gebhart/patrepeval huggingface dataset:
European Emergence of Ciprofloxacin-Resistant Escherichia coli Clonal Groups O25:H4-ST 131 and O15:K52:H1 Causing Community-Acquired Uncomplicated Cystitis (2008)

A total of 148 E. coli strains displaying reduced susceptibility to ciprofloxacin (MIC > or = 2 microg/ml) and causing uncomplicated urinary tract infections in eight European countries during 2003 to 2006 were studied. Their phylogenetic groups, biochemical profiles, and antibiotic susceptibilities were determined. Determination of the O:H serotype, pulsed-field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD) PCR, and multilocus sequence typing provided additional discrimination. The majority (82.4%) of the microorganisms (122/148) carried resistance to two or more additional drugs, with the pattern ciprofloxacin-trimethoprim-sufamethoxazole-tetracycline-ampicillin being the most represented (73 strains out of 148; 49.3%). Extended-spectrum beta-lactamase production was detected in 12/148 strains (8.1%), with CTX-M-15 being the most-common enzyme. Six strains out of the whole collection studied (4.0%) contained a qnrB-like gene. Overall, 55 different PFGE or RAPD PCR profiles could be distinguished, indicating a substantial heterogeneity. However, about one-third (51/148) of the strains belonged to two clonal groups: O15:K52:H1 (phylogenetic group B2, lactose-nonfermenting variant, ciprofloxacin MIC of 16 microg/ml) and O25:H4 sequence type 131 (ST-131) (phylogenetic group D, ciprofloxacin MIC of > or = 32 microg/ml). With the exception of Poland, strains of these two groups were isolated in samples from all participating countries but more frequently in samples from Spain and Italy. In some representative strains of the two main clonal groups, alterations in GyrA and ParC were the basic mechanism of fluoroquinolone resistance. In some members of the O25:H4 ST-131 group, displaying a ciprofloxacin MIC of > 32 microg/ml, additional OmpF loss or pump efflux overexpression was found. In the Mediterranean area, strains belonging to these two clonal groups played a major role in determining the high rate of fluoroquinolone-resistant E. coli strains observed in the community.
Effects of 3-nitrooxypropanol on methane emission, digestion, and energy and nitrogen balance of lactating dairy cows (2014)

The objective was to measure effects of 3-nitrooxypropanol (3 NP) on methane production of lactating dairy cows and any associated changes in digestion and energy and N metabolism. Six Holstein-Friesian dairy cows in mid-lactation were fed twice daily a total mixed ration with maize silage as the primary forage source. Cows received 1 of 3 treatments using an experimental design based on two 3 × 3 Latin squares with 5-wk periods. Treatments were a control placebo or 500 or 2,500 mg/d of 3 NP delivered directly into the rumen, via the rumen fistula, in equal doses before each feeding. Measurements of methane production and energy and N balance were obtained during wk 5 of each period using respiration calorimeters and digestion trials. Measurements of rumen pH (48 h) and postprandial volatile fatty acid and ammonia concentrations were made at the end of wk 4. Daily methane production was reduced by 3 NP, but the effects were not dose dependent (reductions of 6.6 and 9.8% for 500 and 2,500 mg/d, respectively). Dosing 3 NP had a transitory inhibitory effect on methane production, which may have been due to the product leaving the rumen in liquid outflow or through absorption or metabolism. Changes in rumen concentrations of volatile fatty acids indicated that the pattern of rumen fermentation was affected by both doses of the product, with a decrease in acetate:propionate ratio observed, but that acetate production was inhibited by the higher dose. Dry matter, organic matter, acid detergent fiber, N, and energy digestibility were reduced at the higher dose of the product. The decrease in digestible energy supply was not completely countered by the decrease in methane excretion such that metabolizable energy supply, metabolizable energy concentration of the diet, and net energy balance (milk plus tissue energy) were reduced by the highest dose of 3 NP. Similarly, the decrease in N digestibility at the higher dose of the product was associated with a decrease in body N balance that was not observed for the lower dose. Milk yield and milk fat concentration and fatty acid composition were not affected but milk protein concentration was greater for the higher dose of 3 NP. Twice-daily rumen dosing of 3 NP reduced methane production by lactating dairy cows, but the dose of 2,500 mg/d reduced rumen acetate concentration, diet digestibility, and energy supply. Further research is warranted to determine the optimal dose and delivery method of the product.
LRP5 (low density lipoprotein receptor-related protein 5) (2011)

Review on LRP5 (low density lipoprotein receptor-related protein 5), with data on DNA, on the protein encoded, and where the gene is implicated.
A Convenient Preparation of Heteroaryl Sulfonamides and Sulfonyl Fluorides from Heteroaryl Thiols (2006)

