gebhart/patrepeval huggingface dataset:
Strong Impact on the Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Community of a PAH-Polluted Soil but Marginal Effect on PAH Degradation when Priming with Bioremediated Soil Dominated by Mycobacteria (2007)

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by Mycobacterium spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene pdo1. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no pdo1 genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.
The heat shock protein 90 inhibitor IPI‐504 induces apoptosis of AKT‐dependent diffuse large B‐cell lymphomas (2008)

Heat shock protein 90 (HSP90) is a molecular chaperone that stabilizes critical client proteins in multiple cancers. Gene expression profiling was utilized to characterize HSP90 isoform expression in primary human diffuse large B-cell lymphomas (DLBCLs). HSP90 alpha and beta isoforms were differentially expressed in subsets of tumours defined by their transcriptional profiles. Thereafter, we assessed the activity of the HSP90 inhibitor, IPI-504, in an extensive panel of DLBCL cell lines. IPI-504, which interacts with the conserved ATP-binding site in both HSP90 isoforms, inhibited proliferation and induced apoptosis in the majority of DLBCL cell lines at low micromolar concentrations. IPI-504-sensitive cell lines expressed high levels of the HSP90 client protein, pAKT, and exhibited dose-dependent decreases in pAKT levels following IPI-504 treatment and significantly reduced proliferation following AKT RNAi. Furthermore, the combination of low-dose (<1 micromol/l) IPI-504 and the AKT/Pi3K pathway inhibitor, LY24009, was synergistic in IPI-504-sensitive DLBCL cell lines. Low-dose IPI-504 was also synergistic with the chemotherapeutic agent, doxorubicin. The HSP90 inhibitor IPI-504 warrants further investigation in DLBCL alone and in combination with identified client protein inhibitors and active chemotherapeutic agents.
MicroRNAs, development of Barrett’s esophagus, and progression to esophageal adenocarcinoma (2010)

Barrett's esophagus is a premalignant condition caused by gastroesophageal reflux. Once developed, it can progress through varying grades of dysplasia to esophageal adenocarcinoma. Whilst it is well accepted that Barrett's esophagus is caused by gastroesophageal reflux, the molecular mechanisms of its pathogenesis and progression to cancer remain unclear. MicroRNAs (miRNAs) are short segments of RNA that have been shown to control the expression of many human genes. They have been implicated in most cellular processes, and the role of miRNAs in disease development is becoming increasingly evident. Understanding altered miRNA expression is likely to help unravel the molecular mechanisms that underpin the development of Barrett's esophagus and its progression to cancer.
Restrictive Events in the Replication of Hepatitis A Virus in vitro (1985)

Hepatitis A virus was purified from the feces of 2 patients with unrelated, naturally acquired infections and was inoculated into FRhK-4 cells. Analysis of protein synthesis by double-label coelectrophoresis and subtraction allowed the resolution of virus-specific proteins synthesized during infection. In FRhK-4 cells the two strains of virus studied produced markedly different profiles of virus-specified proteins, with an accumulation of high-molecular-weight proteins for strain HM790 relative to strain HM175, suggesting a level of restriction in the processing of the viral polyprotein.
Induction of systemic TNFα in Natalizumab‐treated multiple sclerosis (2008)

The mRNA expression of eight different cytokines in peripheral blood mononuclear cells in 19 individuals with multiple sclerosis was determined at baseline and after 6 months of open-label treatment with natalizumab. Cellular expression of tumor necrosis factor alpha (TNFalpha) mRNA and number of cells secreting TNFalpha and interferon gamma protein significantly increased over the 6 months. Kurtzke EDSS scores improved because of the resolution of relapses, but not fatigue severity scores. The observed increases in systemic proinflammatory cytokines by natalizumab treatment are discussed in relation to fatigue and systemic immunity.
An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching (2011)

