gebhart/patrepeval huggingface dataset:
Library of Synthetic 5' Secondary Structures To Manipulate mRNA Stability in Escherichia coli (1999)

A DNA cassette system has been developed to allow for the convenient introduction of synthetic DNA oligonucleotides between the transcription and translation start sites of a gene in order to examine the effect of 5' hairpin structure and strength on mRNA stabilization. Rationally designed synthetic DNA cassettes were introduced into the 5' untranslated region of a modified lacZ gene to form hairpins at the 5' end of the mRNA. These DNA inserts influenced mRNA half-lives over an order-of-magnitude range, with some groups of predicted structures having half-lives that showed a strong correlation with hairpin strength while half-lives for another group of predicted structures exhibited little or no dependence on this property. These results indicate the importance of 5' hairpin structure and strength in determining stabilization of Escherichia coli mRNA. This synthetic library, as well others generated using the DNA cassette system described here, should prove useful in understanding the mechanisms of mRNA stabilization and in designing structures for recombinant gene expression control.
Ionic Conductivity of Nanostructured Block Copolymer/Ionic Liquid Membranes (2011)

Nanostructured mixtures of ionic liquids and polymers are of great interest for a wide variety of electrochemical applications. Understanding the relationship between composition, structure, and ionic conductivity for these mixtures is essential for designing new materials. In this work, the effect of nanostructure on ionic conductivity, σ, is investigated for model mixtures of diblock copolymers and ionic liquids that are selective for one of the polymer microphases. It is demonstrated that the concentration dependence of σ is a function of the total volume fraction of ionic liquid and described well by percolation theory. This scaling behavior encourages the design of membranes where the amount of a mechanical component in the block copolymer can be increased to improve the strength of the membrane without sacrificing conductivity. The temperature dependence of σ is a function of the amount of ionic liquid exclusively in the conducting domain. Comparing σ for mixtures of the diblock copolymer poly(styrene-block-2-vinylpyridine) (S2VP) and two different ionic liquids, imidazolium bis(trifluoromethylsulfonyl)imide ([Im][TFSI]) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIm][TFSI]), reveals that the chemistry of the polymer/ionic liquid pair affects both the activation energy for σ and the maximum attainable σ but does not affect how σ scales with ionic liquid concentration. The effect of the morphology on σ is also examined, and it is found that as long as the conducting phase morphology is isotropic and well-connected, σ is not affected by morphology.
Overexpression of Protein-tyrosine Phosphatase-1B in Adipocytes Inhibits Insulin-stimulated Phosphoinositide 3-Kinase Activity without Altering Glucose Transport or Akt/Protein Kinase B Activation (2000)

Previous studies suggested that protein-tyrosine phosphatase 1B (PTP1B) antagonizes insulin action by catalyzing dephosphorylation of the insulin receptor (IR) and/or other key proteins in the insulin signaling pathway. In adipose tissue and muscle of obese humans and rodents, PTP1B expression is increased, which led to the hypothesis that PTP1B plays a role in the pathogenesis of insulin resistance. Consistent with this, mice in which the PTP1B gene was disrupted exhibit increased insulin sensitivity. To test whether increased expression of PTP1B in an insulin-sensitive cell type could contribute to insulin resistance, we overexpressed wild-type PTP1B in 3T3L1 adipocytes using adenovirus-mediated gene delivery. PTP1B expression was increased approximately 3-5-fold above endogenous levels at 16 h, approximately 14-fold at 40 h, and approximately 20-fold at 72 h post-transduction. Total protein-tyrosine phosphatase activity was increased by 50% at 16 h, 3-4-fold at 40 h, and 5-6-fold at 72 h post-transduction. Compared with control cells, cells expressing high levels of PTP1B showed a 50-60% decrease in maximally insulin-stimulated tyrosyl phosphorylation of IR and insulin receptor substrate-1 (IRS-1) and phosphoinositide 3-kinase (PI3K) activity associated with IRS-1 or with phosphotyrosine. Akt phosphorylation and activity were unchanged. Phosphorylation of p42 and p44 MAP kinase (MAPK) was reduced approximately 32%. Overexpression of PTP1B had no effect on basal, submaximally or maximally (100 nm) insulin-stimulated glucose transport or on the EC(50) for transport. Our results suggest that: 1) insulin stimulation of glucose transport in adipocytes requires </=45% of maximal tyrosyl phosphorylation of IR or IRS-1 and <50% of maximal activation of PI3K, 2) a novel PI3K-independent pathway may play a role in insulin-induced glucose transport in adipocytes, and 3) overexpression of PTP1B alone in adipocytes does not impair glucose transport.
Exclusive Localization of Colicin A in Cell Cytoplasm of Producing Bacteria (1981)

