gebhart/patrepeval huggingface dataset:
Influenza virion transcriptase: synthesis in vitro of large, polyadenylic acid-containing complementary RNA (1977)

The influenza virion transcriptase is capable of synthesizing in vitro complementary RNA (cRNA) that is similar in several characteristics to the cRNA synthesized in the infected cell, which is the viral mRNA. Most of the in vitro cRNA is large (approximately 2.5 X 10(5) to 10(6) daltons), similar in size to in vivo cRNA. The in vitro transcripts initiate in adenosine (A) or guanosine (G) at the 5' end, as also appears to be the case with in vivo cRNA (R.M. Krug et al., 1976). The in vitro transcripts contain covalently linked polyadenylate [poly(A)] sequences, which are longer and more heterogeneous than the poly(A) sequences found on in vivo cRNA. The synthesis in vitro of cRNA with these characteristics requires both the proper divalent cation, Mg2+, and a specific dinulceside monophosphage (DNMP), ApG or GpG. These DNMPs stimulate cRNA synthesis about 100-fold in the presence of Mg2+ and act as primers to initiate RNA chains, as demonstrated by the fact that the 5'-phosphorylated derivatives of these DNMP's, 32pApG or 32pGpG, are incroporated at the 5' end of the product RNA. The RNA synthesized in vitro differs from in vivo cRNA in that neither capping nor methylation of the in vitro transcripts has been detected. The virion does contain a methylase activity, as shown by its ability to methylate exogenous methyl-deficient Escherichia coli tRNA.
Lactic acid production from cellobiose and xylose by engineered <i>Saccharomyces cerevisiae</i> (2015)

Efficient and rapid production of value-added chemicals from lignocellulosic biomass is an important step toward a sustainable society. Lactic acid, used for synthesizing the bioplastic polylactide, has been produced by microbial fermentation using primarily glucose. Lignocellulosic hydrolysates contain high concentrations of cellobiose and xylose. Here, we constructed a recombinant Saccharomyces cerevisiae strain capable of fermenting cellobiose and xylose into lactic acid. Specifically, genes (cdt-1, gh1-1, XYL1, XYL2, XYL3, and ldhA) coding for cellobiose transporter, β-glucosidase, xylose reductase, xylitol dehydrogenase, xylulokinase, and lactate dehydrogenase were integrated into the S. cerevisiae chromosomes. The resulting strain produced lactic acid from cellobiose or xylose with high yields. When fermenting a cellulosic sugar mixture containing 10 g/L glucose, 40 g/L xylose, and 80 g/L cellobiose, the engineered strain produced 83 g/L of lactic acid with a yield of 0.66 g lactic acid/g sugar (66% theoretical maximum). This study demonstrates initial steps toward the feasibility of sustainable production of lactic acid from lignocellulosic sugars by engineered yeast.
Cloning of Genes of Nontypeable <i>Haemophilus influenzae</i> Involved in Penetration between Human Lung Epithelial Cells (2000)

Haemophilus influenzae penetrates between epithelial cells via an unknown mechanism. A chromosomal library of nonencapsulated H. influenzae strain A960053 DNA was constructed in Escherichia coli DH5alpha to identify bacterial genes contributing to this paracytosis. Two E. coli clones that contained open reading frames (ORFs) homologous to HI0636 to HI0641 of H. influenzae strain Rd and that showed an increased penetration in epithelial cell layers of the human bronchial epithelial cell line NCI-H292 were identified. ORFs HI0636 and HI0638, encoding two small proteins of unknown functions, were further investigated. The clone containing ORFs HI0636 and HI0637 as well as the clone containing ORF HI0638 showed a significant increase in penetration. Disruption of HI0638 by kanamycin box insertion in H. influenzae strain A960053 resulted in loss of penetration into the epithelial cell layers. Disruption of HI0636 had no effect on penetration in this model system. Since a role for HI0637 in the paracytosis of H. influenzae is very unlikely because it encodes TrpS, we conclude that the protein encoded by ORF HI0638 may function as a paracytin, while that encoded by HI0636 may have an auxiliary function.
Macromolecular Crowding Meets Tissue Engineering by Self‐Assembly: A Paradigm Shift in Regenerative Medicine (2014)