Cyan fluorescent proteins (CFPs), such as Cerulean, are widely used as donor fluorophores in Förster resonance energy transfer (FRET) experiments. Nonetheless, the most widely used variants suffer from drawbacks that include low quantum yields and unstable flurorescence. To improve the fluorescence properties of Cerulean, we used the X-ray structure to rationally target specific amino acids for optimization by site-directed mutagenesis. Optimization of residues in strands 7 and 8 of the β-barrel improved the quantum yield of Cerulean from 0.48 to 0.60. Further optimization by incorporating the wild-type T65S mutation in the chromophore improved the quantum yield to 0.87. This variant, mCerulean3, is 20% brighter and shows greatly reduced fluorescence photoswitching behavior compared to the recently described mTurquoise fluorescent protein in vitro and in living cells. The fluorescence lifetime of mCerulean3 also fits to a single exponential time constant, making mCerulean3 a suitable choice for fluorescence lifetime microscopy experiments. Furthermore, inclusion of mCerulean3 in a fusion protein with mVenus produced FRET ratios with less variance than mTurquoise-containing fusions in living cells. Thus, mCerulean3 is a bright, photostable cyan fluorescent protein which possesses several characteristics that are highly desirable for FRET experiments.
A 12V-500&#x00B5;A neuron stimulator with current calibration mechanism in 0.18&#x00B5;m standard CMOS process (2011)

Functional electrical stimulation (FES) has high potential to partially repair or at least improve the physiological function of patients suffering from neuron damage. Stimulators for this purpose usually face two design challenges of the required high supply voltage for compliance voltage, and the residual charge which eventually causes electrode corrosion. Using a voltage limit technique, a stimulator which can withstand 12V supply voltage is proposed in this study. A current calibration mechanism is added to limit the amount of residual charge within a safe range. The simulator has been fabricated using TSMC 0.18μm technology. Experimental results show that stimulation current up to 500μA could be delivered, and the current mismatch is less than 0.2μA. The stimulator successfully generated a 80 Hz biphasic stimulation waveform, whose amplitude and pulse width were tunable. The circuit has been tested for more than 2 hours without any failure due to transistor breakdowns.
Mechanisms of Diesel-Induced Endothelial Nitric Oxide Synthase Dysfunction in Coronary Arterioles (2010)

Acute DE exposure appears to uncouple NOS, increasing reactive oxygen species generation and causing endothelial dysfunction, potentially because of depletion of BH4 limiting its bioavailability.
Presidential address (1980)

For years there has been a struggle for a satisfactory intraar ticular replacement in the anterior cruciate-deficient knee. This paper summarizes our basic and clinical research over the last decade and presents a potential solution to the problem. Instron testing reveals that the anterior cruciate ligament fails at 51.2 kg. Scanning electron microscopy demonstrates that there is little difference whether the ligament is tested just to the point of failure or taken to visible rupture. The technique of the MacIntosh quadriceps-patellar tendon transfer is outlined. Two modifications in the form of a new approach through the defect in the quadriceps mechanism, as well as a new instrument to aid in the passage of the transfer are described. The strength of the tissues about the knee that have been used to substitute for the anterior cruciate ligament are pre sented. Only the distal iliotibial band seems suitable on strength characteristics alone. Intraarticular semitendinosus transfers in rabbits revealed degeneration and a marked decrease in tensile strength at 6 months. We conclude from this experiment and the data from Instron testing on autopsy specimens, substantiated by our clinical impressions, that the long-term success of autogenous intraarticular transfers seems unlikely. We introduce the ligament augmentation device (LAD) as a possible answer. A polypropylene, diamond-braided device is sutured to the prepatellar tissue in the MacIntosh repair to increase its tensile strength. It will sustain the host tissue during the period of degeneration and weakening, and thus allow eventual collagenization. We present our animal work with regard to the LAD and early human clinical application.
Phase I clinical and pharmacokinetic study of hexamethylene bisacetamide (NSC 95580) administered as a five-day continuous infusion. (1987)

