gebhart/patrepeval huggingface dataset:
Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences (1989)

Binding of the Escherichia coli CRP protein to DNA fragments carrying nucleotide sequences closely corresponding to the consensus is very tight with a dissociation time of over 2 h in our conditions. The concentration of cyclic AMP required for this binding is below the physiological range of intracellular cyclic AMP concentrations. Changes in nucleotide sequence at positions that are not well-conserved between different naturally-occurring CRP sites allow a more rapid dissociation of CRP-DNA complexes. There is an inverse correlation between the stability of CRP binding to sites in vitro and the repression by glucose of expression dependent on these sites in vivo: expression that is dependent on the tighter binding sites cannot be repressed by the inclusion of glucose in the growth medium.
Amphetamine Excretion Profile Following Multidose Administration of Mixed Salt Amphetamine Preparation (2004)

Interpretation of drug testing results requires detailed scientific information, particularly in those cases where the question of legitimate use versus illicit use arises. Amphetamine remains a widely abused drug throughout the world, although it is also used therapeutically for weight loss, narcolepsy, and attention-deficit disorder with hyperactivity (ADHD). Treatment of ADHD using stimulant drugs is much more common now than it was in even the recent past. Increasingly, older individuals are diagnosed and treated for ADHD, and treatment often continues into adulthood. Amphetamine is commonly used for the treatment of ADHD and is available by prescription as either the d-enantiomer or a mixture of enantiomers. Although used for many years, there are no data available to describe the excretion profile of amphetamine and its enantiomers following repeated use of the drug. As a result, medical review officers (MROs) and forensic toxicologists have no direct evidence to base their decisions on when it comes to evaluation of use of these drugs. The current study was designed to determine the concentration and enantiomer excretion profile following repeated daily administration of mixed enantiomers of amphetamine. Twenty milligrams of Adderall was administered daily to five healthy subjects with all subsequent ad lib urine samples collected for at least five days following administration of the five-dose regimen. Adderall is a 3:1 mixture of d- and l-enantiomers of amphetamine salts and represents the mixed enantiomer proportion of amphetamine available in the United States through pharmaceutical channels. Peak amphetamine concentrations ranged from 5739 to 19,172 ng/mL. Samples containing > or = 500 ng/mL amphetamine (the administrative cutoff for a positive result by gas chromatography-mass spectrometry) were seen up to 60:15 (h:min) following administration of the last dose. Enantiomer analysis showed the d-enantiomer to be in excess of the l-enantiomer for as long as the drug was administered. After administration of the last dose of drug, the proportion of l-enantiomer increased over time. Not all samples that contained > or = 500 ng/mL total amphetamine were positive when tested by immunoassay because of the differing cross-reactivity of the enantiomers. This study provides the first description of the excretion of amphetamine following repeated administration of Adderall. The presence of the l-enantiomer separates this drug from other formulations composed of only the d-enantiomer (i.e., Dexedrine and much illicit amphetamine), thus readily differentiating them from Adderall use. Some illicit and medicinal amphetamine is, however, a mixture of amphetamine enantiomers. Because the enantiomers are metabolized at different rates, their proportion offers the opportunity to describe excretion versus time. Coupling this data with drug concentration makes it possible for forensic toxicologists and MROs to come to an informed decision regarding the involvement of this drug in a positive drug test result.
Effects of Gabapentin on the Motor Response to Levodopa (2004)

Gabapentin improved parkinsonian symptoms (basal UPDRS III and magnitude of the motor response) following levodopa. This improvement was not reflected in the daily motor situation of patients. Dyskinesias remained unchanged. Gabapentin was well tolerated. Further studies are needed to know the impact of these results in the long-term.
The rehabilitation process of an injured South African rugby player: A discourse analysis (2004)