Heteroaromatic thiols may be oxidized to the sulfonyl chloride at low temperature (-25 degrees C) by using 3.3 equiv of aqueous sodium hypochlorite. The reaction is rapid, avoids the use of chlorine gas, and succeeds with substrates that have previously been found to afford little or none of the sulfonamide product with other procedures. The method allows the preparation of the sulfonyl fluorides, which are stable enough to be purified and stored, making them potentially useful monomers in parallel chemistry efforts.
Serological Relationship between a Pathogenic Strain of Marek's Disease Virus, its Attenuated Derivative and Herpes Virus of Turkeys (1975)

SUMMARY Precipitating antigens present in extracts of chick embryo cells infected with the HPRS-16 attenuated strain of Marek’s disease virus (att-MDV) were separated by gel filtration on Sephadex G200 and some of their properties determined. The two main antigens detected with convalescent MD serum, referred to as ‘B’ and ‘C’ antigens, had mobilities of 0.55 and 0.25 respectively relative to phenol red on electrophoresis in 7.5% acrylamide gel. The B antigen was relatively stable and of low mol. wt. in comparison with the C antigen. B and C antigens were in some instances also detected in culture medium of infected cells, but were distinguishable from the A antigen, a major glycoprotein antigen released into the culture medium of cells infected with HPRS-16. The results of immunodiffusion studies suggest that B antigen is common to MDV and strains of herpes virus of turkeys (HVT) and that at least 2 antigens (including C) are MDV specific. The A antigen was also common to MDV and HVT strains. It was noted however that the capacity of HPRS-16/att to synthesize A antigen was considerably reduced in comparison with HPRS-16 and HVT strains, and in some preparations the A antigen could not be detected. Evidence was also obtained for the presence of HVT-specific antigens associated mainly with the cell fraction.
Stoichiometric growth model for riboflavin‐producing Bacillus subtilis (2001)

Rate equations for measured extracellular rates and macromolecular composition data were combined with a stoichiometric model to describe riboflavin production with an industrial Bacillus subtilis strain using errors in variables regression analysis. On the basis of this combined stoichiometric growth model, we explored the topological features of the B. subtilis metabolic reaction network that was assembled from a large amount of literature. More specifically, we simulated maximum theoretical yields of biomass and riboflavin, including the associated flux regimes. Based on the developed model, the importance of experimental data on building block requirements for maximum yield and flux calculations were investigated. These analyses clearly show that verification of macromolecular composition data is important for optimum flux calculations.
Changes in Sodium Pump Expression Dictate the Effects of Ouabain on Cell Growth (2009)

Here we show that ouabain-induced cell growth regulation is intrinsically coupled to changes in the cellular amount of Na/K-ATPase via the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway. Ouabain increases the endocytosis and degradation of Na/K-ATPase in LLC-PK1, human breast (BT20), and prostate (DU145) cancer cells. However, ouabain stimulates the PI3K/Akt/mTOR pathway and consequently up-regulates the expression of Na/K-ATPase in LLC-PK1 but not BT20 and DU145 cells. This up-regulation is sufficient to replete the plasma membrane pool of Na/K-ATPase and to stimulate cell proliferation in LLC-PK1 cells. On the other hand, ouabain causes a gradual depletion of Na/K-ATPase and an increased expression of cell cycle inhibitor p21(cip), which consequently inhibits cell proliferation in BT20 and DU145 cells. Consistently, we observe that small interfering RNA-mediated knockdown of Na/K-ATPase is sufficient to induce the expression of p21(cip) and slow the proliferation of LLC-PK1 cells. Moreover, this knockdown converts the growth stimulatory effect of ouabain to growth inhibition in LLC-PK1 cells. Mechanistically, both Src and caveolin-1 are required for ouabain-induced activation of Akt and up-regulation of Na/K-ATPase. Furthermore, inhibition of the PI3K/Akt/mTOR pathway by rapamycin completely blocks ouabain-induced expression of Na/K-ATPase and converts ouabain-induced growth stimulation to growth inhibition in LLC-PK1 cells. Taken together, we conclude that changes in the expression of Na/K-ATPase dictate the growth regulatory effects of ouabain on cells.
Therapeutic Efficacy of Transcranial Magnetic Stimulation for Hereditary Spinocerebellar Degeneration. (1999)