Hexamethylene bisacetamide (HMBA), a potent differentiating agent, was tested in patients with refractory, solid tumors. Twenty patients received 25 evaluable courses. HMBA was given by continuous i.v. infusion for 5 consecutive days with courses repeated every 4 wk, provided there was acceptable, reversible toxicity. The starting dose was 4.8 g/m2/day for 5 days with escalations in subsequent cohorts of patients to 43.2 g/m2/day for 5 days. The patients included 12 females and eight males with median age of 56 yr (range 35 to 75 yr) and a median performance status of 80% (range, 60 to 100%). All except two patients had received prior chemotherapy, radiation therapy, or both. Metabolic acidosis and neurotoxicity, consisting of agitation, hallucinations, confusion, and alteration of consciousness, were dose dependent and dose limiting. The one patient treated with 43.2 m/m2/day became acidotic, agitated, and disoriented but recovered to his previous mental and electrolyte status by 8 days after the end of the HMBA infusion. One patient treated with 33.6 g/m2/day became severely acidotic (pH 7.07) and obtunded and also developed myocardial and cerebral infarctions during the HMBA infusion. The other two patients treated with 33.6 g/m2/day became mildly agitated during drug infusion. Six patients were treated at 24 g/m2/day without neurotoxicity. Transient renal insufficiency was seen in the two patients with severe neurotoxicity and in three other patients. Dose-related, mild to moderate nausea and vomiting were observed in ten patients. Four patients developed cutaneous herpes infections during treatment. White blood cell depression was not dose related, and at 24 g/m2/day, the median white blood cell nadir was 4,500/microliter (range, 2,000 to 7,900/microliter). Thrombocytopenia was dose related. At 24 g/m2/day, the median platelet count nadir was 207,000/microliter (range, 66,000 to 542,000/microliter). No objective tumor regressions were noted. HMBA pharmacokinetics was studied at all dosages. Plasma and urine samples from 20 patients were analyzed by gas-liquid chromatography for parent compound. HMBA plasma steady-state concentrations (Css) were achieved in all patients by 12 to 24 h into infusion. Once Css was achieved, daily variation was generally less than or equal to 10% from the mean Css. HMBA plasma Css increased linearly with dose, but there was variation in the Css achieved in individual patients at each dose. Doses of 24 to 33.6 g/m2/day consistently produced plasma HMBA Css of 1 to 2 mM matching concentrations required for differentiation in vitro.(ABSTRACT TRUNCATED AT 400 WORDS)
Cell cycle inhibition preserves endothelial function in genetically engineered rabbit vein grafts. (1997)

We have recently shown that ex vivo gene therapy of rabbit autologous vein grafts with antisense oligodeoxynucleotides (AS ODN) blocking cell cycle regulatory gene expression inhibits not only neointimal hyperplasia, but also diet-induced, accelerated graft atherosclerosis. We observed that these grafts remained free of macrophage invasion and foam cell deposition. Since endothelial dysfunction plays an important role in vascular disease, the current study examined the effect of this genetic engineering strategy on graft endothelial function and its potential relationship to the engineered vessels' resistance to atherosclerosis. Rabbit vein grafts transfected with AS ODN against proliferating cell nuclear antigen (PCNA) and cell division cycle 2 (cdc2) kinase elaborated significantly more nitric oxide and exhibited greater vasorelaxation to both calcium ionophore and acetylcholine than did untreated or control ODN-treated grafts. This preservation of endothelial function was associated with a reduction in superoxide radical generation, vascular cell adhesion molecule-1 (VCAM-1) expression, and monocyte binding activity in grafts in both normal and hypercholesterolemic rabbits. Our data demonstrate that AS ODN arrest of vascular cell cycle progression results in the preservation of normal endothelial phenotype and function, thereby influencing the biology of the vessel wall towards a reduction of its susceptibility to occlusive disease.
The functional coding variant Asn107Ile of the neuropeptide S receptor gene (NPSR1) is associated with schizophrenia and modulates verbal memory and the acoustic startle response (2011)

