gebhart/patrepeval huggingface dataset:
Ornithine Decarboxylase mRNA in Mouse Kidney: A Low Abundancy Gene Product Regulated by Androgens with Rapid Kinetics a (1984)

We have used ODC gene expression in mouse kidney as the biological marker for studies of early androgen action. Some of the characteristics of this regulation involve its strict androgen specificity, the dependency on functional androgen receptors, the lack of requirement for pituitary hormones, and the ability of physiological androgens to bring about activation of the ODC gene. Some recent findings have revealed an additional intriguing feature in the regulation of ODC gene expression in that androgen sensitivity of ODC stimulation is genetically regulated in the mouse kidney (unpublished observations). One of the mechanisms by which androgens regulate renal ODC synthesis is to increase the concentration of ODC mRNA. Increased accumulation of this mRNA was seen as soon as 6 hr after testosterone administration, and it peaked 24 hr posttreatment. In general, acute changes in immunoreactive ODC concentration and ODC mRNA accumulation had very similar kinetics, suggesting that androgens induced de novo synthesis of ODC by increasing the rate of ODC gene transcription. In addition, there was always a highly significant correlation between the catalytic enzyme activity and immunoreactive enzyme protein concentration indicating that androgens do not specifically regulate the active site of ODC by either activating or inhibiting the enzyme by posttranslational modifications. A typical feature of ODC in virtually all eukaryotic tissues is the extremely rapid turnover rate of the enzyme with a biological half-life of 10-30 min. However, no direct information on the turnover rate of ODC mRNA is currently available, although indirect experiments have assigned a half-life of about seven hours for this mRNA. The availability of cDNA clones for ODC mRNA measurements will now permit us to address this question more directly, and also to investigate a possible role of androgens in the stabilization of ODC mRNA. In this regard it is of interest to note that chronic treatment of mice with pharmacological doses of testosterone prolongs the half-life of ODC protein four- to tenfold.
GENERIC ∊-REMOVAL AND INPUT ∊-NORMALIZATION ALGORITHMS FOR WEIGHTED TRANSDUCERS (2002)

We present a new generic ∊-removal algorithm for weighted automata and transducers defined over a semiring. The algorithm can be used with any semiring covered by our framework and works with any queue discipline adopted. It can be used in particular in the case of unweighted automata and transducers and weighted automata and transducers defined over the tropical semiring. It is based on a general shortest-distance algorithm that we briefly describe. We give a full description of the algorithm including its pseudocode and its running time complexity, discuss the more efficient case of acyclic automata, an on-the-fly implementation of the algorithm and an approximation algorithm in the case of the semirings not covered by our framework. We illustrate the use of the algorithm with several semirings. We also describe an input ∊-normalization algorithm for weighted transducers based on the general shortest-distance algorithm. The algorithm, which works with all semirings covered by our framework, admits an on-the-fly implementation.
Cell-free transfer of membrane lipids. (1991)

A latent phospholipase A is concentrated in cis elements of rat liver Golgi apparatus, the presumed sites of fusion of the 50-70-nm transition vesicles formed from endoplasmic reticulum. As a result, conversion of transferred phospholipids to their corresponding lysoforms may provide an index of post transfer lipid processing in a corresponding reconstituted membrane transfer system. To label the phosphatidylcholine of transitional endoplasmic reticulum in vitro, [14C]CDP-choline and endogenous cytidyltransferases were used. In the reconstituted transfer system, the radiolabeled phosphatidylcholine was transferred via transition vesicles to Golgi apparatus immobilized on nitrocellulose strips in a time- and temperature-dependent process. Transfer was promoted by ATP and the ATP-dependent transfer was specific for cis Golgi apparatus elements as acceptor. Trans Golgi apparatus elements were ineffective as acceptors. Median Golgi apparatus elements were intermediate. A portion of the transferred phosphatidylcholine was converted subsequently to lysophosphatidylcholine also in a time- and ATP-dependent manner. The phospholipase A activity of the Golgi apparatus was more than 90% latent (active site located on the lumens of the Golgi apparatus membranes). Therefore, the lipid-containing vesicles derived from endoplasmic reticulum must have combined with cis Golgi apparatus membranes as the basis for Golgi apparatus-dependent phospholipase A processing of endoplasmic reticulum-derived phosphatidylcholine. Since the lipids were processed by phospholipase A in approximately the same proportion as occurs in situ, the findings offer evidence both for the specificity of the ATP-dependent component of cell-free lipid transfer from endoplasmic reticulum to Golgi apparatus and its fidelity to lipid transfer observed in vivo.
Inhibition of apical sodium-dependent bile acid transporter as a novel treatment for diabetes (2011)

