gebhart/patrepeval huggingface dataset:
Discrimination of walking patterns using wavelet-based fractal analysis (2002)

In this paper, we attempted to classify the acceleration signals for walking along a corridor and on stairs by using the wavelet-based fractal analysis method. In addition, the wavelet-based fractal analysis method was used to evaluate the gait of elderly subjects and patients with Parkinson's disease. The triaxial acceleration signals were measured close to the center of gravity of the body while the subject walked along a corridor and up and down stairs continuously. Signal measurements were recorded from 10 healthy young subjects and 11 elderly subjects. For comparison, two patients with Parkinson's disease participated in the level walking. The acceleration signal in each direction was decomposed to seven detailed signals at different wavelet scales by using the discrete wavelet transform. The variances of detailed signals at scales 7 to 1 were calculated. The fractal dimension of the acceleration signal was then estimated from the slope of the variance progression. The fractal dimensions were significantly different among the three types of walking for individual subjects (p < 0.01) and showed a high reproducibility. Our results suggest that the fractal dimensions are effective for classifying the walking types. Moreover, the fractal dimensions were significantly higher for the elderly subjects than for the young subjects (p < 0.01). For the patients with Parkinson's disease, the fractal dimensions tended to be higher than those of healthy subjects. These results suggest that the acceleration signals change into a more complex pattern with aging and with Parkinson's disease, and the fractal dimension can be used to evaluate the gait of elderly subjects and patients with Parkinson's disease.
Fluorescence-Based Approach for Detecting and Characterizing Antibiotic-Induced Conformational Changes in Ribosomal RNA:  Comparing Aminoglycoside Binding to Prokaryotic and Eukaryotic Ribosomal RNA Sequences (2004)

Aminoglycoside antibiotics bind specifically to a conserved sequence of the 16S ribosomal RNA (rRNA) A site and interfere with protein synthesis. One model for the mechanism underlying the deleterious effects of aminoglycosides on protein synthesis invokes a drug-induced conformational change in the rRNA that involves the destacking of two adenine residues (A1492 and A1493 in Escherichia coli) at the A site. We describe here a fluorescence-based approach for detecting and characterizing this drug-induced conformational change in the target rRNA. In this approach, we insert the fluorescent base analogue 2-aminopurine in place of A1492 in an E. coli 16S rRNA A-site model oligonucleotide (EcWT) as well as in a mutant form of this oligomer (A1408G) in which A1408 has been replaced with a guanine. The presence of guanine at 1408 instead of adenine represents one of the major sequence differences between prokaryotic and eukaryotic A sites, with the latter A sites being resistant to the deleterious effects of aminoglycosides. Binding of the aminoglycoside paromomycin to the 2AP-substituted forms of EcWT and A1408G induced changes in fluorescence quantum yield consistent with drug-induced base destacking in EcWT but not A1408G. Isothermal titration calorimetry studies reveal that paromomycin binds to the EcWT duplex with a 31-fold higher affinity than the A1408G duplex, with this differential affinity being enthalpic in origin. In the aggregate, these observations are consistent with both rRNA binding affinity and drug-induced base destacking being important determinants in the prokaryotic specificity of aminoglycosides. Combining fluorescence quantum yield and lifetime data allows for quantification of the extent of drug-induced base destacking, thereby providing a convenient tool for evaluating the relative impacts of both novel and existing A-site targeting ligands on rRNA conformation and potentially for predicting relative antibiotic activities and specificities.
Adaptive modulation techniques for duplex OFDM transmission (2000)

The design tradeoffs of turbo-coded burst-by-burst adaptive orthogonal frequency division multiplex (OFDM) wideband transceivers are analyzed. We demonstrate that upon aiming for a higher throughput a higher proportion of low-quality OFDM subcarriers has to be used for the transmission of inherently vulnerable high-order modem modes, transmitting several bits per subcarrier. Upon invoking turbo coding and adjusting the modem mode switching regime near-error-free performance can be achieved at the cost of a reduced throughput. Various blind modem mode detection techniques have also been investigated and the most complex channel coding trellis-based detection algorithm was found to be the most powerful. Last, the design tradeoffs of spectral pre-equalization have been explored and quantified. We concluded that AOFDM provides a convenient framework for adjusting the required target integrity and throughput both with and without turbo channel coding.
Meningococcal vaccines—present and future (1991)

