gebhart/patrepeval huggingface dataset:
Elevated Circulating P-Selectin in Insulin Dependent Diabetes Mellitus (1996)

Based on findings that showed increased P-selectin expression on platelets and on choroidal microvessels of patients with insulin dependent diabetes mellitus (IDDM), we hypothesized that also plasma concentrations of circulating (c)P-selectin would be increased in these patients. The aim of this study was to compare the plasma levels of cP-selectin between non-smoking patients with IDDM, treated with an intensified insulin therapy, and healthy controls. The study design was prospective, cross-sectional and analyst-blinded. Subjects were matched individually for sex, age and body mass index. Plasma levels of cP-selectin and of von Willebrand antigen (vWF-Ag) were determined by enzyme linked immunoassays. Forty-two pairs were available for intergroup comparison. Median plasma concentrations of cP-selectin in patients with IDDM (285 ng/ml; interquartile range: 233-372) were on average 21% higher than those of controls (236 ng/ml; interquartile range: 175-296; p = 0.004). Also, median plasma levels of vWF-Ag were 10% higher in patients (96 U/dl; interquartile range: 82-127) than controls (87 U/dl; interquartile range: 70-104; p = 0.025). There was no correlation between plasma concentrations of cP-selectin and vWF-Ag levels in either group (p > 0.05). In conclusion, our results of increased cP-selectin levels are in line with increased P-selectin expression on platelets and on choroidal microvessels found in patients with IDDM. In view of the currently developed small molecule inhibitors of cell adhesion molecules, these independent observations together may provide a sound rationale to select P-selectin as a target for treating or preventing IDDM-associated micro- or macrovascular complications.
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization (2012)

CTCF is a highly conserved transcriptional regulator protein that performs diverse functions such as regulating gene expression and organizing the 3D structure of the genome. Here, we describe recent updates to a database of CTCF-binding sites, CTCFBSDB (http://insulatordb.uthsc.edu/), which now contains almost 15 million CTCF-binding sequences in 10 species. Since the original publication of the database, studies of the 3D structure of the genome, such as those provided by Hi-C experiments, have suggested that CTCF plays an important role in mediating intra- and inter-chromosomal interactions. To reflect this important progress, we have integrated CTCF-binding sites with genomic topological domains defined using Hi-C data. Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate experiments.
Novel, Highly Specific N -Demethylases Enable Bacteria To Live on Caffeine and Related Purine Alkaloids (2012)

The molecular basis for the ability of bacteria to live on caffeine as a sole carbon and nitrogen source is unknown. Pseudomonas putida CBB5, which grows on several purine alkaloids, metabolizes caffeine and related methylxanthines via sequential N-demethylation to xanthine. Metabolism of caffeine by CBB5 was previously attributed to one broad-specificity methylxanthine N-demethylase composed of two subunits, NdmA and NdmB. Here, we report that NdmA and NdmB are actually two independent Rieske nonheme iron monooxygenases with N(1)- and N(3)-specific N-demethylation activity, respectively. Activity for both enzymes is dependent on electron transfer from NADH via a redox-center-dense Rieske reductase, NdmD. NdmD itself is a novel protein with one Rieske [2Fe-2S] cluster, one plant-type [2Fe-2S] cluster, and one flavin mononucleotide (FMN) per enzyme. All ndm genes are located in a 13.2-kb genomic DNA fragment which also contained a formaldehyde dehydrogenase. ndmA, ndmB, and ndmD were cloned as His(6) fusion genes, expressed in Escherichia coli, and purified using a Ni-NTA column. NdmA-His(6) plus His(6)-NdmD catalyzed N(1)-demethylation of caffeine, theophylline, paraxanthine, and 1-methylxanthine to theobromine, 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NdmB-His(6) plus His(6)-NdmD catalyzed N(3)-demethylation of theobromine, 3-methylxanthine, caffeine, and theophylline to 7-methylxanthine, xanthine, paraxanthine, and 1-methylxanthine, respectively. One formaldehyde was produced from each methyl group removed. Activity of an N(7)-specific N-demethylase, NdmC, has been confirmed biochemically. This is the first report of bacterial N-demethylase genes that enable bacteria to live on caffeine. These genes represent a new class of Rieske oxygenases and have the potential to produce biofuels, animal feed, and pharmaceuticals from coffee and tea waste.
Monosomy 3 Predicts Death but Not Time until Death in Choroidal Melanoma (2005)