MMC, the addition of inert polydispersed macromolecules in the culture media, effectively emulates the dense in vivo extracellular space, resulting in amplified deposition of ECM in vitro and subsequent production of cohesive, ECM-rich living substitutes.
Hypoxia Selectively Enhances Integrin α5β1 Receptor Expression in Breast Cancer to Promote Metastasis (2017)

Metastasis is the leading cause of breast cancer mortality. Previous studies have implicated hypoxia-induced changes in the composition and stiffness of the extracellular matrix (ECM) in the metastatic process. Therefore, the contribution of potential ECM-binding receptors in this process was explored. Using a bioinformatics approach, the expression of all integrin receptor subunits, in two independent breast cancer patient datasets, were analyzed to determine whether integrin status correlates with a validated hypoxia-inducible gene signature. Subsequently, a large panel of breast cancer cell lines was used to validate that hypoxia induces the expression of integrins that bind to collagen (ITGA1, ITGA11, ITGB1) and fibronectin (ITGA5, ITGB1). Hypoxia-inducible factors (HIF-1 and HIF-2) are directly required for ITGA5 induction under hypoxic conditions, which leads to enhanced migration and invasion of single cells within a multicellular 3D tumor spheroid but did not affect migration in a 2D microenvironment. ITGB1 expression requires HIF-1α, but not HIF-2α, for hypoxic induction in breast cancer cells. ITGA5 (α<sub>5</sub> subunit) is required for metastasis to lymph nodes and lungs in breast cancer models, and high ITGA5 expression in clinical biopsies is associated with an increased risk of mortality.<b>Implications:</b> These results reveal that targeting ITGA5 using inhibitors that are currently under consideration in clinical trials may be beneficial for patients with hypoxic tumors. <i>Mol Cancer Res; 15(6); 723-34. ©2017 AACR</i>.
Nosocomial Outbreak of Multiple Bloodborne Viral Infections (2001)

In resource-limited countries, nosocomial transmission of bloodborne pathogens is a major public health concern. After a major outbreak of human immunodeficiency virus (HIV) infection in approximately 400 children in 1998 in Libya, we tested HIV, hepatitis C virus (HCV), and hepatitis B virus (HBV) markers in 148 children and collected epidemiological data in a subgroup of 37 children and 46 parents. HIV infection was detected in all children but one, with HCV or HBV coinfection in 47% and 33%, respectively. Vertical transmission was ruled out by analysis of parents' serology. The children visited the same hospital 1-6 times; at each visit, invasive procedures with potential blood transmission of virus were performed. HIV and HCV genotypic analyses identified a HIV monophyletic group, whereas 4 clusters of HCV sequences were identified. To our knowledge, this is the largest documented outbreak of nosocomial HIV transmission.
Borate Minerals Stabilize Ribose (2004)

Evidence for an “RNA world,” an episode of life on Earth during which RNA was the only genetically encoded component of biological catalysts, is found in the ribosome ([ 1 ][1]), catalytic RNA molecules ([ 2 ][2]), and contemporary metabolism ([ 3 ][3]). That RNA could form spontaneously and
Immune complex–Fc<i>γ</i>R interaction modulates monocyte/macrophage molecules involved in inflammation and immune response (2003)

The interaction between receptors for the Fc portion of IgG (FcgammaRs) from monocytes/macrophages and immune complexes (IC) triggers regulatory and effector functions. Recently, we have demonstrated that IC exert a drastic inhibition of basal and IFN-gamma-induced expression of MHC class II on human monocytes. Taking into account that the regulation of MHC class II molecules is a crucial event in the immune response, in this report we extend our previous studies analysing the effect of STAT-1 phosphorylation in the down-regulatory process, the fate of the intracellular pool of MHC class II molecules and the effect of complement on MHC class II down-regulation induced by IC. We also studied the effect of IC on the expression of MHC class II (I-A(d)) in macrophages using a mouse model of chronic inflammation. We demonstrate that IC induce a depletion not only on surface expressed but also on intracellular MHC class II content and that IC-induced down-regulation of MHC class II is not mediated by the inhibition of STAT-1 phosphorylation. On the other hand, the effect of IC is not specific for the down-regulation of MHC class II, for it could be restricted to other molecules involved in inflammatory processes. Our experiments also show that the activation of the complement system could be a crucial step on the regulation of the effect of IC on MHC class II expression. In agreement with our in vitro experiments using human monocytes, IC treatment reduces the expression of MHC class II in a mouse model of chronic inflammation.
An economic assessment of the benefits of mosquito abatement in an organized mosquito control district. (1987)