Over 20 years after the development of the meningococcal A and C vaccines, an effective vaccine against Neisseria meningitidis group B is still lacking. Major obstacles in the development of a B vaccine have been the remarkable capacity of the organism to evade the immune defences of the host and the lack of a predictive animal model. Three group B vaccines based on outer membrane proteins have been, or are currently being, evaluated in field trials. Nevertheless, a number of important questions remain such as the identity of the active components, the degree of efficacy against heterologous group B subtypes, and the duration of protection. In addition, work on a variety of alternative approaches to a group B vaccine is rapidly progressing. Among these are use of chemically modified group B polysaccharide, synthetic or natural lipopolysaccharide epitopes, synthetic peptides corresponding to bactericidal epitopes on the class 1 outer membrane protein, and iron binding proteins. Although each of these approaches has some problems associated with it, the prospects remain good for an effective solution to the group B problem.
Kinetic Study on the Acid-Catalyzed Hydrolysis of Cellulose to Levulinic Acid (2007)

A variety of interesting bulk chemicals is accessible by the acid-catalyzed hydrolysis of cellulose. An interesting example is levulinic acid, a versatile precursor for fuel additives, polymers, and resins. A detailed kinetic study on the acid-catalyzed hydrolysis of cellulose to levulinic acid is reported in this paper. The kinetic experiments were performed in a temperature window of 150-200 degrees C, sulfuric acid concentrations between 0.05 and 1 M, and initial cellulose intakes between 1.7 and 14 wt %. The highest yield of levulinic was 60 mol %, obtained at a temperature of 150 degrees C, an initial cellulose intake of 1.7 wt %, and a sulfuric acid concentration of 1 M. A full kinetic model covering a broad range of reaction conditions was developed using the power-law approach. Agreement between the experimental data and the kinetic model is good. The kinetic expressions were used to gain insights into the optimum process conditions for the conversion of cellulose to levulinic acid in continuous-reactor configurations. The model predicts that the highest obtainable levulinic acid yield in continuous-reactor configurations is about 76 mol %, which was obtained when using reactors with a large extent of backmixing.
Postnatal Hyperplasic Effects of ActRIIB Blockade in a Severely Dystrophic Muscle (2016)

The efficacy of two ActRIIB ligand-trapping agents (RAP-031 and RAP-435) in treating muscular dystrophy was examined by determining their morphological effects on the severely dystrophic triangularis sterni (TS) muscle of the mdx mouse, a model for Duchenne muscular dystrophy. These agents trap all endogenous ligands to the ActRIIB receptor and thereby block myostatin signaling in a highly selective manner. Short-term (1 month) and long-term (3 months) in vivo treatment of 1-month-old mdx mice increased myonuclei and fiber cross section (FCS) density but did not alter individual fiber size. Vehicle-treated mdx mice exhibited age-dependent increases in myonuclei and FCS density, and age-dependent reductions in centronucleation that were each enhanced by treatment with RAP-435. Distributions of FCS area (FCSA) in the mdx TS were 90% identical to those from untreated age-matched nondystrophic mice and were unaltered by the substantial fiber hyperplasia observed with age and RAP-435 treatment. These results were inconsistent with injury-induced fiber regeneration which produces altered FCSA distributions characterized by a distinct class of smaller regenerated fibers. Nondystrophic mice exhibited a constant postnatal density of fiber cross sections and myonuclei, and RAP-435 treatment of nondystrophic mice increased TS mean FCSA but had no effects on myonuclei or FCS density. These results demonstrating a continual postnatal proliferation and fusion of satellite cells and a response to myostatin blockade characteristic of developing prenatal muscle suggest that the lack of dystrophin directly results in unrestrained postnatal satellite cell activation that is not necessarily dependent upon prior fiber degeneration. J. Cell. Physiol. 232: 1774-1793, 2017. © 2016 Wiley Periodicals, Inc.
Development of enucleated mouse oocytes reconstituted with embryonic nuclei (1991)