Monosomy 3 is an important predictor of death in melanoma and is in some cases predicted by histology. However, death of metastatic disease occurs in a significant number of patients without monosomy 3. There is no significant difference in time until death between metastatic melanomas, with and without monosomy 3. However, survival of patients with tumors displaying monosomy 3 is generally short.
ConCORD: Tracking and Exploiting Cross-Node Memory Content Redundancy in Large-Scale Parallel Systems (2013)

In large-scale parallel systems scientific workloads consist of numerous processes running across many nodes. Their memory footprint is massive, however many studies from both our and others ’ works have shown that significant amount of memory content redundancy usually exists in these systems. This has consequences for services that enhance performance, reliability, or power. For example, leveraging content sharing could significantly reduce the size of a checkpoint of a group of nodes. As another example, it could speed VM migration by allowing the reconstruction of a VM’s memory from multiple source VMs. Finally, a service that improves reliability by introducing memory redundancy could leverage existing content sharing to minimize the memory costs of any particular level of redundancy. I argue that, a facility that continuously tracks and identifies the sharing of memory content, both within individual machines, and across machines, should be included in the infrastructure of a large-scale HPC system. To support my claim, I consider 1) the opportunity that this service could unveil, 2) the feasibility of creating the service, and 3)
Photoacid generators for catalytic decomposition of polycarbonate (2007)

Abstract The photo‐activated, acid catalyzed decomposition of polycarbonate was investigated in this study. The impact of the chemical and physical properties of the photoacid generators (PAG) and the ambient atmosphere effect on polycarbonate decomposition were discussed. The photo‐patterns resulted from the photoacid catalyzed decomposition of a polycarbonate can be used as a sacrificial placeholder for fabrication of microelectromechanical and microfluidic devices. The effects of acid strength, vapor pressure of the acid, PAG activation process, and ambient conditions (temperature, moisture, and oxygen concentrations) on polymer film decomposition were studied. Several superacids (e.g. triflic and nonaflic based PAGs) were not suitable for decomposition of the polycarbonate because of their high vapor pressures resulting in the high volatility properties. From the decomposition experiments it was found that the nonfluorinated sulfonic acid based PAGs do not posses the superacidity needed for decomposition. Perfluorinated methide and a tetrakis (pentafluoropheyl)borate PAG were effective in the decomposition of polycarbonate films. The combination of two PAGs, one which generates high vapor pressure acid (thus, highly volatile) and the other with a lower vapor pressure acid (thus, less volatile) showed very low residue levels. This is because of the volatility of the generated high vapor pressure acid (usually remaining acid in the film was the cause of the residue left behind) and the remaining nonvolatile low vapor pressure acid was sufficient to decompose the polycarbonate that was not decomposed by the generated high volatile acid. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2007
AID/APOBEC deaminases and cancer (2015)

Mutations are the basis for evolution and the development of genetic diseases. Especially in cancer, somatic mutations in oncogenes and tumor suppressor genes alongside the occurrence of passenger mutations have been observed by recent deep-sequencing approaches. While mutations have long been considered random events induced by DNA-replication errors or by DNA damaging agents, genome sequencing led to the discovery of non-random mutation signatures in many human cancer. Common non-random mutations comprise DNA strand-biased mutation showers and mutations restricted to certain DNA motifs, which recently have become attributed to the activity of the AID/APOBEC family of DNA deaminases. Hence, APOBEC enzymes, which have evolved as key players in natural and adaptive immunity, have been proposed to contribute to cancer development and clonal evolution of cancer by inducing collateral genomic damage due to their DNA deaminating activity. This review focuses on how mutagenic events through AID/APOBEC deaminases may contribute to cancer development.
Isolation and Characterization of Kidney-Derived Stem Cells (2006)