A case study application of contingent valuation to the measurement of mosquito program benefits is presented. Annual program benefits in Jefferson County, TX are estimated to exceed costs by 1.8 times. Mean household benefits are $22.44 for owners and $18.96 for renters. Using ordinary least squares procedures these household benefits were found to be related to household socioeconomic characteristics, effectiveness of control efforts and environmental concerns.
Glycoprotein IIIa is phosphorylated in intact human platelets (1990)

The glycoprotein IIb-IIIa complex (GP IIb-IIIa) is a multifunctional transmembrane protein on platelets. Its most completely described function is as a fibrinogen receptor that mediates platelet aggregation, but it is also involved in clot retraction, signal transduction, calcium transport, and other events. However, the mechanisms that regulate the functions of GP IIb-IIIa during platelet activation are largely unknown. One possible mechanism is phosphorylation, since several other receptors are regulated by this process. We found that GP IIIa, but not GP IIb, was phosphorylated in 32P-labeled platelets, predominantly on threonine residues. Furthermore, GP IIIa phosphorylation increased four-fold in platelets activated with thrombin or phorbol 12-myristate 13-acetate, but not at all in platelets treated with prostacyclin, an inhibitor of platelet activation. The thrombin-induced increase in phosphorylation was inhibited by pretreating platelets with prostacyclin or with staurosporin, a specific protein kinase C inhibitor. Thus, there is an increase in the level or turnover of phosphate on GP IIIa during platelet activation, most likely involving protein kinase C. This phosphorylation may regulate some aspect(s) of GP IIb-IIIa function.
Ring-Opening Metathesis Polymerizations in <scp>d</scp>-Limonene:  A Renewable Polymerization Solvent and Chain Transfer Agent for the Synthesis of Alkene Macromonomers (2006)

d-Limonene has been utilized as a renewable solvent and chain transfer agent for the ring-opening metathesis polymerization (ROMP) of alkene macromonomers. The polymerization of various strained monomers, such as norbornene and 1,5-cyclooctadiene (COD), and low-strain monomers, such as cyclopentene, trans,trans,trans-1,5,9-cyclododecatriene and cycloheptene, have been initiated with a ruthenium carbene complex. The metathesis reactions with d-limonene resulted in decreased weight-average (Mw) molecular weight values compared to ROMP in toluene and hydrogenated d-limonene. For the ROMP of COD in d-limonene, the amount of chain transfer and chain degradation increased with increasing time (1−20 h) and temperature (23−70 °C). The formation of the trisubstituted alkene during chain transfer, as evidenced by a model compound, was characterized by 1H NMR (δ 5.14 ppm). Optimization of the reaction conditions for the ROMP of COD resulted in the synthesis of alkene macromonomers without the need for postpolymerization reactions.
Niños expósitos y medicina infantil en España a principios del siglo XIX (1991)

Se pretende analizar los conocimientos pediatricos y la influencia que en el tratamiento medico podia tener el pertenecer a un sector de la sociedad desfavorecido como el de los ninos expositos y como la persistencia de unas estructuras politco-sociales atrasadas condicionaron la introduccion de nuevas tecnicas y medios medicos
Description of a closed plastic bag system for the collection and cryopreservation of leukapheresis‐derived blood mononuclear leukocytes and CFUc from human donors (1980)

