gebhart/patrepeval huggingface dataset:
Differential effect of rpoB mutations on antibacterial activities of rifampicin and KRM-1648 against Staphylococcus aureus (2001)

The in vitro antibacterial activities of the rifamycin derivatives rifampicin and KRM-1648 against 150 Staphylococcus aureus isolates were determined. The MICs of rifampicin and KRM-1648 for 90% of rifampicin-susceptible S. aureus isolates (n = 100) were 0.016 and 0.001 mg/L, respectively. In rifampicin-resistant S. aureus isolates (n = 50), different levels of resistance to rifamycins were associated with mutations at different sites in rpoB. Mutations at some sites were associated with high-level resistance to both rifamycins, while certain mutations were associated with the activity of KRM-1648 being < or = 100-fold better than that of rifampicin.
Exercise‐induced muscle damage and inflammation: fact or fiction? (2001)

Physical exercise is necessary for maintaining normal function of skeletal muscle. The mechanisms governing normal muscle function and maintenance are vastly unknown but synergistic function of hormones, neurosignalling, growth factors, cytokines and other factors, is undoubtedly important. Because of the complex interaction among these systems the lack of complete understanding of muscle function is not surprising. The purpose of exercise-induced changes in muscle cell function is to adapt the tissue to a demand of increased physical work capacity. Some of the approaches used to investigate changes in skeletal muscle cell function are exercise and electrical stimulation in animals and human models and isolated animal muscle. From these models, it has been concluded that during physical exercise, in an intensity and duration dependent manner, skeletal muscle is damaged and subsequently inflamed. The purpose of the inflammation would be to repair the exercise-induced damage. Because of the design and methods used in a majority of these studies, concerns must be raised, and the question asked whether the paradigm of exercise-induced muscle inflammation in fact is fiction. In a majority of conducted studies, a non-exercising control group is lacking and because of the invasive nature of the sampling methods used to study inflammation it does not appear impossible that observed inflammatory events in human skeletal muscle after physical exercise are methodological artefacts.
Stapled Peptides with Improved Potency and Specificity That Activate p53 (2012)

By using a phage display derived peptide as an initial template, compounds have been developed that are highly specific against Mdm2/Mdm4. These compounds exhibit greater potency in p53 activation and protein-protein interaction assays than a compound derived from the p53 wild-type sequence. Unlike Nutlin, a small molecule inhibitor of Mdm2/Mdm4, the phage derived compounds can arrest cells resistant to p53 induced apoptosis over a wide concentration range without cellular toxicity, suggesting they are highly suitable for cyclotherapy.
Galactose-extended glycans of antibodies produced by transgenic plants (2001)

Plant-specific N-glycosylation can represent an important limitation for the use of recombinant glycoproteins of mammalian origin produced by transgenic plants. Comparison of plant and mammalian N-glycan biosynthesis indicates that beta1,4-galactosyltransferase is the most important enzyme that is missing for conversion of typical plant N-glycans into mammalian-like N-glycans. Here, the stable expression of human beta1,4-galactosyltransferase in tobacco plants is described. Proteins isolated from transgenic tobacco plants expressing the mammalian enzyme bear N-glycans, of which about 15% exhibit terminal beta1,4-galactose residues in addition to the specific plant N-glycan epitopes. The results indicate that the human enzyme is fully functional and localizes correctly in the Golgi apparatus. Despite the fact that through the modified glycosylation machinery numerous proteins have acquired unusual N-glycans with terminal beta1,4-galactose residues, no obvious changes in the physiology of the transgenic plants are observed, and the feature is inheritable. The crossing of a tobacco plant expressing human beta1,4-galactosyltransferase with a plant expressing the heavy and light chains of a mouse antibody results in the expression of a plantibody that exhibits partially galactosylated N-glycans (30%), which is approximately as abundant as when the same antibody is produced by hybridoma cells. These results are a major step in the in planta engineering of the N-glycosylation of recombinant antibodies.
Synthesis and evaluation of novel bioconjugates as antiviral agents (2000)