The chromosomes of mouse oocytes at telophase of the first meiotic division were removed using micromanipulation and differential interference microscopy. The enucleated oocytes were used as recipients for nuclear transplantation, after culture for 4-6 h. The newly synthesized proteins of the enucleated oocytes showed the same pattern as those of secondary oocytes matured in vivo. When the enucleated oocytes received a nucleus from late 2- and 8-cell embryos, or a cell from the inner cell mass (ICM) of blastocysts, 23, 4 and 10%, respectively, of reconstituted embryos developed to blastocysts. After transfer to recipient females, live young were produced from the reconstituted eggs that received a nucleus from late 2-cell embryos.
Synthesis, SAR, and Biological Evaluation of Oximino-Piperidino-Piperidine Amides. 1. Orally Bioavailable CCR5 Receptor Antagonists with Potent Anti-HIV Activity (2002)

We previously reported the discovery of 4-[(Z)-(4-bromophenyl)(ethoxyimino)methyl]-1'-[(2,4-dimethyl-3-pyridinyl)carbonyl]-4'-methyl-1,4'-bipiperidine N-oxide 1 (SCH 351125) as an orally bioavailable human CCR5 antagonist for the treatment of HIV-1 infection. Herein, we describe in detail the discovery of 1 from our initial lead compound as well as the synthesis and SAR studies directed toward optimization of substitution at the phenyl, oxime, and right-hand side amide groups in the oximino-piperidino-piperidine series. Substitutions (4-Br, 4-CF(3), 4-OCF(3), 4-SO(2)Me, and 4-Cl) at the phenyl group are well-tolerated, and small alkyl substitutions (Me, Et, (n)()Pr, (i)()Pr, and cyclopropyl methyl) at the oxime moiety are preferred for CCR5 antagonism. The 2,6-dimethylnicotinamide N-oxide moiety is the optimal choice for the right-hand side. Several compounds in this series, including compound 1, exhibited excellent antiviral activity in vitro. Compound 1, which has a favorable pharmacokinetic profile in rodents and primates, excellent oral bioavailability, and potent antiviral activity against a wide range of primary HIV-1 isolates, is a potentially promising new candidate for treatment of HIV-1 infection.
S -Adenosylhomocysteine toxicity in normal and adenosine kinase-deficient lymphoblasts of human origin (1979)

The human lymphoblast line WI-L2 is subject to growth inhibition by a combination of the adenosine deaminase (ADA; adenosine aminohydrolase, EC 3.5.4.4.) inhibitor erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA) and adenosine. Although adenosine-induced pyrimidine starvation appears to contribute to this effect, uridine only partially reverses adenosine toxicity in WI-L2 and not at all in strain 107, an adenosine kinase-(ATP:adenosine 5'-phosphotransferase, EC 2.7.1.20) deficient derivative of WI-L2. Treatment of both cell lines with EHNA and adenosine leads to striking elevations in intracellular S-adenosyl-L-homocysteine (AdoHcy), a potent inhibitor of S-adenosyl-L-methionine (AdoMet)-dependent methylation reactions. The methylation in vivo of both DNA and RNA is inhibited by concentrations of EHNA and adenosine that elevate intracellular AdoHcy. Addition of 100 muM L-homocysteine thiolactone to cells treated with EHNA and adenosine enhances adenosine toxicity and further elevates AdoHcy to levels approximately 60-fold higher than those obtained in the absence of this amino acid, presumably by combining with adenosine to form AdoHcy in a reaction catalyzed by S-adenosylhomocysteine hydrolase (EC 3.3.1.1). In the adenosine kinase-deficient strain 107, a combination of ADA inhibition and L-homocysteine thiolactone markedly increases intracellular AdoHcy and inhibits growth even in the absence of exogenous adenosine. These results demonstrate a form of toxicity from endogenously produced adenosine and support the view that AdoHcy, by inhibiting methylation, is a mediator of uridine-resistant adenosine toxicity in these human lymphoblast lines. Furthermore, they suggest that AdoHcy may play a role in the pathogenesis of the severe combined immunodeficiency disease found in most children with heritable ADA deficiency.
Biomimetic Carbohydrate Substrates of Tunable Properties Using Immobilized Dextran Hydrogels (2008)