Hemopoietic stem cells were collected from blood by means of continuous-flow centrifugation. The therapeutic use of large quantities of autologous blood stem cells requires a suitable, reliable and easily practicable cryopreservation technique which prevents loss of cell number and viability. This paper describes a closed plastic bag system consisting of one part for the collection and freezing of blood-derived mononuclear cells (MNC), among them granulocyte/macrophage progenitor cells (CFUc), and of a second part for thawing the cryopreserved cells and washing them free of DMSO before transfusion to a patient. In a series of 20 leukaphereses, the average number of collected MNC and CFUc was about 11 x 10(9) and 8 x 10(5) respectively. The recovery rate of the leukapheresis derived MNC and CFUc after cryopreservation, thawing, and washing was demonstrated to be 90 per cent of better. Sequential leukaphereses in the same donor showed little effect on red and white blood cell concentration. However, there was a significant decrease in the donor's blood platelet concentration prior to the third leukapheresis.
Micro-RNAs as Potential New Molecular Biomarkers in Oncology: Have They Reached Relevance for the Clinical Imaging Sciences? (2013)

Minimally invasive biomarkers for early cancer detection and monitoring of personalized therapies are of high importance to further improve prognosis in oncological disease. MicroRNAs (miRNAs) are small regulatory RNAs in humans and play a key role in carcinogenesis. In recent years they have emerged as promising biomarkers in oncology. miRNA profiling has demonstrated its capacity for sub-classifying tumors and monitoring of therapeutic effects. Different expression profiles of miRNAs in cancer and the stability of circulating miRNAs potentially provide a clinically accessible molecular monitoring tool of malignant tissues and its response to therapies. Clinical imaging including the modalities PET/CT and MRI is well established for characterizing tumor tissue and sub-classifying morphological, metabolic or vascular treatment response in cancer. Sophisticated clinical imaging biomarkers for cancer detection and monitoring should now been correlatively applied to further validate the potential of miRNAs as oncologic biomarkers for the clinic.
The expression of Ki‐67, MCM3, and p27 defines distinct subsets of proliferating, resting, and differentiated cells (2001)

The mini-chromosome maintenance proteins (MCM), which are involved in the control of DNA replication, and the cyclin-dependent kinase inhibitors, such as p27/KIP1, represent two groups of proteins that are currently under investigation as diagnostic tumour markers. The expression of p27 and MCM3 was compared with the expression of the Ki-67 protein, an approved marker for proliferating cells, extensively used in histopathology and cancer research. The expression pattern of all three proteins was assessed on germinal centres and oral mucosa, which display a well-defined spatio-temporal organization. The expression of the p27 protein was closely related to differentiated cells, whereas MCM3 and Ki-67 were predominantly localized to the regions of proliferating cells. However, it is important to note that considerable numbers of cells that were growth-arrested, as confirmed by the absence of the Ki-67 protein, stained positive for the MCM3 protein. These results were verified in vitro using growth-arrested Swiss 3T3. The MCM3 protein is therefore expressed in cells that have ceased to proliferate, but are not terminally differentiated, according to the absence of p27 protein expression. In conclusion, a combined analysis of Ki-67, MCM3, and p27 protein expression may provide a more detailed insight into the cell proliferation and differentiation processes that determine individual tumour growth.
Coupled Electron- and Proton-Transfer Processes in the Reduction of α-[P<sub>2</sub>W<sub>18</sub>O<sub>62</sub>]<sup>6</sup><sup>-</sup> and α-[H<sub>2</sub>W<sub>12</sub>O<sub>40</sub>]<sup>6</sup><sup>-</sup> As Revealed by Simulation of Cyclic Voltammograms (1999)

Quantitative analysis of the complex problem of coupled electron- and proton-transfer steps during reduction of the polyoxo anions α-[P(2)W(18)O(62)](6)(-) and α-[H(2)W(12)O(40)](6)(-) in aqueous NaCl (0.5 M) has been achieved by simulation of cyclic voltammograms (Rudolph, M.; Reddy, D. P.; Feldberg, S. W. Anal. Chem. 1994, 66, 589A) over wide ranges of anion concentration, pH, and scan rate. Since there are too many unknown parameters to attempt a one-step global form of simulation, a systematic, stepwise approach has been adopted by progressively accessing regimes of increasing voltammetric complexity. This protocol allows experimental behavior in each system over 5 orders of magnitude in proton concentration to be simulated by estimation of three protonation constants combined with experimentally determined reversible half-wave potentials for the two one-electron processes involved. Fast electron transfer and protonation kinetics are assumed. The importance of the values chosen for the diffusion coefficients of the proton and polyoxo anion species is considered. The simulations account for the fact that pairs of one-electron processes coalesce to give an apparent two-electron process in the pH range 1-6 for reduction of both anions.
Investigations on vitamin D esters synthesized in rats. Detection and identification (1968)