Recently, the neuropeptide S (NPS) neurotransmitter system has been identified as a promising psychopharmacological drug target given that NPS has shown anxiolytic-like and stress-reducing properties and memory-enhancing effects in rodent models. NPS binds to the G-protein-coupled receptor encoded by the neuropeptide S receptor gene (NPSR1). A functional variant within this gene leads to an amino-acid exchange (rs324981, Asn107Ile) resulting in a gain-of-function in the Ile107 variant which was recently associated with panic disorder in two independent studies. A potential psychopharmacological effect of NPS on schizophrenia psychopathology was demonstrated by showing that NPS can block NMDA antagonist-induced deficits in prepulse inhibition. We therefore explored a potential role of the NPSR1 Asn107Ile variation in schizophrenia. A case-control sample of 778 schizophrenia patients and 713 healthy control subjects was successfully genotyped for NPSR1 Asn107Ile. Verbal declarative memory and acoustic startle response were measured in subsamples of the schizophrenia patients. The case-control comparison revealed that the low-functioning NPSR1 Asn107 variant was significantly associated with schizophrenia (OR 1.19, p=0.017). Moreover, specifically decreased verbal memory consolidation was found in homozygous Asn107 carriers while memory acquisition was unaffected by NPSR1 genotype. The schizophrenia patients carrying the Ile107 variant demonstrated significantly reduced startle amplitudes but unaffected prepulse inhibition and habituation. The present study confirms findings from rodent models demonstrating an effect of NPS on memory consolidation and startle response in schizophrenia patients. Based on these findings, we consider NPS as a promising target for antipsychotic drug development.
Purification and properties of an exo-.ALPHA.-amylase from Pseudomonas stutzeri. (1982)

A maltotetraose-forming amylase from Pseudomonas stutzeri was highly purified by adsorption on starch granules and by chromatographies on Sephadex G-100 and DEAE-cellulose. The purified enzyme showed a single band in polyacrylamide gel electrophoreses with or without sodium dodecylsulfate. The optimum pH for enzyme action on starch was 6.0-6.5, and the optimum temperature was 45°C. The purified enzyme attacked starch from the non-reducing end to produce α-anomer oligosaccharides. This indicated that the enzyme was an exo-α-amylase which had not hitherto been found. The enzyme activity was markedly inhibited by the addition of Cu2+, Hg2+, N-bromosuccinimide and 2, 3-butanedione. The molecular weight of the enzyme determined by the method of Weber and Osborn was about 5.7×104. The isoelectric point of the enzyme was estimated to be 5.3 by polyacrylamide gel electrofocusing. The Km and ko values of this enzyme for starch, glycogen, short chain amylose and some maltooligosaccharides were calculated from Lineweaver-Burk plots.
Chemistry of nucleic acids: impacts in multiple fields (2011)

Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.
Improved Control of Emesis and Quality of Life with Ondansetron in Breast Cancer (1993)

Cyclophosphamide-based chemotherapy is often given to patients for the treatment of breast cancer. This chemotherapy can induce severe nausea and vomiting in these patients, which can adversely affect their quality of life, especially as these regimens are often given on an outpatient basis over several courses. This paper reviews 5 randomised, double-blind, multicenter comparative studies which have been carried out in breast cancer patients to evaluate the efficacy and safety profile of the potent and highly selective 5-HT3 receptor antagonist, ondansetron. These studies have shown that ondansetron is superior to placebo in the control of emesis induced by a 14-day CMF schedule and that it is superior to conventional anti-emetics (metoclopramide and alizapride) in the control of acute and delayed emesis induced by regimens containing high-dose cyclophosphamide. Ondansetron was well tolerated in these studies and did not induced any extrapyramidal reactions. The efficacy and tolerability of ondansetron was reflected in a better quality of life for patients given this anti-emetic which was formally assessed in 2 of the studies using the Rotterdam Symptom Checklist or the Functional Living Index-Emesis. In conclusion, ondansetron is an effective and well-tolerated anti-emetic for patients receiving cyclophosphamide-based chemotherapy for the treatment of breast cancer. Ondansetron provides significant benefits for patients' quality of life compared with conventional anti-emetics particularly as these patients are often treated on an outpatient basis and can be treated with oral ondansetron at home.
Virulence Characteristics and Genetic Affinities of Multiple Drug Resistant Uropathogenic Escherichia coli from a Semi Urban Locality in India (2011)