The production of colicin A in Citrobacter freundii and in Escherichia coli was studied. After induction with low concentrations of mitomycin C, these organisms differed with regards to cell growth, cell viability, and kinetics of colicin A biosynthesis. Despite these differences, immunoferritin labeling on ultra‐thin sections of induced frozen cells demonstrated that colicin A was located exclusively within the cell cytoplasm in both types of bacteria. By using protein markers, it was shown that at no times after induction was colicin A accumulated in the periplasmic space or in inner or outer membranes. These results were confirmed by a biochemical approach. For at least 3 h after induction, colicin A remained associated with producing cells and no colicin A activity was found in the periplasmic space. These results are discussed with reference to the synthesis and export of other bacteriocins.
A 6-kb Promoter Fragment Mimics in Transgenic Mice the Prostate-Specific and Androgen-Regulated Expression of the Endogenous Prostate-Specific Antigen Gene in Humans (1997)

Prostate-specific antigen (PSA) is a kallikrein-like serine protease, which is almost exclusively synthesized in the luminal epithelial cells of the human prostate. PSA expression is androgen regulated. Previously, we characterized in vitro the proximal promoter, and a strong enhancer region, approximately 4 kb upstream of the PSA gene. Both regions are needed for high, androgen-regulated activity of the PSA promoter in LNCaP cells. The goal of the present study is the in vivo characterization of the PSA promoter. Three transgenic mouse lines carrying the Escherichia coli LacZ gene, driven by the 632-bp proximal PSA promoter, and three lines with LacZ, driven by the 6-kb PSA promoter, were generated. Expression of the LacZ reporter gene was analyzed in a large series of tissues. Transgene expression could not be demonstrated in any of the transgenic animals carrying the proximal PSA promoter. All three lines carrying the 6-kb PSA promoter showed lateral prostate-specific beta-galactosidase activity. Transgene expression was undetectable until 8 weeks after birth. Upon castration, beta-galactosidase activity rapidly declined. It could be restored by subsequent androgen administration. A search for mouse PSA-related kallikrein genes expressed in the prostate led to the identification of mGK22, which was previously demonstrated to be expressed in the submandibular salivary gland. Therefore, the 6-kb PSA-LacZ transgene followed the expression pattern of the PSA gene in humans, which is almost completely prostate-specific, rather than that of mGK22 in mice. In conclusion, the 6-kb promoter fragment appears to contain most, if not all, information for androgen regulation and prostate specificity of the PSA gene.
Proton coupled membrane transport of anions mediated by cryptate carriers (1988)

B. Dietrich, T. M. Fyles, M. W. Hosseini, J. Lehn and K. C. Kaye, J. Chem. Soc., Chem. Commun., 1988, 691 DOI: 10.1039/C39880000691
Duality for Monomorphisms and Almost Open Operators Between Locally Convex Spaces (2001)

A continuous and linear operator T : E → F between Banach spaces E and F is a bounded below, resp. surjective (and open), if and only if its transposed operator T': F' b → E' b is surjective (and open), resp. bounded below. This survey paper presents a complete analysis of the possible extensions of these two results when E and F are both Frechet spaces or both complete (DF)-spaces.
Isolation and expression in Escherichia coli of hepB and hepC, genes coding for the glycosaminoglycan-degrading enzymes heparinase II and heparinase III, respectively, from Flavobacterium heparinum (1996)