We applied transcranial magnetic stimulation (TMS) as a therapeutic approach for patients with spinocerebellar degeneration (SCD). The subjects were four familial SCD patients (three men and one woman) aged from 27 to 76 years old. They were genetically analysed as two spinocerebellar ataxia type 6 (SCA 6), one SCA 1, and one SCA 7. The durations of their illness ranged from 1 to 7 years. Ten consecutive magnetic pulses were delivered over the scalp corresponding to the right cerebellar hemisphere, the middle of the cerebellum and the left cerebellar hemisphere, respectively, every day for 21 days. In all patients, the time and the number of steps required for a 10 m walk examination were significantly decreased after TMS trial compared with those before TMS. The number of feasible steps in tandem gait test increased. The total length of tracing body balance for 30 seconds measured by gravinometer was significantly decreased. However, nystagmus, dysarthria or incoordination of the upper limbs did not change after TMS trial. It is of interest that the blood flow of the cerebellar hemisphere, putamen and pons were significantly increased during the TMS trial. Although we do not know the exact mechanism by which TMS improved the ataxic gait, we speculate the increase of blood flow in the cerebellum, putamen and pons takes part in the improvement. These findings suggest that TMS over the cerebellum may be an effective therapy for patients with SCD.
Hepadnavirus envelope proteins regulate covalently closed circular DNA amplification (1990)

Primary duck hepatocytes were infected with a mutant duck hepatitis B virus defective in envelope protein but competent for viral DNA synthesis. Cells infected by this mutant accumulated higher levels of viral covalently closed, circular DNA (cccDNA) than those infected by wild-type virus. The accumulation of high levels of cccDNA was due to a failure of the mutant-infected cells to suppress de novo cccDNA synthesis compared with suppression by cells infected by the wild type. The envelope-defective virus failed to establish a persistent infection in vitro, possibly because of a virus-mediated cell death. Therefore, one or both viral envelope proteins are required for regulation of cccDNA synthesis and for maintenance of persistent infection in vitro.
Tracking feature points: a new algorithm (2002)

A new algorithm is presented for feature point based motion tracking in long image sequences. Dynamic scenes with multiple, independently moving objects are considered in which feature points may temporarily disappear enter and leave the view field. The existing approaches to feature point tracking have limited capabilities in handling incomplete trajectories, especially when the number of points and their speeds are large, and trajectory ambiguities are frequent. The proposed algorithm was designed to efficiently resolve these ambiguities.
Effect of ethanol ingestion on plasma vasopressin and water balance in humans (1982)

The effects of 75 ml ethanol ingested over 60 min on plasma osmolality (Posmol) and plasma vasopressin (PAVP) in four normal subjects were studied. In the 1st h of the investigation PAVP fell, then rose, even though plasma ethanol levels were still rising. The rise in PAVP was preceded by a rise in Posmol corrected for the influence of ethanol. The fall in PAVP was followed by an increase in free water clearance and a decrease in urine osmolality, while the later rise in PAVP was followed by a decrease in free water clearance (CH2O) and a rise in urine osmolality. The relationship between PAVP and Posmol was then studied during intravenous (iv) hypertonic saline infusion in five subjects. The results were compared with those from a second infusion in the same subjects after ingestion of ethanol (0.5 ml/kg). Ethanol reduced vasopressin release in response to iv hypertonic saline infusion, and this correlated with a reduced decrease in CH2O. We conclude that ethanol inhibits PAVP release by decreasing the response of the osmosodium receptors to changes in plasma tonicity.
ChemProt: a disease chemical biology database (2010)

Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700,000 unique chemicals with biological annotation for 30,578 proteins. We gathered over 2-million chemical-protein interactions, which were integrated in a quality scored human PPI network of 428,429 interactions. The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A, an endocrine disruptor, with certain types of cancer, respectively. The server can be accessed at http://www.cbs.dtu.dk/services/ChemProt/.
Small Ti clusters for catalysis of hydrogen exchange in NaAlH4 (2003)

Colloidal Ti has been synthesized following a method described in the literature. Extended x-ray absorption fine structure measurements indicate the presence of small colloidal entities, consisting of only a few core Ti atoms which are coordinated by O atoms from tetrahydrofuran (THF). The results can be explained by the proposed structure of Ti13 · 6THF, in which the Ti cluster has the shape of a distorted icosahedron. The Ti colloid was used to prepare a functional nanocomposite by ball-milling the clusters with NaAlH4. The nanocomposite showed superior hydrogen exchange kinetics when compared to the state of the art in the literature.
Increased (superscript 99m)Tc-MDP Uptake in a Hemithorax Associated with Acute Radiation Effect: A Case Report (2008)

Extraosseous uptake of bone seeking agents on a bone scan can result from a variety of causes, which need further verification. We present a 61-year-old woman with breast cancer post surgery and adjuvant chemotherapy who underwent radiotherapy over the left chest. The (superscript 99m)Tc-MDP bone scan performed one hour after one fraction of external beam irradiation showed increased MDP uptake in the irradiated left hemithorax. Acute radiation effect induced (superscript 99m)Tc-MDP uptake and the follow-up results are discussed.
Unmodified device driver reuse and improved system dependability via virtual machines (2004)