Bile acids are recognized as metabolic modulators. The present study was aimed at evaluating the effects of a potent Asbt inhibitor (264W94), which blocks intestinal absorption of bile acids, on glucose homeostasis in Zucker Diabetic Fatty (ZDF) rats. Oral administration of 264W94 for two wk increased fecal bile acid concentrations and elevated non-fasting plasma total Glp-1. Treatment of 264W94 significantly decreased HbA1c and glucose, and prevented the drop of insulin levels typical of ZDF rats in a dose-dependent manner. An oral glucose tolerance test revealed up to two-fold increase in plasma total Glp-1 and three-fold increase in insulin in 264W94 treated ZDF rats at doses sufficient to achieve glycemic control. Tissue mRNA analysis indicated a decrease in farnesoid X receptor (Fxr) activation in small intestines and the liver but co-administration of a Fxr agonist (GW4064) did not attenuate 264W94 induced glucose lowering effects. In summary, our results demonstrate that inhibition of Asbt increases bile acids in the distal intestine, promotes Glp-1 release and may offer a new therapeutic strategy for type 2 diabetes mellitus.
Organic Radical Contrast Agents for Magnetic Resonance Imaging (2012)

We report a molecular design that provides an intravenously injectable organic radical contrast agent (ORCA) for which the molecular (1)H water relaxivity (r(1)) is ca. 5 mM(-1) s(-1). The ORCA is based on spirocyclohexyl nitroxide radicals and poly(ethylene glycol) chains conjugated to a fourth-generation polypropylenimine dendrimer scaffold. The metal-free ORCA has a long shelf life and provides selectively enhanced magnetic resonance imaging in mice for over 1 h.
Replicated Data Management in Mobile Environments: Anything New Under the Sun? (1994)

The mobile wireless computing environment of the future will contain large numbers of low powered palmtop machines. Replication will be an essential technique in this environment, providing data availability to the system. In a mobile environment it is important to have dynamic replicated data management algorithms that allow for instance copies to migrate from one site to another or for new copies to be generated. In this paper we show that such dynamic algorithms can be obtained simply by letting transaction update the directory that specifies sites holding copies. Thus we argue that no fundamentally new algorithms are needed to cope with mobility. However, exisiting algorithms may have to be &amp;quot;tuned&amp;quot; for a mobile environment, and we discuss what this may entail. As an illustration, we present a variation of the primary copy algorithm, Primary By Row, that is well suited for migrating copies 1 . Keywords: Distributed Data Bases, replication, mobility, availability. 1 Intr...
Shear-dependent changes in the three-dimensional structure of human von Willebrand factor (1996)

The three-dimensional tertiary structure of human von Willebrand Factor (vWF) on a hydrophobic surface under aqueous conditions and different shear stress regimes was studied by atomic force microscopy (AFM). vWF was imaged by AFM at molecular level resolution under negligible shear stress, under a local applied shear force (7.4 to 19 nN) using the AFM probe in contact mode scanning, and after subjecting vWF to a range of shear stress (0 to 42.4 dyn/cm2) using a rotating disk system. The results demonstrate that vWF undergoes a shear stress-induced conformational transition from a globular state to an extended chain conformation with exposure of intra-molecular globular domains at a critical shear stress of 35 +/- 3.5 dyn/cm2. The globular vWF conformation (149 nm by 77 nm and height 3.8 nm) is representative of native vWF after simple diffusion to the hydrophobic surface, followed by adhesion and some spreading. In a shear stress field above the critical value, protein unfolding occurs and vWF is observed in extended chain conformations oriented in the direction of the shear stress field with molecular lengths ranging from 146 to 774 nm and 3.4 nm mean height. The shear stress-induced structural changes to vWF suggest a close conformation-function relationship in vWF properties for thrombogenesis in regions of high shear stress.
Experiments on the automatic construction of hypertext from texts (1995)