Glycidylmethacrylate-modified dextran macromers (Dex-GMA) of different degrees of substitution (DS) were synthesized. The elastic modulus of the hydrogels produced using one-component and two-component macromer systems was measured using rheometry. When one macromer of DS 1/10 was used, a hydrogel modulus in the range of 0.2 Pa to 42 kPa was obtained by varying the Dex-GMA concentration from 80 to 200 mg/mL. When a mixture of two macromers of different DS (1/10 and 1/23) was used, a more uniform variation of modulus in the range of 0.4 Pa to 42 kPa was achieved by controlling the ratio of the two macromers. When dextran hydrogels were functionalized with fibronectin and immobilized onto glass substrates, the attachment, spreading, and growth of human aortic smooth muscle cells were modulated by the elastic properties of the dextran matrix. The dextran hydrogel system with tunable mechanical and biochemical properties appears promising for applications in cell culture and tissue engineering.
SC68896, a Novel Small Molecule Proteasome Inhibitor, Exerts Antiglioma Activity In vitro and In vivo (2009)

Abstract Purpose: Glioblastomas are among the most lethal neoplasms, with a median survival of &amp;lt;1 year. Modulation of the proteasome function has emerged as a novel approach to cancer pharmacotherapy. Here, we characterized the antitumor properties of SC68896, a novel small molecule proteasome inhibitor. Experimental Design: Different tumor cell lines were tested by crystal violet staining for sensitivity to SC68896, given alone or in combination with death ligands. The molecular mechanisms mediating SC68896-induced cell death and changes in cell cycle progression were assessed by immunoblot and flow cytometry. An orthotopic human glioma xenograft model in nude mice was used to examine the in vivo activity of SC68896. Results: SC68896 inhibits the proliferation of cell lines of different types of cancer, including malignant glioma. Exposure of LNT-229 glioma cells to SC68896 results in a concentration- and time-dependent inhibition of the proteasome, with a consequent accumulation of p21 and p27 proteins, cell cycle arrest, caspase cleavage, and induction of apoptosis. Using RNA interference, we show that the effect of SC68896 on glioma cells is facilitated by wild-type p53. SC68896 sensitizes glioma cells to tumor necrosis factor–related apoptosis–inducing ligand and CD95 ligand and up-regulates the cell surface expression of the tumor necrosis factor–related apoptosis–inducing ligand receptor cell death receptors 4 and 5, which may contribute to this sensitization. Intracerebral glioma–bearing nude mice treated either i.p. or intratumorally with SC68896 experience prolonged survival. Conclusions: SC68896 is the first proteasome inhibitor that exerts antiglioma activity in vivo. It may represent a novel prototype agent for the treatment of malignant gliomas and warrants clinical evaluation. (Clin Cancer Res 2009;15(21):6609–18)
A novel rhodopsin-like gene expressed in zebrafish retina (2011)

The visual pigment rhodopsin (rh1) constitutes the first step in the sensory transduction cascade in the rod photoreceptors of the vertebrate eye, forming the basis of vision at low light levels. In most vertebrates, rhodopsin is a single-copy gene whose function in rod photoreceptors is highly conserved. We found evidence for a second rhodopsin-like gene (rh1-2) in the zebrafish genome. This novel gene was not the product of a zebrafish-specific gene duplication event and contains a number of unique amino acid substitutions. Despite these differences, expression of rh1-2 in vitro yielded a protein that not only bound chromophore, producing an absorption spectrum in the visible range (λmax ≈ 500 nm), but also activated in response to light. Unlike rh1, rh1-2 is not expressed during the first 4 days of embryonic development; it is expressed in the retina of adult fish but not the brain or muscle. Similar rh1-2 sequences were found in two other Danio species, as well as a more distantly related cyprinid, Epalzeorhynchos bicolor. While sequences were only identified in cyprinid fish, phylogenetic analyses suggest an older origin for this gene family. Our study suggests that rh1-2 is a functional opsin gene that is expressed in the retina later in development. The discovery of a new previously uncharacterized opsin gene in zebrafish retina is surprising given its status as a model system for studies of vertebrate vision and visual development.
TRPA1 mediates formalin-induced pain (2007)