1. Vitamin D-deficient rachitic rats were given [1-(3)H]cholecalciferol by gastric intubation. After 24hr., diethyl ether extracts of liver and kidney contained 5-11% and 4.5-20% respectively of total vitamin D apparently esterified with long-chain fatty acids. 2. A two-dimensional thin-layer chromatographic technique was devised that completely separated seven synthetic vitamin D esters according to the chain length and number of double bonds in the fatty acid component. When the ;vitamin D ester' fraction from liver or kidney was co-chromatographed with the standard esters, radioactivity appeared mainly in vitamin D palmitate, stearate, oleate and linoleate regions. The proportion of radioactivity in the saturated fatty acid esters was higher in kidney than in liver. 3. The same percentage of tissue vitamin D in the esterified form was found at each of two dosages of vitamin D. 4. The possible specificity of a vitamin D esterification mechanism is discussed.
Non-invasive adaptation of black-box user interfaces (2003)

In this paper a new method for the non-invasive adaptation of user interfaces is presented. The main idea is not to implement the user interface toolkit as an API, but instead as an object file that redefines the functionality of the API of an already existing toolkit in a generic way based on a so-called preloading technique. Compared to common approaches, the presented method allows us to evaluate prototypical user interfaces with a large number of real-world applications with very little e#ort. If the prototype proves useful, the new user interface is instantly available for all applications based on the redefined toolkit, which significantly simplifies the spreading of new interaction techniques and ideas. We illustrate the procedure by means of adapting the user interface of a 3D graphical application based on a widely used toolkit for use on handheld computers.
Purification and Properties of N-Acetylglucosaminide β1↑4 Galactosyltransferase from Embryonal Carninoma Cells12 (1987)

N-Acetylglucosaminide beta 1----4 galactosyltransferase was chromatographically purified about 1,700-fold from F9 embryonal carcinoma cells after solubilization with Triton X-100, using N-acetylglucosamine as the acceptor. As the last step of the purification, affinity chromatography was performed either on N-acetylglucosamine-Sepharose or on alpha-lactalbumin-Sepharose: in both cases, two protein bands with molecular weights of around 68,000 and 59,000 were detected by SDS-polyacrylamide gel electrophoresis of the purified preparations. The enzymological properties including behavior toward alpha-lactalbumin were very similar to those of the enzyme from other sources. The specificity of the enzyme was confirmed by determining the structure of the product; it was mostly Gal beta 1----4GlcNAc. beta-Galactosidase-treated embryoglycan (poly-N-acetyllactosamine) and asialo-agalactofetuin could serve as acceptors with the purified enzyme. Thus, the embryonic enzyme, apparently involved in the synthesis of poly-N-acetyllactosamines, has properties similar in several respects to those of the beta-galactosyltransferases so far studied.
Nucleotide sequence of feline panleukopenia virus: comparison with canine parvovirus identifies host-specific differences (1990)

The nucleotide sequence of feline panleukopenia virus (FPV) strain 193 was determined and compared with the sequence of canine parvovirus (CPV) strain N and partial sequences of FPV strain Carl and CPV strain b. Base differences were identified at 115 positions in these 5.1 kb genomes and predicted amino acid differences occurred at 40 positions. The two overlapping capsid protein genes contained almost twice as many base differences as the single non-structural protein gene (49 compared to 26) and about the same ratio was calculated for predicted amino acid differences (27 compared to 13). The 27 variant amino acids in the capsid proteins were clustered at three sites in the primary sequence, whereas 10 of the 13 variant amino acids in the non-structural protein occurred in the 130 C-terminal amino acids. The two FPV strains differed consistently from the two CPV strains at 31 bases: 12 base changes in the capsid protein genes resulted in six amino acid changes, six base changes in the non-structural protein gene resulted in three amino acid changes, and 13 base changes occurred in the non-coding sequence.