Upon induction with heparin, Flavobacterium heparinum synthesizes and secretes into its periplasmic space heparinase I (EC 4.2.2.7), heparinase II, and heparinase III (heparitinase; EC 4.2.2.8). Heparinase I degrades heparin, and heparinase II degrades both heparin and heparan sulfate, while heparinase III degrades heparan sulfate predominantly. We isolated the genes encoding heparinases II and III (designated hepB and hepC, respectively). These genes are not contiguous with each other or with the heparinase I gene (designated hepA). hepB and hepC were found to contain open reading frames of 2,316 and 1,980 bp, respectively. Enzymatic removal of pyroglutamate groups permitted sequence analysis of the amino termini of both mature proteins. It was determined that the mature forms of heparinases II and III contain 746 and 635 amino acids, respectively, and have calculated molecular weights of 84,545 and 73,135, respectively. The preproteins have signal sequences consisting of 26 and 25 amino acids. Truncated hepB and hepC genes were used to produce active, mature heparinases II and III in the cytoplasm of Escherichia coli. When these enzymes were expressed at 37 degrees C, most of each recombinant enzyme was insoluble, and most of the heparinase III protein was degraded. When the two enzymes were expressed at 25 degrees C, they were both present predominantly in a soluble, active form.
PHYSICOCHEMICAL CHARACTERIZATION OF CAPSTONE DEPLETED URANIUM AEROSOLS II: PARTICLE SIZE DISTRIBUTIONS AS A FUNCTION OF TIME (2009)

The Capstone Depleted Uranium (DU) Aerosol Study, which generated and characterized aerosols containing DU from perforation of armored vehicles with large-caliber DU penetrators, incorporated a sampling protocol to evaluate particle size distributions. Aerosol particle size distribution is an important parameter that influences aerosol transport and deposition processes as well as the dosimetry of the inhaled particles. These aerosols were collected on cascade impactor substrates using a pre-established time sequence following the firing event to analyze the uranium concentration and particle size of the aerosols as a function of time. The impactor substrates were analyzed using proportional counting, and the derived uranium content of each served as input to the evaluation of particle size distributions. Activity median aerodynamic diameters (AMADs) of the particle size distributions were evaluated using unimodal and bimodal models. The particle size data from the impactor measurements were quite variable. Most size distributions measured in the test based on activity had bimodal size distributions with a small particle size mode in the range of between 0.2 and 1.2 microm and a large size mode between 2 and 15 microm. In general, the evolution of particle size over time showed an overall decrease of average particle size from AMADs of 5 to 10 microm shortly after perforation to around 1 microm at the end of the 2-h sampling period. The AMADs generally decreased over time because of settling. Additionally, the median diameter of the larger size mode decreased with time. These results were used to estimate the dosimetry of inhaled DU particles.
Activation of the Fibrinolytic Cascade Early in Pregnancy Among Women With Spontaneous Preterm Birth (2008)

II.
HyperText: State of the Art (1990)

Preface Navigation and browsing Hypertext and learning Prototypes Designing Hypertext and Hypertext design Index.
Oncolytic herpes simplex virus vector with enhanced MHC class I presentation and tumor cell killing (2001)

Oncolytic herpes simplex virus type 1 (HSV-1) vectors are promising therapeutic agents for cancer. Their efficacy depends on the extent of both intratumoral viral replication and induction of a host antitumor immune response. To enhance these properties while employing ample safeguards, two conditionally replicating HSV-1 vectors, termed G47Delta and R47Delta, have been constructed by deleting the alpha47 gene and the promoter region of US11 from gamma34.5-deficient HSV-1 vectors, G207 and R3616, respectively. Because the alpha47 gene product is responsible for inhibiting the transporter associated with antigen presentation (TAP), its absence led to increased MHC class I expression in infected human cells. Moreover, some G47Delta-infected human melanoma cells exhibited enhanced stimulation of matched antitumor T cell activity. The deletion also places the late US11 gene under control of the immediate-early alpha47 promoter, which suppresses the reduced growth properties of gamma34.5-deficient mutants. G47Delta and R47Delta showed enhanced viral growth in a variety of cell lines, leading to higher virus yields and enhanced cytopathic effect in tumor cells. G47Delta was significantly more efficacious in vivo than its parent G207 at inhibiting tumor growth in both immune-competent and immune-deficient animal models. Yet, when inoculated into the brains of HSV-1-sensitive A/J mice at 2 x 10(6) plaque forming units, G47Delta was as safe as G207. These results suggest that G47Delta may have enhanced antitumor activity in humans.
Azoles. Part 9. Synthesis of derivatives of thieno[2,3-d]thiazole, 4H-pyrrolo-[2,3-d]thiazole, 2H-pyrazolo[3,4-d]thiazole and isoxazolo[3,4-d]thiazole from thiazolidine-2,4-dione (1992)