The formalin model is widely used for evaluating the effects of analgesic compounds in laboratory animals. Injection of formalin into the hind paw induces a biphasic pain response; the first phase is thought to result from direct activation of primary afferent sensory neurons, whereas the second phase has been proposed to reflect the combined effects of afferent input and central sensitization in the dorsal horn. Here we show that formalin excites sensory neurons by directly activating TRPA1, a cation channel that plays an important role in inflammatory pain. Formalin induced robust calcium influx in cells expressing cloned or native TRPA1 channels, and these responses were attenuated by a previously undescribed TRPA1-selective antagonist. Moreover, sensory neurons from TRPA1-deficient mice lacked formalin sensitivity. At the behavioral level, pharmacologic blockade or genetic ablation of TRPA1 produced marked attenuation of the characteristic flinching, licking, and lifting responses resulting from intraplantar injection of formalin. Our results show that TRPA1 is the principal site of formalin's pain-producing action in vivo, and that activation of this excitatory channel underlies the physiological and behavioral responses associated with this model of pain hypersensitivity.
DNA demethylation in the human FOXP3 locus discriminates regulatory T cells from activated FOXP3+ conventional T cells (2007)

The transcription factor FOXP3 is critical for development and function of regulatory T cells (Treg). Their number and functioning appears to be crucial in the prevention of autoimmunity and allergy, but also to be a negative prognostic marker for various solid tumors. Although expression of the transcription factor FOXP3 currently constitutes the best-known marker for Treg, in humans, transient expression is also observed in activated non-Treg. Extending our recent findings for the murine foxp3 locus, we observed epigenetic modification of several regions in the human FOXP3 locus exclusively occurring in Treg. Importantly, activated conventional CD4(+) T cells and TGF-beta-treated cells displayed no FOXP3 DNA demethylation despite expression of FOXP3, whereas subsets of Treg stable even upon extended in vitro expansion remained demethylated. To investigate whether a whole set of genes might be epigenetically imprinted in the Treg lineage, we conducted a genome-wide differential methylation hybridization analysis. Several genes were found displaying differential methylation between Treg and conventional T cells, but none beside FOXP3 turned out to be entirely specific to Treg when tested on a broad panel of cells and tissues. We conclude that FOXP3 DNA demethylation constitutes the most reliable criterion for natural Treg available at present.
Nuclear reprogramming and stem cell creation (2003)

The transplantation of a somatic cell nucleus to an enucleated egg results in a major reprogramming of gene expression and switch in cell fate. We review the efficiency of nuclear reprogramming by nuclear transfer. The serial transplantation of nuclei from defective first-transfer embryos and the grafting of cells from such embryos to normal host embryos greatly increases the proportion of nuclei that can be seen to have been reprogrammed. We discuss possible reasons for the early failure of most nuclear transfers from differentiated cells and describe the potential value of growing oocytes, rather than unfertilized eggs, as a source of nuclear reprogramming molecules and for the eventual identification of these molecules. Nuclear transfer provides a possible route for the creation of stem cells from adult somatic cells.
Functional Interactions of a Homolog of Proliferating Cell Nuclear Antigen with DNA Polymerases inArchaea (1999)

Proliferating cell nuclear antigen (PCNA) is an essential component of the DNA replication and repair machinery in the domain Eucarya. We cloned the gene encoding a PCNA homolog (PfuPCNA) from an euryarchaeote, Pyrococcus furiosus, expressed it in Escherichia coli, and characterized the biochemical properties of the gene product. The protein PfuPCNA stimulated the in vitro primer extension abilities of polymerase (Pol) I and Pol II, which are the two DNA polymerases identified in this organism to date. An immunological experiment showed that PfuPCNA interacts with both Pol I and Pol II. Pol I is a single polypeptide with a sequence similar to that of family B (alpha-like) DNA polymerases, while Pol II is a heterodimer. PfuPCNA interacted with DP2, the catalytic subunit of the heterodimeric complex. These results strongly support the idea that the PCNA homolog works as a sliding clamp of DNA polymerases in P. furiosus, and the basic mechanism for the processive DNA synthesis is conserved in the domains Bacteria, Eucarya, and Archaea. The stimulatory effect of PfuPCNA on the DNA synthesis was observed by using a circular DNA template without the clamp loader (replication factor C [RFC]) in both Pol I and Pol II reactions in contrast to the case of eukaryotic organisms, which are known to require the RFC to open the ring structure of PCNA prior to loading onto a circular DNA. Because RFC homologs have been found in the archaeal genomes, they may permit more efficient stimulation of DNA synthesis by archaeal DNA polymerases in the presence of PCNA. This is the first stage in elucidating the archaeal DNA replication mechanism.