Abstract The problem of (semi-)automatically turning text into hypertext is one that has been identified as important to the growth and development of hypertext as a way of organising information. In this paper we describe an approach we have developed to semi-automatically generate a hypertext from linear texts. This is based on initially creating nodes and composite nodes composed of ‘mini-hypertexts’. Following this we then compute node-node similarity values using standard information retrieval techniques. These similarity measures are then used to selectively create node-node links based on the strength of similarity between nodes. What makes our process novel is that the link creation process also uses values from a dynamically computed metric which measures the topological compactness of the overall hypertext being generated. Thus link creation is a selective process based not only on node-node similarity but also on the overall layout of the hypertext. Experiments on generating a hypertext from a collection of 846 software product descriptions comprising 8.5 Mbytes of text are described. Our experiments with a variety of IR techniques and link creation approaches yield some guidelines on how the process should be automated. Finally, this text to hypertext conversion method is put into the context of an overall hypertext authoring tool currently under development.
Cloning and Detection of HIV-1-Encoded MicroRNA (2006)

MicroRNAs (miRNAs) are 21-to 25-nucleotides (nt) long and interact with messenger RNAs to trigger either translational repression or RNA cleavage through RNA interference (RNAi). We have shown that HIV-1 nef double-stranded RNA from AIDS patients who are long-term nonprogressors, inhibits HIV-1 transcription; and that nef-derived miRNA, miR-N367, is produced in human T-cells persistently infected with HIV-1. The miR-N367 can block HIV-1 Nef expression and long terminal repeat (LTR) transcription, suggesting that miR-N367 might suppress both Nef function and HIV-1 transcription through the RNAi pathway. Protocols are presented here for cloning HIV-1-encoded miRNA and confirming miRNA expression by Northern blot hybridization.
Clinical predictors of erosion-free status in rheumatoid arthritis: a prospective cohort study (2011)

In our cohort, 21% of subjects were erosion free at baseline and 2 years. Few baseline clinical characteristics significantly predicted erosion-free status.
Gradient substrate assembly for quantifying cellular response to biomaterials (2006)

Using quantitative fluorescence microscopy in conjunction with a method of gradient substrate assembly established in their group, the authors were able to introduce and measure reproducible changes in cellular morphology and cell density by manipulating polymer grafting density. The mechanism behind this change in cellular behavior was explained by a semiempirical, geometric model that describes the effect of the spatial distribution of the polymer on protein attachment. A 10-fold increase in graft density of poly(2-hydroxyethyl methacrylate) [PHEMA] along the surface of a gradient sample, preexposed to bovine fibronectin, caused a change in the size of fibroblasts on the surface (i.e., cell spreading) from (1238 +/- 704) to (377 +/- 216) microm(2). The results were in quantitative agreement with those obtained on three separate gradient samples. Both cellular response and fibronectin adsorption (as measured via ellipsometry) were found to vary sigmoidally with graft density of PHEMA, demonstrating the high degree of correlation between the two phenomena. A simple, rigid-disk model accounting for the surface coverage of PHEMA was able to predict the amount of adsorbed fibronectin with a correlation coefficient of 0.97. Maximal cell adhesion and cell spreading were found to occur at fibronectin surface densities of 50 and 100 ng/cm(2), respectively. The results demonstrate the role of gradient substrate assembly as a method for quantifying the relationship between protein and cellular response to technologically relevant polymeric materials.
Memristor-Based Edge Detection for Spike Encoded Pixels (2020)

Memristors have many uses in machine learning and neuromorphic hardware. From memory elements in dot product engines to replicating both synapse and neuron wall behaviours, the memristor has proved a versatile component. Here we demonstrate an analogue mode of operation observed in our silicon oxide memristors and apply this to the problem of edge detection. We demonstrate how a potential divider exploiting this analogue behaviour can prove a scalable solution to edge detection. We confirm its behaviour experimentally and simulate its performance on a standard testbench. We show good performance comparable to existing memristor based work with a benchmark score of 0.465 on the BSDS500 dataset, while simultaneously maintaining a lower component count.
Control‐oriented modeling of sheet and film processes (1997)