Novel lipid (mannito-stearate) antiviral nucleoside and oligonucleotide conjugates were prepared with improved lipophilic and membrane associating properties of drugs. Potential advantages of these liponucleotide prodrugs are lower toxicity, increased cellular uptake, nuclease resistivity and antiviral activity. Oligonucleotide conjugate complementary to a unique segment of viral genome may selectively disrupt the processes dependent on the segment by hybridisation.
Coypu insulin. Primary structure, conformation and biological properties of a hystricomorph rodent insulin (1986)

Insulin from a hystricomorph rodent, coypu (Myocaster coypus), was isolated and purified to near homogeneity. Like the other insulins that have been characterized in this Suborder of Rodentia, coypu insulin also exhibits a very low (3%) biological potency, relative to pig insulin, on lipogenesis in isolated rat fat-cells. The receptor-binding affinity is significantly higher (5-8%) in rat fat-cells, in rat liver plasma membranes and in pig liver cells, indicating that the efficacy of coypu insulin on receptors is about 2-fold lower than that of pig insulin. The primary structures of the oxidized A- and B-chains were determined, and our sequence analysis confirms a previous report [Smith (1972) Diabetes 21, Suppl. 2, 457-460] that the C-terminus of the A-chain is extended by a single residue (i.e. aspartate-A22), in contrast with most other insulin sequences, which terminate at residue A21. In spite of a large number of amino acid substitutions (relative to mammalian insulins), computer-graphics model-building studies suggest a similar spatial arrangement for coypu insulin to that for pig insulin. The substitution of the zinc-co-ordinating site (B10-His----Gln) along with various substitutions on the intermolecular surfaces involved in the formation of higher aggregates are consistent with the observation that this insulin is predominantly 'monomeric' in nature. The c.d. spectrum of coypu insulin is relatively similar to those of casiragua insulin and of bovine insulin at low concentration.
Photonic Band Gaps Based on Tetragonal Lattices of Slanted Pores (2003)

We describe broad new classes of three-dimensional (3D) structures which, when made of silicon, exhibit robust 3D photonic band gaps of up to 25% of the gap center frequency. The proposed photonic crystals are readily amenable to very high precision microfabrication using established techniques such as x-ray lithography and template inversion. Each architecture consists of a set of oriented cylindrical pores emanating from a two-dimensional (2D) square lattice mask with a two-point basis. Large bandwidth, microcircuits for light may be incorporated within the resulting photonic band gaps using an intercalated 2D photonic crystal layer.
Bland prinsessor och häxor : turtagning i barns interaktion med en smartplatta (2012)

Som del av ett storre projekt om svenskundervisning och IKT (Informations- och Kommunikations- Teknologi), undersoker vi har hur barn i skolans tidiga aldrar samspelar med varandra i det forst ...
An interplanetary cause of large geomagnetic storms: Fast forward shock overtaking preceding magnetic cloud (2003)

In the event that occurred during October 3–6, 2000, at least one magnetosonic wave and one fast forward shock advanced into the preceding magnetic cloud (MC). By using the field and plasma data from the ACE and WIND spacecraft, we analyze the evolution of this event, including the characteristics and changes of the magnetic fields and plasma. At the rear part of the cloud, a large southward magnetic field is caused by a shock compression. The shock intensified a preexisting southward magnetic field. This increased the geoeffectiveness of this event and produced an intense geomagnetic storm with Dst = −175 nT . We also describe another event with a shock overtaking a MC on Nov. 6, 2001. A great geomagnetic storm of intensity Dst = 292 nT resulted. These observations are used to argue that shock compression of magnetic cloud fields is an important interplanetary cause of large geomagnetic storms. Our analyses suggest that the geoeffectiveness is related to the direction of preexisting magnetic fields, the intensity of overtaking shock, and the amount of shock penetration into the preceding MC.
The Intracellular Signaling Pathways Involved in MCP-1-Stimulated T Cell Migration across Microvascular Endothelium (1996)