We propose a method to reuse unmodified device drivers and to improve system dependability using vir-tual machines. We run the unmodified device driver, with its original operating system, in a virtual machine. This approach enables extensive reuse of existing and unmod-ified drivers, independent of the OS or device vendor, significantly reducing the barrier to building new OS en-deavors. By allowing distinct device drivers to reside in separate virtual machines, this technique isolates faults caused by defective or malicious drivers, thus improving a system’s dependability. We show that our technique requires minimal support infrastructure and provides strong fault isolation. Our prototype’s network performance is within 3–8 % of a native Linux system. Each additional virtual machine in-creases the CPU utilization by about 0.12%. We have successfully reused a wide variety of unmodified Linux network, disk, and PCI device drivers. 1
Multiple-exposure interferometric lithography (1993)

Interference effects between two coherent laser beams have long been used to create simple grating patterns in photoresist. With the addition of multiple exposures with variations in period, phase, and orientation, in the same level of photoresist, highly complex one- and two-dimensional patterns of potential interest for device application are demonstrated. The spatial scale of the lines forming these patterns is ∼1/4 of the writing wavelength λ (period to λ/2 and line to space ratio of 1:1) and is in the extreme submicron range, ∼0.1 μm, for readily available laser sources, such as an Ar+-ion laser operating at 364 nm. Importantly, the depth-of-focus for these pairwise exposures is unlimited on the scale of typical semiconductor device topographies and large area, uniform exposures to scales much larger than projected integrated circuit die sizes (e.g., to 30×30 cm2) are easily achieved. These patterns are closely related to moiré interference patterns; relationships are illustrated. Diffractive readout is shown to be a powerful and intuitive technique for monitoring these structures. Additional flexibility in pattern fabrication is provided with conventional lithography to define areas on a larger scale and by the use of aperture and phase masks to isolate areas. An example is the fabrication of an interdigitated structure with submicron spaces over a large area.
Ultrahigh resolution Fourier domain optical coherence tomography (2004)

We present, for the first time, in vivo ultrahigh resolution (~2.5 microm in tissue), high speed (10000 A-scans/second equivalent acquisition rate sustained over 160 A-scans) retinal imaging obtained with Fourier domain (FD) OCT employing a commercially available, compact (500x260mm), broad bandwidth (120 nm at full-width-at-half-maximum centered at 800 nm) Titanium:sapphire laser (Femtosource Integral OCT, Femtolasers Produktions GmbH). Resolution and sampling requirements, dispersion compensation as well as dynamic range for ultrahigh resolution FD OCT are carefully analyzed. In vivo OCT sensitivity performance achieved by ultrahigh resolution FD OCT was similar to that of ultrahigh resolution time domain OCT, although employing only 2-3 times less optical power (~300 microW). Visualization of intra-retinal layers, especially the inner and outer segment of the photoreceptor layer, obtained by FDOCT was comparable to that, accomplished by ultrahigh resolution time domain OCT, despite an at least 40 times higher data acquisition speed of FD OCT.
Effective Immunotherapy against Murine Gliomas Using Type 1 Polarizing Dendritic Cells—Significant Roles of CXCL10 (2009)

In an attempt to develop effective vaccines against central nervous system (CNS) tumors, we evaluated the ability of vaccines with standard dendritic cells (DC) versus type 1 polarizing DCs (DC1) to induce glioma-specific type 1 CTLs with CNS tumor-relevant homing properties and the mechanism of their action. C57BL/6 mouse-derived bone marrow cells were cultured with mouse granulocyte/macrophage colony-stimulating factor (GM-CSF) for 6 days, and CD11c(+) cells were subsequently cultured with GM-CSF, rmIFN-gamma, rmIFN-alpha, rmIL-4, and polyinosinic-polycytidylic acid stabilized by lysine and carboxymethylcellulose for 24 hours to generate DC1s. In analogy to their human counterparts, mouse DC1s exhibited surface marker profiles of mature DCs and produced high levels of IL-12 and CXCL10. Importantly for their application as cancer vaccines, such DC1s stably retained their type 1 phenotype even when exposed to type 2-promoting or regulatory T cell (Treg)-promoting environments. Consistently, mouse DC1s induced antigen-specific type 1 CTLs more efficiently than nonpolarized DCs in vitro. DC1s given s.c. migrated into draining lymph nodes, induced antigen-specific CTLs, and suppressed Treg accumulation. In addition, s.c. immunization with DC1s loaded with glioma-associated antigen (GAA)-derived CTL epitope peptides prolonged the survival of CNS GL261 glioma-bearing mice, which was associated with efficient CNS glioma homing of antigen-specific CTLs. Intratumoral injections of GAA peptide-loaded DC1s further enhanced the anti-CNS glioma effects of DC1-based s.c. immunization. Interestingly, the antitumor functions were abrogated with CXCL10(-/-) mouse-derived DC1s. Collectively, these findings show the anti-CNS glioma effects of DC1-based therapy and a novel role of CXCL10 in the immunologic and therapeutic activity of DC-based cancer vaccines.