Abstract Sheet and film processes pose a challenging identification and control problem due to high complexity, poor conditioning, and limited input–output data. The interaction between model accuracy and closed‐loop performance is explored for sheet and film processes using a model decomposition in terms of two static orthogonal matrices in series with a diagonal transfer‐function matrix. It is shown that the accuracy of the diagonal elements of the transfer‐function matrix directly specifies the closed‐loop performance achievable by a model‐based controller. This motivates the development of a combined identification and control procedure in which the controller is designed to be robust to model inaccuracies quantified during identification. The resulting controller is compared to an industrially accepted controller design method for two examples, including a simulated blown‐film process. Based on the theoretical results and simulations, it was concluded that the poor performance often reported for existing industrial sheet and film process‐control systems is likely due to signs of the model gains being incorrectly identified.
Red Blood Cell Distribution Width and the Risk of Death in Middle-aged and Older Adults (2009)

Red blood cell distribution width is a widely available test that is a strong predictor of mortality in the general population of adults 45 years or older.
A Unique Heparin-Binding Domain in the Envelope Protein of the Neuropathogenic PVC-211 Murine Leukemia Virus May Contribute to Its Brain Capillary Endothelial Cell Tropism (2001)

ABSTRACT Previous studies from our laboratory demonstrated that PVC-211 murine leukemia virus (MuLV), a neuropathogenic variant of Friend MuLV (F-MuLV), had undergone genetic changes which allowed it to efficiently infect rat brain capillary endothelial cells (BCEC) in vivo and in vitro. Two amino acid changes from F-MuLV in the putative receptor binding domain (RBD) of the envelope surface protein of PVC-211 MuLV (Glu-116 to Gly and Glu-129 to Lys) were shown to be sufficient for conferring BCEC tropism on PVC-211 MuLV. Recent examination of the unique RBD of PVC-211 MuLV revealed that the substitution of Lys for Glu at position 129 created a new heparin-binding domain that overlapped a heparin-binding domain common to ecotropic MuLVs. In this study we used heparin-Sepharose columns to demonstrate that PVC-211 MuLV, but not F-MuLV, can bind efficiently to heparin and that one or both of the amino acids in the RBD of PVC-211 MuLV that are associated with BCEC tropism are responsible. We further showed that heparin can enhance or inhibit MuLV infection and that the mode of action is dependent on heparin concentration, sulfation of heparin, and the affinity of the virus for heparin. Our results suggest that the amino acid changes that occurred in the envelope surface protein of PVC-211 MuLV may allow the virus to bind strongly to the surface of BCEC via heparin-like molecules, increasing the probability that the virus will bind to its cell surface receptor and efficiently infect these cells.
Plasma Viral Load and CD4+ Lymphocytes as Prognostic Markers of HIV-1 Infection (1997)

Plasma viral load strongly predicts the rate of decrease in CD4+ lymphocyte count and progression to AIDS and death, but the prognosis of HIV-infected persons is more accurately defined by combined measurement of plasma HIV-1 RNA and CD4+ lymphocytes.
A Fully Synthetic Globo H Carbohydrate Vaccine Induces a Focused Humoral Response in Prostate Cancer Patients: A Proof of Principle (1999)

Human trials on the globo H carbohydrate vaccine (see picture, KLH=the carrier protein keyhole limpet hemocyanin) show that it produces strong IgM, and in some cases IgG, responses in patients with progressive and recurrent prostate cancer. Furthermore, these antibodies not only recognize synthetic antigens, but also globo H-positive tumors in biopsy extracts and tumor tissues.
[P-8502--a new mu selective opioid receptor ligand]. (1989)

The analgesic potencies of 3-[beta-(p-amino)-phenethyl)-9 beta-methoxy-9 alpha-(m-methoxyphenyl)-3- azabicyclo [3,3,1] nonane (P-8502) and 3-[beta-(p-monoester fumarylamido)-phenethyl]-9 beta-methoxy-9 alpha-(m-methoxyphenyl)-3-azabicyclo [3,3,1] nonane (P-8511) were examined. The analgesic ED50 of P-8502 and P-8511 were 55 and 200 micrograms/kg (mice, ip, hot plate), and 30 and 95 micrograms/kg (rat, sc, tail flick), respectively. The duration of the analgesic action of P-8511 (about 4 h) was longer than that of P-8502 (about 1.5 h, rat, sc, tail flick). Binding assay showed that P-8502 had a high ratio of delta/mu, kappa/mu: IC50 (DPDPE)/IC50 (DAGO) = 399; IC50(DAD-LE)/IC50 (DAGO) = 1498; IC50 (kappa)/IC50 (DAGO) = 159. In conclusion, P-8502 appears to be a new mu selective opioid receptor ligand, whereas P-8511 has no such selectivity.
Epitope Localization of a Monoclonal Antibody, LO-22, with Broad Specificity for Interferon-α Subtypes (1986)