The adherence and transmigration of T cells through microvascular endothelium is an essential step for recruitment into inflammatory lesions, although the factors that stimulate the directional migration of T cells have not been fully characterized. In the present study we investigated the capacity of chemokines to induce migration of T cells across dermal microvascular endothelial cell monolayer. The results showed that recombinant MCP-1 significantly induced transendothelial migration of both resting and activated T cells. Maximal induction of migration was observed at a concentration of 10 ng/ml and a 3- to 4-hr incubation period. In contrast, the chemokines IL-8, RANTES, and MIP-1 alpha failed to stimulate T cell migration at doses as high as 100 ng/ml. In studies designed to investigate the intracellular signaling pathways mediating the MCP-1 effect, the results showed that MCP-1 at doses ranging from 10 to 100 ng/ml did not cause an increase in intracellular calcium ions in T cells, even though this chemokine induced rapid calcium mobilization in monocytes. Furthermore, pretreatment of T cells with either bisindolymaleimide HCl, a specific inhibitor of protein kinase C, or genistein, a protein tyrosine kinase inhibitor, significantly decreased the MCP-1-induced transmigration in a dose-dependent manner. In contrast, T cells pretreated with the protein kinase A-specific inhibitor H89 responded normally to MCP-1 stimulation. Finally, T cell transmigration was inhibited by antibodies against CD11a, thereby confirming the importance of beta 2-integrin in the transmigration process.
Essential fatty acid requirements of cats: Pathology of essential fatty acid deficiency (1984)

The pathologic changes of essential fatty acid (EFA) deficiency were studied in specific-pathogen-free, domestic shorthair cats which were fed purified diets for 1.5 to 2.5 years. Cats fed an EFA-deficient diet exhibited signs of deficiency: severe fatty degeneration of the liver, excessive fat in the kidneys, dystrophic mineralization of the adrenal glands, degeneration of the testes, and hyperkeratosis of the skin. Minor clinical pathologic changes were consistent with liver damage. Fatty acid analyses of plasma lipids revealed low concentrations of linoleate and other n6-fatty acids, and high concentrations of n7- and n9-fatty acids, consistent with EFA deficiency. These signs of deficiency were prevented by including safflower seed oil in the diet at a concentration to supply linoleate at 6.7% of dietary energy. Therefore, linoleate is an EFA for the cat, despite negligible conversion of linoleate to arachidonate in cat liver. However, in cats fed a diet containing linoleate, but lacking arachidonate, there was mild mineralization of the kidneys, and the neutral fat content of the liver was slightly higher than that of cats fed a diet containing arachidonate and other long-chain polyunsaturated fatty acids. Also, 2 of the 19 cats fed arachidonate-deficient diets developed unusual inflammatory skin lesions. In cats fed a diet containing hydrogenated coconut oil, safflower seed oil, and chicken fat, fatty livers developed despite the presence of high levels of linoleate. The fatty livers appeared to result from a specific deleterious effect of the medium-chain triglycerides in hydrogenated coconut oil. Most of the organ pathologic changes of EFA deficiency in the cat can be prevented by feeding dietary linoleate. Linoleate meets the EFA requirement for functions which depend on proper membrane structure: growth, lipid transport, normal skin and coat condition, and maintenance of the epidermal permeability barrier. However, dietary arachidonate is required by the cat for functions which depend on eicosanoid formation, such as reproduction and blood platelet aggregation.
Bio-inspired tactile sensor sleeve for surgical soft manipulators (2014)

Robotic manipulators for Robot-assisted Minimally Invasive Surgery (RMIS) pass through small incisions into the patient's body and interact with soft internal organs. The performance of traditional robotic manipulators such as the da Vinci Robotic System is limited due to insufficient flexibility of the manipulator and lack of haptic feedback. Modern surgical manipulators have taken inspiration from biology e.g. snakes or the octopus. In order for such soft and flexible arms to reconfigure itself and to control its pose with respect to organs as well as to provide haptic feedback to the surgeon, tactile sensors can be integrated with the robot's flexible structure. The work presented here takes inspiration from another area of biology: cucumber tendrils have shown to be ideal tactile sensors for the plant that they are associated with providing useful environmental information during the plant's growth. Incorporating the sensing principles of cucumber tendrils, we have created miniature sensing elements that can be distributed across the surface of soft manipulators to form a sensor network capable of acquire tactile information. Each sensing element is a retractable hemispherical tactile measuring applied pressure. The actual sensing principle chosen for each tactile makes use of optic fibres that transfer light signals modulated by the applied pressure from the sensing element to the proximal end of the robot arm. In this paper, we describe the design and structure of the sensor system, the results of an analysis using Finite Element Modeling in ABAQUS as well as sensor calibration and experimental results. Due to the simple structure of the proposed tactile sensor element, it is miniaturisable and suitable for MIS. An important contribution of this work is that the developed sensor system can be ”loosely” integrated with a soft arm effectively operating independently of the arm and without affecting the arm's motion during bending or elongation.
Anxious and nonanxious depression (1993)