Extraintestinal pathogenic Escherichia coli (ExPEC) are of significant health concern. The emergence of drug resistant E. coli with high virulence potential is alarming. Lack of sufficient data on transmission dynamics, virulence spectrum and antimicrobial resistance of certain pathogens such as the uropathogenic E. coli (UPEC) from countries with high infection burden, such as India, hinders the infection control and management efforts. In this study, we extensively genotyped and phenotyped a collection of 150 UPEC obtained from patients belonging to a semi-urban, industrialized setting near Pune, India. The isolates representing different clinical categories were analyzed in comparison with 50 commensal E. coli isolates from India as well as 50 ExPEC strains from Germany. Virulent strains were identified based on hemolysis, haemagglutination, cell surface hydrophobicity, serum bactericidal activity as well as with the help of O serotyping. We generated antimicrobial resistance profiles for all the clinical isolates and carried out phylogenetic analysis based on repetitive extragenic palindromic (rep)-PCR. E. coli from urinary tract infection cases expressed higher percentages of type I (45%) and P fimbriae (40%) when compared to fecal isolates (25% and 8% respectively). Hemolytic group comprised of 60% of UPEC and only 2% of E. coli from feces. Additionally, we found that serum resistance and cell surface hydrophobicity were not significantly (p = 0.16/p = 0.51) associated with UPEC from clinical cases. Moreover, clinical isolates exhibited highest resistance against amoxicillin (67.3%) and least against nitrofurantoin (57.3%). We also observed that 31.3% of UPEC were extended-spectrum beta-lactamase (ESBL) producers belonging to serotype O25, of which four were also positive for O25b subgroup that is linked to B2-O25b-ST131-CTX-M-15 virulent/multiresistant type. Furthermore, isolates from India and Germany (as well as global sources) were found to be genetically distinct with no evidence to espouse expansion of E. coli from India to the west or vice-versa.
Suitability of datamodels as canonical models for federated databases (1991)

We develop a framework of characteristics, essential and recommended, that a data model should have to be suitable as canonical model for federated databases. This framework is based on the two factors of the representation ability of a model: expressiveness and semantic relativism . Several data models are analyzed with repect to the characteristics of the framework, to evaluate their adequacy as canonical models.
A mutual coupling study of linear and circular polarized microstrip antennas for diversity wireless systems (2003)

In this paper, an analysis of mutual coupling is presented to examine the benefits of orthogonal polarizations and patterns for adjacent microstrip antennas. The mutual coupling between two linear polarized antennas orientated in parallel polarizations (E and H plane) is reduced using low dielectric constant materials. The mutual coupling can be reduced an additional 20-35dB at the same inter-element spacing when adjacent elements are orientated in orthogonal polarizations, O plane. Similarly, the mutual coupling between two circular polarized antennas orientated in the parallel polarization is reduced using low dielectric constant materials. However, the reduction in mutual coupling between two circular polarized antenna elements orientated in the O plane is only an additional 1-6 dB. The mutual coupling between a linear polarized sum beam (1/2/spl lambda/) and difference beam (1/spl lambda/) antenna is reduced 20-35 dB below the case when using identical antennas only in the H- and O-planes. Compact two- and four-element multielement antennas with inter-element spacings less than 0.15/spl lambda/ are fabricated and the S parameters and radiation patterns are measured.