Acute kidney injury is followed by regeneration of damaged renal tubular epithelial cells. The purpose of this study was to test the hypothesis that renal stem cells exist in the adult kidney and participate in the repair process. A unique population of cells that behave in a manner that is consistent with a renal stem cell were isolated from rat kidneys and were termed multipotent renal progenitor cells (MRPC). Features of these cells include spindle-shaped morphology; self-renewal for >200 population doublings without evidence for senescence; normal karyotype and DNA analysis; and expression of vimentin, CD90 (thy1.1), Pax-2, and Oct4 but not cytokeratin, MHC class I or II, or other markers of more differentiated cells. MRPC exhibit plasticity that is demonstrated by the ability of the cells to be induced to express endothelial, hepatocyte, and neural markers by reverse transcriptase–PCR and immunohistochemistry. The cells can differentiate into renal tubules when injected under the capsule of an uninjured kidney or intra-arterially after renal ischemia-reperfusion injury. Oct4 expression was seen in some tubular cells in the adult kidney, suggesting these cells may be candidate renal stem cells. It is proposed that MRPC participate in the regenerative response of the kidney to acute injury.
Hyaluronic acid hydrogel added with ibuprofen‐lysine for the local treatment of chondral lesions in the knee: In vitro and in vivo investigations (2005)

The effect of hyaluronan-based hydrogel with a cross-linking degree of 50% (i.e., the amount of carboxylate groups involved in the cross-lining reaction) (Hyal 50%), loaded with an anti-inflammatory drug (ibuprofen-lysine) for local administration in the osteoarthritic knee was evaluated. The kinetic of drug release from Hyal 50% hydrogel was performed in vitro by a continuous flow system. The release was studied at three different rates (0.375, 0.073, and 0.005 mL/s), and for the slowest one a period of 8 days was necessary to receive the complete release of the drug. A chondral defect was caused in the right femoral medial condyle of 24 rabbits. Twelve animals were treated with Hyal 50%+ibuprofen-lysine and 12 with Hyal 50% by percutaneous injection. The treatments were repeated every 10 days, for three or five times. At 30 and 50 days, no significant differences were observed between the groups (mean score at 30 days: 4.4+/-0.6 in Hyal 50%-treated group and 5.1+/-0.7 in Hyal 50% +Ibuprofen-lysine-treated group; mean score at 50 days: 6.9+/-0.6 in Hyal 50%-treated group and 7.1+/-0.6 in Hyal 50%+ Ibuprofen-lysine-treated group). A significant difference was observed in bone mineral density of the total tibia of rabbits treated by Hyal 50% + Ibuprofen-lysine in comparison with those treated only by Hyal 50%. The positive effects of Hyal 50% on chondral lesions were maintained in the presence of ibuprofen-lysine with the adjunctive effect of an increased limb usage, most likely due to less pain and discomfort.
A 65nm CMOS wide-band LNA with continuously tunable gain from 0dB to 24dB (2013)

A bi-directional active resistor structure with quasifloating gate MOS transistors and non-linearity compensation is used in a resistive negative feedback wide-band LNA implementation enabling a continuously tunable gain from 0dB to 24dB. The LNA has been realized in 65nm CMOS with a minimum noise figure of 2.5dB and IIP3 of -8dBm at highest gain. The LNA bandwidth is from 100MHz to 2GHz, with a power consumption of 12mW and an active area of 0.0375mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
The Removal of Egg Shell Membranes by Enzyme Treatment to Facilitate the Study of Shell Microstructure (1980)

A procedure is described for the enzymatic hydrolysis of the outer shell membrane of hen eggs using a nonspecific protease. This method is less rigorous than the conventional method of boiling in NaOH and it eliminates the possibility of damage to shell fragments during removal of the adhering membrane.
Semi-batch absorption and regeneration studies for CO2 capture by aqueous ammonia (2005)