The authors used the anxiety summary score described by Clayton and associates to assess anxious and nonanxious subtypes of depression in a group of 134 outpatients with major depression. Patients with anxious depression were only slightly less likely to respond to their first tricyclic antidepressant than patients with nonanxious depression. When functional severity or symptom severity was controlled for, this differential treatment response did not hold.
Novel suppressor loci on chromosome 14q in primary bladder cancer. (1995)

Two hundred eighty-five primary human carcinomas of the urinary bladder were examined for allelic loss on chromosome 14q. Seventeen highly polymorphic dinucleotide markers spanning the long arm of this acrocentric chromosome were selected for fine PCR-based mapping. Loss of heterozygosity for at least one marker was observed in 72 (25.3%) tumors. Thirty-four of these 72 tumors (47.2%) lost the entire long arm (monosomy), as suggested by loss of heterozygosity at all informative sites. Allelic loss on 14q occurred in all grades and stages of bladder cancer but was more commonly associated with muscle-invasive tumors (Ta, 9.4%; T1, 24.1%; and > or = T2, 41%). A deletion map of 16 primary tumors with partial losses delineated two minimal regions of loss. One region (approximately 2 cM) was bounded by markers D14S75 and D14S288 and the other (approximately 3 cM) by D14S51 and D14S267. Our results demonstrate that 14q loss is common in invasive bladder cancer and suggest that two potential suppressor loci at 14q12 and 14q32.1-32.2 may contribute to the genetic progression of this common cancer.
Mini-rank: Adaptive DRAM architecture for improving memory power efficiency (2008)

The widespread use of multicore processors has dramatically increased the demand on high memory bandwidth and large memory capacity. As DRAM subsystem designs stretch to meet the demand, memory power consumption is now approaching that of processors. However, the conventional DRAM architecture prevents any meaningful power and performance trade-offs for memory-intensive workloads. We propose a novel idea called mini-rank for DDRx (DDR/DDR2/DDR3) DRAMs, which uses a small bridge chip on each DRAM DIMM to break a conventional DRAM rank into multiple smaller mini-ranks so as to reduce the number of devices involved in a single memory access. The design dramatically reduces the memory power consumption with only a slight increase on the memory idle latency. It does not change the DDRx bus protocol and its configuration can be adapted for the best performance-power trade-offs. Our experimental results using four-core multiprogramming workloads show that using x32 mini-ranks reduces memory power by 27.0% with 2.8% performance penalty and using x16 mini-ranks reduces memory power by 44.1% with 7.4% performance penalty on average for memory-intensive workloads, respectively.
Wearable micro-fluidic pH sweat sensing device based on colorimetric imaging techniques (2011)

In this paper a wearable electronic-free micro-fluidic device for the continuous monitoring of pH in sweat during exercise is described. The sensing capability is based on ionogels, ionic liquid hydrogels, containing pH sensitive dyes capable of reporting pH activity in the range from 3 to 10. Previously, we reported a flexible micro-fluidic barcode capable of measuring the pH of sweat in real time [1]. Here we have improved the device in terms of wearability, physical robustness, chemistry of the sensor and its optical response by using a mobile phone for data collection and a more accurate algorithm for colorimetric image analysis.
Hole Cleaning in Large, High-Angle Wellbores (1994)