The goal of this article is to explore the dominant, positive epistemology that describes the understanding and management of sports injury and rehabilitation, and to compare it with an alternative epistemology, namely social constructionism. A single case study was used within a qualitative research design. One male rugby player who gave consent was interviewed six times by using unstructured interview techniques to collect data regarding his rugby-related injuries. A discourse analysis was done to try and come to the understanding of the cultural discourses that informed the player's personal narratives regarding his injuries. It seemed as if different cultural discourses were ‘at play' with the various rugby injuries, which led to the construction of distinct personal narratives about the rugby injuries. With the player's first rugby injury the discourse of national colours mainly informed the rehabilitation process, while with the second injury, the discourse of embodiment mainly influenced his rehabilitation from the injury. Key Words: Rugby injuries, rehabilitation, discourse analysis, positivistic epistemology, social constructionism AJPHERD . Vol.10(1) 2004: 20-41
Evaluation of an enzyme‐linked immunosorbent assay for the detection of Mycoplasma hyopneumoniae antibody in porcine serum (1992)

An enzyme-linked immunosorbent assay (ELISA) for detecting antibody to Mycoplasma hyopneumoniae in porcine serum is described. The results are presented as an ELISA ratio, calculated by dividing the absorbance of the test sample by the mean absorbance of control negative sera. In known infected pigs, the ELISA ratio was highest when the serum concentration applied to the ELISA plate was diluted 1 in 20 in PBS - Tween. Mean ELISA ratios ranged from 1.2 +/- 0.3 for pigs without porcine enzootic pneumonia (PEP) lesions to 5.5 +/- 1.5 for pigs observed with a PEP lesion reacting positively with immunofluorescent histopathology. Pigs observed with typical PEP lesions at slaughter, but not confirmed by immunofluorescent histopathology had a mean ELISA ratio of 4.9 +/- 1.7. The ELISA was highly sensitive (95.6%) and specific (98.8%) when pig sera from commercial piggeries of known M hyopneumoniae infection status were assessed. No cross-reactivity with serum from a pig hyperimmunised with killed M flocculare was detected, and reactivity with serum from another pig hyperimmunised with killed M hyorhinis showed only weak cross-reactivity, which failed to reach the ELISA positive threshold (ELISA ratio 3) for M hyopneumoniae.
Efficient transfection of mosquito cells is influenced by the temperature at which DNA‐calcium phosphate coprecipitates are prepared (1991)

Transient expression of a heat-shock protein-chloramphenicol acetyltransferase (hsp-CAT) recombinant plasmid was used to define the parameters that influence transfection of cultured mosquito cells using DNA-calcium phosphate coprecipitates. The efficiency of the calcium phosphate procedure was strongly influenced by the growth state of recipient cells, and by the temperature at which the coprecipitate was prepared. Under optimal conditions, which included formation of the DNA-calcium phosphate coprecipitate at 50 degrees C, transfection frequencies were up to tenfold higher than those obtained using the previously described polybrene procedure.
Ipsilateral fractures of the femoral neck and shaft. A treatment protocol. (1984)

Ipsilateral fractures of the femoral neck and shaft present diagnostic difficulties and complex choices as to treatment. A review of the eighty-three cases reported in the literature revealed that one-third of the fractures of the femoral neck were missed initially. No consistent method of treatment can be recommended on the basis of this review. Our present protocol for this double fracture is treatment with immediate internal fixation: the femoral neck fracture is given first priority and is reduced and immobilized with multiple cancellous screws, and the femoral shaft fracture is then treated with retrograde closed intramedullary Küntscher nailing. Appropriate exceptions to the protocol exist. We reviewed the cases of fifteen patients who were treated at Harborview Medical Center and University Hospital from 1971 through 1981. Our experience with the first two patients led to the development of our protocol, which was applied in the thirteen subsequent double fractures. Two of the fifteen femoral-neck fractures were missed initially. All of the fractures had united four months postoperatively. Of the nine patients who were followed for three years or more, two had aseptic necrosis of the femoral head. Compared with other reports, our protocol seems to have produced somewhat better functional results.
Monitoring Plasma HIV-1 RNA Levels in Addition to CD4+ Lymphocyte Count Improves Assessment of Antiretroviral Therapeutic Response (1997)

For an individual patient, a change in plasma HIV-1 RNA level of 2.5-fold or more probably indicates a true biological change. Monitoring HIV-1 RNA levels and CD4+ lymphocytes before a change in antiretroviral treatment and monitoring HIV-1 RNA levels shortly thereafter improves prediction of disease progression and decline in CD4+ counts for 1 year compared with monitoring CD4+ counts of HIV-1 RNA levels alone. Additional monitoring of infectious HIV-1 titers in mononuclear cells of peripheral blood is not useful.
Anti‐CCP Antibody, a Marker for the Early Detection of Rheumatoid Arthritis (2008)

Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation of synovial joints. In most cases this will lead to the formation of pannus tissue, ultimately leading to joint destruction. Early diagnosis, coupled with aggressive use of disease-modifying antirheumatic drugs, has been shown to have a favorable effect on the course of the disease. Therefore, early and accurate diagnosis has become increasingly important. Several sets of criteria have been published to achieve such an early diagnosis, and all of them include measurement of antibodies directed to citrullinated peptides or proteins. This review summarizes our present knowledge about the most well-known and established test to measure these antibodies, the anti-CCP test, which measures antibodies directed to cyclic citrullinated peptides. We describe the current views on how these antibodies are generated and how genetic and environmental parameters are important in this process. The anti-CCP test is more specific than the commonly used RF test (95% versus less than 90%) and has a comparable sensitivity (more than 70%). These antibodies are detectable very early in the disease and are reported to predict the development of erosive RA. Increasing evidence supports a role for these antibodies in the pathology of the disease. In conclusion, testing for anti-CCP autoantibodies is widely accepted as an indispensable tool for diagnosis and early treatment in the management of rheumatoid arthritis patients.
1′, 5′ ‐Anhydrohexitol Oligonucleotides: Synthesis, Base Pairing and Recognition by Regular Oligodeoxyribonucleotides and Oligoribonucleotides (1997)

Abstract Oligonucleotides constructed of 1′, 5′‐anhydrohexitol nucleoside building blocks (hexitol nucleic acids, HNA) are completely stable towards 3′‐exonuclease and form very stable self‐complementary duplexes as well as sequence‐selective stable duplexes with the natural DNA and RNA. Triple‐helix formation has also been observed. These hybridisation characteristics are highly dependent on the base sequence and the experimental conditions. When using a phosphate buffer containing 0.1M NaCl, a homopurine HNA dodecamer gives a δ T m of +3.0 °C/ base pair with RNA as complement. These oligomers may therefore be of considerable interest as antisense constructs.
Pneumocystis cariniiCytochrome b Mutations Are Associated with Atovaquone Exposure in Patients with AIDS (2001)

This retrospective cohort study was conducted to determine whether Pneumocystis carinii cytochrome b gene mutations in patients with AIDS and P. carinii pneumonia (PCP) are associated with atovaquone exposure. Portions of the P. carinii cytochrome b genes that were obtained from 60 patients with AIDS and PCP from 6 medical centers between 1995 and 1999 were amplified and sequenced by using polymerase chain reaction. Fifteen patients with previous atovaquone prophylaxis or treatment exposure were matched with 45 patients with no atovaquone exposure. Cytochrome b coenzyme Q binding site mutations were observed in 33% of isolates from patients exposed to atovaquone, compared with 6% from those who were not (P=.018). There was no difference in survival 1 month after treatment between patients with or without cytochrome b mutations (P=.14). Thus, cytochrome b mutations are significantly more common in patients with AIDS and PCP with atovaquone exposure, but the clinical significance of these mutations remains unknown.
Laminates of Thin Ferromagnetic Films for Microwave Applications (2007)

Thin ferromagnetic films are known to exhibit the highest possible microwave permeability of known magnetic materials. Magnetic materials with high microwave magnetic performance are useful for many technical applications. However, bulk rather than planar materials are frequently needed for the applications. Bulk materials with high microwave permeability may be produced as laminated structures of thin ferromagnetic films, possibly patterned. The paper presents experimental data on the microwave permeability of such laminated structures based on Fe films. Possible technical applications of the materials under study include thin wideband radar absorbers and miniaturized patch antennas.
A novel class of cardiotonics. Synthesis and pharmacological properties of [4-(substituted-amino)phenyl]pyridazinones and related derivatives (1987)