The aldehyde group of 2,4-dichlorothiazole-5-carbaldehyde was protected and the chlorine atom at position 2 was replaced by hydrogen and a methylthio group, via Cl → Li exchange, to give 4-chloro-thiazole-5-carbaldehyde and its 2-methylthio derivative, respectively. Ethyl 2-mercaptoacetate reacted with 4-chlorothiazole-5-carbaldehydes to give thieno[2,3-d]thiazoles. Saponification of ethyl thieno[2,3-d]thiazole-5-carboxylate and attempted decarboxylation of the resulting acid failed to yield enough of the parent thieno[2,3-d]thiazole to allow full characterisation owing to its high volatility.4-Azidothiazole-5-carbaldehydes were prepared by nucleophilic displacement of the chlorine atom in the corresponding 4-chlorothiazole-5-carbaldehyde and converted into alkenes and Schiff's bases by standard procedures. On being heated in toluene these afforded the corresponding 4H-pyrrolo-[2,3-d]thiazole or 2H-pyrazolo[3,4-d]thiazole. lsoxazolo[3,4-d]thiazole and its 2-methylthio derivative, both unstable, were obtained by heating the corresponding 4-azidothiazole-5-carbaldehyde in bromobenzene.
Pathogenesis, Diagnosis, and Management of Primary Antibody Deficiencies and Infections (2009)

Primary antibody deficiencies are the most common primary immunodeficiency diseases. They are a heterogeneous group of disorders with various degrees of dysfunctional antibody production resulting from a disruption of B-cell differentiation at different stages. While there has been tremendous recent progress in the understanding of some of these disorders, the etiology remains unknown for the majority of patients. As there is a large spectrum of underlying defects, the age at presentation varies widely, and the clinical manifestations range from an almost complete absence of B cells and serum immunoglobulins to selectively impaired antibody responses to specific antigens with normal total serum immunoglobulin concentrations. However, all of these disorders share an increased susceptibility to infections, affecting predominantly the respiratory tract. A delay of appropriate treatment for some diseases can result in serious complications related to infections, while timely diagnosis and adequate therapy can significantly decrease morbidity and increase life expectancy and quality of life.
Analysis of Enterococcus faecalis isolates from intercontinental sources by multilocus enzyme electrophoresis and pulsed-field gel electrophoresis (1995)

Pulsed-field gel electrophoresis (PFGE) and multilocus enzyme electrophoresis (MLEE) were compared in this study of 65 Enterococcus faecalis isolates recovered over a 20-year period from diverse geographic sources. Clonal relationships recognized by PFGE were also recognized by MLEE; however, MLEE recognized as greater number of isolates as belonging to clonal groups than did PFGE. Both techniques were reproducible and discriminatory, but MLEE more readily recognized relationships among large numbers of isolates. MLEE confirmed the previously reported clonal spread of beta-lactamase-producing E. faecalis to six hospitals in five states. MLEE provided a useful population framework of the E. faecalis isolates in this sample, while PFGE was able to differentiate among isolates within some MLEE clonal groups.
Summary: the modified nucleosides of RNA (1994)

A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sources, and initial literature citations for structural characterization or occurrence, and for chemical synthesis. The listing is categorized by type of RNA: tRNA, rRNA, mRNA, snRNA, and other RNAs. A total of 93 different modified nucleosides have been reported in RNA, with the largest number and greatest structural diversity in tRNA, 79; and 28 in rRNA, 12 in mRNA, 11 in snRNA and 3 in other small RNAs.
Doing Dutch Pronouns Automatically in Optimality Theory (2003)