Carbon dioxide transfer capacities of aqueous ammonia solution and monoethanolamine (MEA) solution were compared. The ammonia process for CO2 capture was simulated using a semibatch reactor, where the flow of gas is continuous. The CO2 carrying capacity in g CO2 per g of NH3 solution (8 wt.%) circulated is 0.07 as compared with 0.036 g CO2 per g MEA solution (20 wt.%). The energy requirement for liquid mass circulation of ammonia solution is approximately 50% of MEA solution for equal weight of CO2 carried. In another comparison, the thermal energy required to regenerate CO2 from the rich solution is substantially less as compared to the MEA process. A 3-cycle absorption–regeneration test was conducted in the semibatch reactor to simulate an approach-to-steady state in a flow system. pH values of the absorbent solution was found to oscillate between 9.6 (CO2-lean) and 8.8 (CO2-rich) under the test conditions. Thermodynamics study shows that ammonium bicarbonate required the least thermal energy among the ammonium compounds for CO2 regeneration.
Centering in Hierarchical Linear Modeling (2008)

This paper examines the implications of centering choices when using hierarchical linear modeling. Compared to using a level-1 predictor in its raw metric or as a grand-mean centercept, centering around the group mean can yield different outcomes when estimating and interpreting the level-1 intercept and slope. Additionally, when including level-2 predictors hypothesized to explain the variance in the level-1 intercept and slope, what each coefficient represents differs with the centering choice. As a result, it often but not always becomes possible, that researchers with different centering choices can reach different conclusions about the effects of the predictors and the interactions among them. These implications are illustrated with graphic and numeric examples and conceptual examples.
Efficacy of intralesional immunotherapy for the treatment of warts: A review of the literature (2016)

Warts are common epidermal growths caused by human papillomavirus that often cause significant discomfort and embarrassment. Current treatment options include topical therapies, cryotherapy, laser vaporization, and surgical excision. Many of these options are destructive and may result in scarring, while less aggressive approaches can lead to lesion recurrence. Additionally, these local modalities are not practical for patients with a large number of warts. Systemic approaches such as immunotherapy have demonstrated success in treating multiple lesions by combining a targeted approach with upregulation of the host immune system. An extensive literature review was performed to evaluate the various vaccine antigens that have been used intralesionally to treat cutaneous and anogenital warts. The specific intralesional immunotherapies that have been studied include: Candida albicans; measles, mumps, and rubella; Trichophyton; and tuberculin antigens such as purified protein derivative, Mycobacterium w vaccine, and Bacillus Calmette-Guerin. Intralesional vaccine injection represents a safe, effective, and tolerable treatment for warts, including recalcitrant and anogenital warts. This approach has been somewhat overlooked in the past despite substantial evidence of high response rates with a low side effect profile. Large comparative trials are necessary to determine the most effective immunotherapy treatment option as well as the most appropriate dosing parameters.
DNA affinity capture and protein profiling by SELDI-TOF mass spectrometry: effect of DNA methylation (2002)

We report here that surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry, as performed on a Ciphergen Biosystems ProteinChip System, can be used in conjunction with DNA affinity capture (DACA) to study specific DNA-protein binding. Using DNA molecules bound to a surface, sequence-specific interactions can be detected as demonstrated by a mutation affecting the binding profile for TBP, a transcription factor. Also, a comparison between methylated and unmethylated promoter-containing DNA fragments shows numerous binding profile differences over a mass range extending to >60 kDa. The binding of several proteins is inhibited by methylation of the DNA.
Neuroimmune Mechanisms in Alzheimer Disease Pathogenesis (1994)

Lesions in Alzheimer disease are characterized by the assembly of a variety of cells and proteins associated with the immune system. Activated microglia express high levels of major histocompatibility complex glycoproteins and receptors for complement. Small numbers of T lymphocytes infiltrate tissue. Proteins of the classical complement pathway are closely connected with beta-amyloid deposits. beta-Amyloid protein binds C1q in vitro and activates the pathway. The membrane attack complex of complement, as well as proteins that defend against that complex, colocalize with dystrophic neurites. These data imply that an autodestructive process is occurring in Alzheimer disease, that overactive microglia might be responsible, and that antiinflammatory drugs might be an effective form of therapy.
Human Melanoma Patients Recognize an HLA-A1-Restricted CTL Epitope from Tyrosinase Containing Two Cysteine Residues: Implications for Tumor Vaccine Development (1998)