A series of [4-(substituted-amino)phenyl]pyridazinones and [4-(substituted-methyl)amino]phenyl]pyridazinones was synthesized and evaluated for inotropic activity in vitro and for cardiohemodynamic effects in vivo. Above all, 6-[4-(4-pyridylamino)phenyl]-4,5-dihydro-3(2H)-pyridazinone hydrochloride (4, MCI-154) and 6-[4-(4-pyridylamino)phenyl]-5-methyl-4,5-dihydro-3(2H)-pyridazinone hydrochloride (5) showed extremely potent positive inotropic activity along with vasodilating activity. Regarding dP/dtmax (an indicator for cardiac contractility), ED30's (doses that increased dP/dtmax by 30%) of compounds 4 and 5 were 8.5 +/- 1.9 and 4.4 +/- 0.6 micrograms/kg, respectively, where that of amrinone was 471.9 +/- 94.1 micrograms/kg. Structure-activity relationships of these series are presented, and a plausible model of receptor binding is discussed.
Stencil computation optimization and auto-tuning on state-of-the-art multicore architectures (2008)

Understanding the most efficient design and utilization of emerging multicore systems is one of the most challenging questions faced by the mainstream and scientific computing industries in several decades. Our work explores multicore stencil (nearest-neighbor) computations --- a class of algorithms at the heart of many structured grid codes, including PDF solvers. We develop a number of effective optimization strategies, and build an auto-tuning environment that searches over our optimizations and their parameters to minimize runtime, while maximizing performance portability. To evaluate the effectiveness of these strategies we explore the broadest set of multicore architectures in the current HPC literature, including the Intel Clovertown, AMD Barcelona, Sun Victoria Falls, IBM QS22 PowerXCell 8i, and NVIDIA GTX280. Overall, our auto-tuning optimization methodology results in the fastest multicore stencil performance to date. Finally, we present several key insights into the architectural tradeoffs of emerging multicore designs and their implications on scientific algorithm development.
Horizontal Transfer of Tamoxifen Resistance in MCF-7 Cell Derivates: Proteome Study (2017)

Using estrogen-dependent MCF-7 breast cancer cells and tamoxifen-resistant MCF-7/T subline we have shown that their co-cultivation lead to increase in tamoxifen resistance in the parent MCF-7 cells. The proteome analysis of MCF-7/T cells and new-generated resistant cells revealed 21 common proteins differently expressed in both the resistant cell lines, among them - 6 proteins were associated with the drug or hormonal resistance. Both resistant lines were characterized with suppression of estrogen receptor and activation of SNAIL1-signaling - mesenchymal pathway playing an important role in the down-regulation of estrogen receptor and maintaining of the estrogen-independent phenotype.
High-Throughput RNA Sequencing-Based Virome Analysis of 50 Lymphoma Cell Lines from the Cancer Cell Line Encyclopedia Project (2014)

Viruses cause cancer in humans. In lymphomas the Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV) and human T-lymphotropic virus type 1 are major contributors to oncogenesis. We assessed virus-host interactions using a high throughput sequencing method that facilitates the discovery of new virus-host associations and the investigation into how the viruses alter their host environment. We found a previously unknown murine leukemia virus infection in one cell line. We identified cellular genes, including cytokine regulators, that are disrupted by virus integration, and we determined mechanisms through which virus integration causes deregulation of cellular gene expression. Investigation into the KSHV transcriptome in the BCP-1 cell line revealed high-level expression of immune signaling genes. EBV transcriptome analysis showed expression of vIL-10 transcripts in a Hodgkin's lymphoma that was uncoupled from lytic genes. These findings illustrate unique mechanisms of viral gene regulation and to the importance of virus-mediated host immune signaling in lymphomas.
The FtsH Protein Accumulates at the Septum of Bacillus subtilis during Cell Division and Sporulation (2000)

The ftsH gene encodes an ATP- and Zn(2+)-dependent metalloprotease which is anchored to the cytoplasmic membrane via two transmembrane segments in such a way that the very short amino- and the long carboxy termini are exposed to the cytoplasm. Deletion of the ftsH gene in Bacillus subtilis results in a pleiotropic phenotype such as filamentous growth. This observation prompted us to ask whether ftsH is involved in cell division. A translational fusion was constructed between the complete coding region of ftsH and gfp(+) the latter carrying five point mutations to obtain enhanced fluorescence. We detected that the FtsH protein accumulates in the midcell septum of dividing cells, and during sporulation first in the asymmetrically located septa of sporulating cells and later in the membrane which engulfs the forespore. These observations revealed a new function of FtsH.
Antitumor activity of recombinant interleukin 6 in mice. (1990)