A murine monoclonal antibody, LO-22, with broad cross-reactivity to human interferon-alpha (HuIFN-alpha) subtypes and some animal IFN-alpha species was found to bind less efficiently to IFN-alpha A (IFN-alpha 2a). In contrast, LO-22 bound strongly to IFN-alpha 2 (IFN-alpha 2b) and IFN-alpha 2C (IFN-alpha 2c) which differ by one or two amino acids, respectively, from IFN-alpha A; the latter has lysine at position 23 whereas the other closely related IFNs have arginine. LO-22 also bound efficiently to IFN-alpha D which is only 83% related to IFN-alpha A, but which also has arginine at position 23. These results strongly suggest that LO-22 recognizes a conserved epitope among IFN-alpha subtypes in which arginine at position 23 is involved. The specificity of a second monoclonal antibody, MT4/E4, is also reported and compared to that of LO-22.
Studies of the Human c- myb Gene and Its Product in Human Acute Leukemias (1986)

The myb gene is the transforming oncogene of the avian myeloblastosis virus (AMV); its normal cellular homolog, c-myb, is conserved across a broad span of evolution. In humans, c-myb is expressed in malignant hematopoietic cell lines and in primary hematopoietic tumors. Partial complementary DNA clones were generated from blast cells of patients with acute myelogenous leukemia. The sequences of the clones were compared to the c-myb of other species, as well as the v-myb of AMV. In addition, the carboxyl terminal region of human c-myb was placed in an expression vector to obtain protein for the generation of antiserum, which was used to identify the human c-myb gene product. Like v-myb, this protein was found within the nucleus of leukemic cells where it was associated with the nuclear matrix. These studies provide further evidence that c-myb might be involved in human leukemia.
Single-Pot Extraction-Analysis of Dyed Wool Fibers with Ionic Liquids (2012)

Analytical capabilities to identify dyes associated with structurally robust wool fibers would critically assist crime-scene and explosion-scene forensics. Nondestructive separation of dyes from wool, removal of contaminants, and dye analysis by MALDI- or ESI-MS, were achieved in a single-pot, ionic liquid-based method. Ionic liquids (ILs) that readily denature the wool α-keratin structure have been identified and are conducive to small volume, high-throughput analysis for accelerated threat-response times. Wool dyed with commercial or natural, plant-based dyes have unique signatures that allow classification and matching of samples and identification of dyestuffs. Wool released 0.005 mg of dye per mg of dyed wool into the IL, allowing for analysis of single-thread sample sizes. The IL + dye mixture promotes sufficient ionization in MALDI-MS: addition of common MALDI matrices does not improve analysis of anionic wool dyes. An inexpensive, commercially available tetrabutylphosponium chloride IL was discovered to be capable of denaturing wool and was determined to be the most effective for this readily fieldable method.
Peripheral Mechanisms in Irritable Bowel Syndrome (2012)

Various peripheral mechanisms have been implicated in the pathogenesis of irritable bowel syndrome, including intraluminal intestinal irritants, alteration in the bowel microbiome, enteroendocrine-cell products, and susceptibility to inflammation. Recent evidence is summarized.
Optimization of tumor-targeted gene delivery by engineered attenuated Salmonella typhimurium. (2003)

Our results indicate the need to define an OTD, probably for each species, when using genetically engineered Salmonella as a tumor- and species-selective vector in cancer therapy.
Phase 1/2 Placebo-Controlled, Double-Blind, Dose-Escalating Trial of Myocardial Vascular Endothelial Growth Factor 2 Gene Transfer by Catheter Delivery in Patients With Chronic Myocardial Ischemia (2002)

This phase 1/2, double-blind, randomized trial provides preliminary data that support safety of phVEGF2 catheter-mediated myocardial gene transfer. The statistically significant reduction in anginal class and strong positive trends for remaining end points suggest that a larger phase 2/3 trial is warranted.