Pronoun resolution algorithms often use elaborate and complicated rules and weighted factors. In this paper I will use the framework of Optimality Theory to implement an automatic pronoun resolution system for Dutch. By ranking constraints, Optimality Theory can be used to model complex behaviour and preferences, whilst keeping the constraints clear and simple. The system is developed by quantative evaluation of different configurations on a small corpus of newspaper articles, containing 222 pronouns. Even though, from a practical perspective, the performance is wanting, some linguistically interesting results are given. 1
A Novel Endothelial L-Selectin Ligand Activity in Lymph Node Medulla That Is Regulated by α(1,3)-Fucosyltransferase-IV (2003)

Lymphocytes home to peripheral lymph nodes (PLNs) via high endothelial venules (HEVs) in the subcortex and incrementally larger collecting venules in the medulla. HEVs express ligands for L-selectin, which mediates lymphocyte rolling. L-selectin counterreceptors in HEVs are recognized by mAb MECA-79, a surrogate marker for molecularly heterogeneous glycans termed peripheral node addressin. By contrast, we find that medullary venules express L-selectin ligands not recognized by MECA-79. Both L-selectin ligands must be fucosylated by alpha(1,3)-fucosyltransferase (FucT)-IV or FucT-VII as rolling is absent in FucT-IV+VII(-/-) mice. Intravital microscopy experiments revealed that MECA-79-reactive ligands depend primarily on FucT-VII, whereas MECA-79-independent medullary L-selectin ligands are regulated by FucT-IV. Expression levels of both enzymes paralleled these anatomical distinctions. The relative mRNA level of FucT-IV was higher in medullary venules than in HEVs, whereas FucT-VII was most prominent in HEVs and weak in medullary venules. Thus, two distinct L-selectin ligands are segmentally confined to contiguous microvascular domains in PLNs. Although MECA-79-reactive species predominate in HEVs, medullary venules express another ligand that is spatially, antigenically, and biosynthetically unique. Physiologic relevance for this novel activity in medullary microvessels is suggested by the finding that L-selectin-dependent T cell homing to PLNs was partly insensitive to MECA-79 inhibition.
Adoptive transfer of tumor-infiltrating lymphocytes in melanoma: a viable treatment option (2018)

The treatment of metastatic melanoma patients with autologous tumor-infiltrating lymphocytes (TIL) shows robust, reproducible, clinical responses in clinical trials executed in several specialized centers over the world. Even in the era of targeted therapy and immune checkpoint inhibition, TIL therapy can be an additional and clinically relevant treatment line. This review provides an overview of the clinical experiences with TIL therapy thus far, including lymphodepleting regimens, the use of interleukin-2 (IL-2) and the associated toxicity. Characteristics of the TIL products and the antigen recognition pattern will be discussed, as well as the current and upcoming production strategies, including the selective expansion of specific fractions from the cell product. In addition, the future potential of TIL therapy in melanoma and other tumor types will be covered.
Efficient coding for integrated information systems and multimedia databases (2003)

Schemes that can be used to compress image data as well as nonimage database files efficiently are presented. An initial transformation (coding) step is applied to image data in order to induce desirable properties that enable the efficient application of popular lossless compression schemes that are normally well suited to text and database files. Further improvement is obtained by a scheme that utilizes the correlation properties of the transformed image files.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vaccine-Induced Immunopathology during Bovine Respiratory Syncytial Virus Infection: Exploring the Parameters of Pathogenesis (2003)

The bovine and human respiratory syncytial viruses cause severe lower respiratory tract infections. Effective vaccines against the respiratory syncytial viruses have been lacking since vaccine failures in the 1960s and 1970s. In this report, we describe a bovine respiratory syncytial virus (bRSV) challenge model in which both classical bRSV respiratory infection and vaccine-enhanced immune pathology were reproduced. The classical, formalin-inactivated (FI) bRSV vaccine that has been associated with vaccine failure was efficient in inducing high antibody titers and reducing viral loads but also primed calves for a far more serious enhanced respiratory disease after a bRSV challenge, thereby mimicking the enhanced clinical situation in FI human RSV (hRSV)-immunized and hRSV-infected infants in the 1960s. We show that immunization with FI-bRSV mainly primes a Th2-like inflammatory response that is characterized by a significant eosinophilic influx in the bronchial alveolar lung fluid and lung tissues and high levels of immunoglobulin E serum antibodies. The current model may be useful in the evaluation of new bRSV candidate vaccines for potency and safety.