ABSTRACT Beds of cuttings are usually formed on the bottom of large, high-angle wellbores during drilling. When the drill string is moved axially along the wellbore, large bottom-hole assembly elements such as drill bit and stabilizers tend to plow the cuttings bed, thereby causing the formation of plugs of cuttings which give rise to high overpulls, loss of circulation, continuous need for operations such as backreaming, and stuck pipe. To reduce the likelihood of these costly hole problems occurring, it is necessary to minimize the height of the cuttings bed which forms while drilling, and to minimize the tendency of the bottom-hole assembly to form plugs of cuttings. This can be done with a new hole cleaning tool described in this paper. This tool was developed using a combination of analytical modeling based on fluid mechanics first principles, experimental data, and field data. The tool enables establishment of pump flow rates, drilling fluid rheological properties, drill string configurations, and well profiles for minimal risk of experiencing problems associated with the existence of a cuttings bed.
New high‐yield, one‐step synthesis of polyglycolide from haloacetic acids (1984)

Abstract In a new, one‐step synthesis, polyglycolide was prepared by the reaction of bromo‐ or chloroacetic acid with triethylamine in a nitromethane solution. It was discolored, by iodoacetic acid possibly as a result of iodine formed by the decomposition of triethylammonium iodide. The structure of polyglycolide was characterized by hydrolysis, 1 H‐NMR and IR spectra, and x‐ray powder diffraction, which indicated partial crystallinity. A mechanism is proposed for the formation of polyglycolide. A lower limiting value of the number‐average molecular weight of 10 4 was determined by cryoscopy in 1,3‐dinitrobenzene for polyglycolide prepared from bromoacetic acid; the measurement was inaccurate because of the low solubility of the polymer. No significant effect of solvent (acetone, ether, or chloroform) on yield or melting point was observed; a higher yield was obtained in nitromethane. The polymer obtained with tri‐ n ‐propylamine and bromoacetic acid had properties similar to that obtained with triethylamine. No polymer was obtained with N , N ‐dimethylaniline and bromoacetic acid or with triethylamine and bromoacetic acid in aqueous solution.
[A novel reporter system monitoring sortase A catalyzed protein ligation efficiency]. (2014)

Efforts on directed evolution of sortase A to optimize its catalytic properties have been undertaken and shown the promise. To facilitate screening of sortase A mutants with expected catalytic properties, a novel ligation efficiency monitoring system, including reporter substrates GFP-LPETG and GGGYK-Biotin, was developed. GFP-LPETG, wild type sortase A, and a recently reported high activity sortase A mutant were prepared recombinantly from Escherichia coli BL21 (DE3). Taking advantage of the newly designed reporter system, the ligation efficiency catalyzed by wild type and mutant form of sortase A could be sensitively monitored via SDS-PAGE directly. Consistent with previous report, the mutant sortase A displayed much higher catalytic activity compared to wild type enzyme, indicating the new reporter system is easily and fast handled and sensitive. The application of this reporter system into systemic screening will facilitate future directed optimization of sortase A.
BioInfer: a corpus for information extraction in the biomedical domain (2007)

We introduce a corpus targeted at protein, gene, and RNA relationships which serves as a resource for the development of information extraction systems and their components such as parsers and domain analyzers. The corpus will be maintained and further developed with a current version being available at http://www.it.utu.fi/BioInfer.
Recommendation system for automatic design of magazine covers (2013)

In this paper, we present a recommendation system for the automatic design of magazine covers. Our users are non-designer designers: individuals or small and medium businesses who want to design without hiring a professional designer while still wanting to create aesthetically compelling designs. Because a design should have a purpose, we suggest a number of semantic features to the user, e.g., "clean and clear," "dynamic and active," or "formal," to describe the color mood for the purpose of his/her design. Based on these high level features and a number of low level features, such as the complexity of the visual balance in a photo, our system selects the best photos from the user's album for his/her design. Our system then generates several alternative designs that can be rated by the user. Consequently, our system generates future designs based on the user's style. In this fashion, our system personalizes the designs of a user based on his/her preferences.
Efficient frequency domain postfiltering for multibandexcited linear predictive coding of speech (1996)

A frequency domain postfilter for multiband excited linear predictive (MBELP) coders is proposed. It is based on the principle of multiplying the signal band magnitudes by the postfilter magnitudes obtained by sampling the postfilter response at the pitch harmonics. This approach offers two major advantages: first, the signal energies before and after postfiltering can be equalised by simply rescaling the signal band magnitudes; secondly, the phase information will be retained owing to only the magnitude spectra being modified. A fast method is given for sampling the postfilter magnitude spectrum characterised by line spectral pair (LSP) parameters.