
Carrier lifetime and radiative recombination in quantum dot LEDs (2002)

We have measured the differential carrier lifetime as a function of current density for QD LED samples and used this data to calculate the functional relationship between the carrier lifetime, carrier density and radiative efficiency. The results indicate that carrier filling on the different dot energy levels has a strong influence on the radiative behavior of the devices and that the radiative rate coefficient, B, for different QD levels can vary considerably.
IL-12, as an adjuvant, promotes a T helper 1 cell, but does not suppress a T helper 2 cell recall response (1996)

IL-12 is a potent inducer of NK and cytolytic T cell activity, IFN-gamma production, and T cell proliferation, and is necessary for differentiation of naive T cells to the Th1 subset. We have previously shown that IL-12 promotes a primary Th1 response and suppresses a primary Th2 response in lymph nodes of mice primed with a model hapten-protein conjugate, 2,4,6-trinitrophenyl (TNP)-keyhole limpet hemocyanin (KLH). We have now extended these studies to determine the Th phenotype of the recall response following immunization with soluble Ag and IL-12. For these experiments, mice were primed with TNP-KLH with or without treatment with IL-12, allowed to progress beyond the primary immune response, and challenged by i.p. injection of TNP-KLH. The phenotype of the recall response was monitored by measuring ex vivo production of IFN-gamma and IL-4 in Ag-stimulated lymph node and spleen cell cultures. Titer and isotype of TNP-specific serum Abs were also evaluated. Mice primed with Ag+IL-12 developed a Th1 recall response, as detected by KLH-specific IFN-gamma production from cultured spleen cells and the presence of TNP-specific IgG2a Ab in serum. However, they also developed an Ag-specific Th2 recall response, as characterized by Ag-induced IL-4 production from spleen cells and the presence of high titers of anti-TNP IgG1 in the serum. Studies of the cytokine profile during the primary response revealed that IL-12 induced in spleen cells the capacity to express both IL-4 and IFN-gamma. CD4+ T cells are necessary for production of IL-4 in the spleens of IL-12-treated mice, and most likely account for the Th2 recall response detected in mice primed with Ag+IL-12. These results indicate that the Th1 phenotype induced by immunization with IL-12 and Ag is maintained so that a Th1 recall response is expressed upon subsequent challenge with Ag. However, immunization with IL-12 also supports the development of a Th2 recall response, indicating that the Th1-inducing effect of IL-12 in vivo is not accompanied by a long lasting suppression of Th2 development.
The Galvanization of Biology: A Growing Appreciation for the Roles of Zinc (1996)

Zinc ions are key structural components of a large number of proteins. The binding of zinc stabilizes the folded conformations of domains so that they may facilitate interactions between the proteins and other macromolecules such as DNA. The modular nature of some of these zinc-containing proteins has allowed the rational design of site-specific DNA binding proteins. The ability of zinc to be bound specifically within a range of tetrahedral sites appears to be responsible for the evolution of the side range of zinc-stabilized structural domains now known to exist. The lack of redox activity for the zinc ion and its binding and exchange kinetics also may be important in the use of zinc for specific functional roles.