To identify shared epitopes for melanoma-reactive CTL restricted by MHC molecules other than HLA-A*0201, six human melanoma patient CTL lines expressing HLA-A1 were screened for reactivity against the melanocyte differentiation proteins Pmel-17/gp100, MART-1/Melan-A, and tyrosinase, expressed via recombinant vaccinia virus vectors. CTL from five of the six patients recognized epitopes from tyrosinase, and recognition of HLA-A1+ target cells was strongly correlated with tyrosinase expression. Restriction by HLA-A1 was further demonstrated for two of those tyrosinase-reactive CTL lines. Screening of 119 synthetic tyrosinase peptides with the HLA-A1 binding motif demonstrated that nonamer, decamer, and dodecamer peptides containing the sequence KCDICTDEY (residues 243-251) all reconstituted the CTL epitope in vitro. Epitope reconstitution in vitro required high concentrations of these peptides, which was hypothesized to be a result of spontaneous modification of cysteine residues, interfering with MHC binding. Substitution of serine or alanine for the more N-terminal cysteine prevented modification at that residue and permitted target cell sensitization at peptide concentrations 2 to 3 orders of magnitude lower than that required for the wild-type peptide. Because spontaneous modification of sulfhydryl groups may also occur in vivo, tumor vaccines using this or other cysteine-containing peptides may be improved by amino acid substitutions at cysteine residues.
Systemic lupus erythematosus presenting as hypoglycaemia with insulin receptor antibodies and insulin autoantibodies (2009)

A 37-year-old man presented with sweating, confusion, palpitations, hunger and tremor of 3 months duration. The symptoms disappeared after ingestion of food. After 3 months, he suffered from irregular fever, arthritis, rash, photosensitivity, and was admitted to the hospital. His antinuclear antibody, anti-double stranded DNA antibody, anti-smith antibody and lupus erythematosus cell phenomenon were all positive. Urine analysis showed albuminuria; his 24-h urine protein was 4.7 g. During hospitalisation, the patient presented with loss of consciousness three times because of hypoglycaemia. His serum insulin level during the hypoglycaemic episode was high at 490-1080 mmol/L (normal range: 6.00-27.00 mmol/L). He had never received an insulin rejection. Both insulin autoantibody and insulin receptor antibody were positive. Investigations confirmed systemic lupus erythematosus (SLE) with autoimmune hypoglycaemia. High-dose of corticosteroids, chloroquine and cyclophosphamide therapy had resulted in remission of hypoglycaemia associated with resolution of circulating antibodies to insulin and insulin receptor, and improvement in clinical and laboratory features of SLE.
A New Fluorescent Chemosensor for Copper Ions Based on Tripeptide Glycyl−Histidyl−Lysine (GHK) (2001)

[structure: see text]. A new fluorescent chemosensor for Cu2+ ions was synthesized by modifying the tripeptide glycyl-histidyl-lysine (GHK) with 9-carbonylanthracene via the standard Fmoc solid-phase peptide synthesis method. While significant fluorescence quenching was observed from the molecule upon binding with Cu2+, addition of Fe2+, Co2+, Ni2+, and Zn2+ to the peptide solution caused a minimum fluorescence emission spectral change, indicating a high specificity of this chemosensor for Cu2+ ions. Effects of pH were also investigated.
Regulation of neuronal differentiation by the α and ϵ isoforms of protein kinase C (1996)

Previous studies utilizing cell-permeant inhibitors and intracellular delivery of anti-PKC antibodies and active enzyme have indicated that inhibition of protein kinase C (PKC) promotes the initial stage(s) of neurite elaboration, while PKC activation inhibits and reverses this phenomenon. In the present study we treated SH-SY-5Y human neuroblastoma cells with antisense oligonucleotides directed against unique sequences of the α, β, and ϵ PKC isoforms for a length of time (5 days) sufficient to reduce immunocytochemical levels of their specific target isoforms. We observed that treatment for 5 days with antisense oligonucleotides directed against PKCα and PKCϵ, but not PKCβ, induced a marked increase in the percentage of cells elaborating neurites. By contrast, treatment with the corresponding sense-oriented oligonucleotides for each isoform had no detectable effect. These data confirm the participation of PKC in regulation of the initial stage(s) of neuronal differentiation, and further imply specific roles for the PKCα and ϵ isoforms in this regulation.