IL-6 possesses multiple biologic activities that affect a broad range of cells including those directly involved in immune responses as well as cells important in the systemic response to infection or trauma. We now show that purified human rIL-6, when administered alone at relatively high doses that are comparable to therapeutic levels of IL-2, mediated substantial reductions in the number of pulmonary and hepatic micrometastases from four distinct syngeneic tumors. Unlike IL-2, IL-6 injections resulted in neither observable toxicity nor death of the treated mice at the dose regimens used. Host immunosuppression by sublethal total-body irradiation before the initiation of therapy prevented the IL-6 antitumor effect, thus suggesting that IL-6 acted through a radiosensitive host component rather than directly on the tumor itself. Moreover, the systemic administration of relatively low doses of IL-6 in combination with subtherapeutic doses of TNF to mice bearing an established weakly immunogenic, syngeneic tumor at a subcutaneous site resulted in marked tumor regression and cure rates. These studies represent the first demonstration of tumor regression mediated by recombinant IL-6 in vivo.
The Photopolymer Science and Technology Award (2007)

The photopolymer Science and Technology Award No. 071100, the Outstanding Achievement Award 2007, was presented to Hiroshi Ito (IBM Almaden Research Center) for his outstanding achievements in photopolymer science and technology, "Development of new advanced resist materials for microelectronics".
Synthesis and Some Properties of Nematic Compounds Containing Three Ring Systems (1984)

Abstract Four series of nematic compounds: 1-(i>truns-4′-n-alkylcyclohexyl)-2-{4”-(trans-4”'-n-alkylcyclohexyl)phenyl}ethanes,trans-4-n-alkylcyclohexylmethyl 4′-(trans-4”-n-alkylcyclohexyl)phenyl ethers and 4-(trans-4′-n-alkylcyclohexyl)methoxyphenyl trans-4”-n-alkylcyclohexane-1”-carboxylates, were prepared and their transition temperatures and transition entropies measured. Their flow-aligned viscosities and birefringences were determined by extrapolation. The N-I transition temperatures and entropies for the 1-(trans-4′-n-propylcyclohexyl)-2-{4”-(trans-4”'-n-alkylcyclohexyl)phenyl}ethanes and 4-{β-(trans-4′-n-propylcyclohexyl)ethyl}phenyl trans-4”'-n-alkylcyclohexane-1”-carboxylates exhibit odd-even effects in relation to the number of carbon atoms in the alkyl chain. The viscosity of 1-(trans-4′-n-propylcyclohexyl)-2-(4”-(truns-4”'-n-pro-pylcyclohexyl)phenyl}ethane is 17.0 c.p. at 20[ddot]C and the viscosity of 4-(β-(trans-4′-n-propylcyclohexyl)ethyl}phenyl trans-4”-n-propylcyclohexane-1”-carboxylate is 34.0 c.p. at 20[ddot]C.
The carrier effects on the change of refractive index for n-type GaAs at λ=1.06,1.3, and 1.55 μm (1990)

A numerical Kramers–Kronig analysis is used to calculate the refractive-index change Δn caused by the injection/depletion of free carriers in various doped n-type GaAs. The analysis makes use of a carrier-related absorption spectrum, which is established by using quantum theory as well as empirical relations and is confirmed by the experimental absorption data in the literature. We obtain the Δn values for various doping concentrations ND and carrier concentrations N at three wavelengths; λ=1.06, 1.3, and 1.55 μm. The Δn value is positive for low-N region, and increases gradually to its maximum which is around 10−4 for λ=1.06 μm. Thereafter, Δn decreases rapidly to 0 as N increases. The linear relation between Δn and N, as predicted by the Drude theory, only happens when N is beyond a certain value. In this region, the Δn value may attain to −10−2 at N=5×1018 cm−3 for λ=1.55 μm. Because of this significant Δn value and its linear relation with N, the free-carrier induced index-change effect may find the applications in integrated optics and optical probing.