gebhart/patrepeval huggingface dataset:
Three-dimensional solution structure of the N-terminal receiver domain of NTRC (1995)

NTRC is a transcriptional enhancer binding protein whose N-terminal domain is a member of the family of receiver domains of two-component regulatory systems. Using 3D and 4D NMR spectroscopy, we have completed the 1H, 15N, and 13C assignments and determined the solution structure of the N-terminal receiver domain of the NTRC protein. Determination of the three-dimensional structure was carried out with the program X-PLOR (Brünger, 1992) using a total of 915 NMR-derived distance and dihedral angle restraints. The resultant family of structures has an average root mean square deviation of 0.81 A from the average structure for the backbone atoms involved in well-defined secondary structure. The structure is comprised of five alpha-helices and a five-stranded parallel beta-sheet, in a (beta/alpha)5 topology. Comparison of the solution structure of the NTRC receiver domain with the crystal structures of the homologous protein CheY in both the Mg(2+)-free and Mg(2+)-bound forms [Stock, A.M., Mottonen, J. M., Stock, J. B., & Schutt, C. E. (1989) Nature 337, 745-749; Volz, K., & Matsumura, P. (1991) J. Biol. Chem. 296, 15511-15519; Stock, A. M., Martinez-Hackert, E., Rasmussen, B. F., West, A. H., Stock, J. B., Ringe, D., & Petsko, G. A. (1993) Biochemistry 32, 13375-13380; Bellsolell, L., Prieto, J., Serrano, L., & Coll, M. (1994) J. Mol. Biol. 238, 489-495] reveals a very similar fold, with the only significant difference occurring in the positioning of helix 4 relative to the rest of the protein. Examination of the conformation of consensus residues of the receiver domain superfamily [Volz, K. (1993) Biochemistry 32, 11741-11753] in the structures of the NTRC receiver domain and CheY establishes the structural importance of residues whose side chains are involved in hydrogen bonding or hydrophobic core interactions. The importance of some nonconsensus residues which may be conserved for their ability to fulfill helix capping roles is also discussed.
Molecular Analysis of Drug Delivery Systems Controlled by Dissolution of the Polymer Carrier (1997)

Dissolution-controlled drug delivery systems are characterized by a phase erosion of the polymer carrier that is associated with fast or slow dissolution of the macromolecular chains. The molecular nature of the dissolution phenomenon was examined by analyzing the water transport process and the subsequent polymer chain disentanglement that is usually characterized by a snake-like motion of the chain (reptation). The results indicate that the polymer molecular weight, water, polymer and drug diffusion coefficients, equilibrium water concentration in the polymer, and water-polymer interaction parameter can control the mechanism and rate of drug release. A new model for this process was developed, and its predictions are compared with experimental studies of drug delivery from poly(vinyl alcohol)-based systems.
Interference Management for Future Cellular OFDMA Systems Using Coordinated Multi-Point Transmission (2010)

Todays cellular systems reach their limits for data rate due to the continuously increasing amount of subscribers using wireless service for business purposes or in leisure time (smartphone effect). Thus, recent research focuses on concepts for interference management for cellular OFDMA systems. This paper addresses various techniques related to this topic, while considering the concepts with lowest complexity and backhaul costs as promising candidates to be applied first. Starting from interference canceling receivers over multi-user MIMO using fixed precoding to multi-cell interference estimation, which improves the precision of link adaptation, we discuss closed-loop cooperative transmit beamforming using multiple base stations grouped into a wireless distributed network (WDN), which is denoted as coordinated multi-point joint transmission in the 3GPP LTE-Advanced standardization. It is obvious, the more sophisticated these techniques are, the higher the demands for feedback and backhaul become. Performance results are provided by employing multi-cell simulations according to recommendations from 3GPP. In addition, feasibility of coordinated multi-point joint transmission is demonstrated in a real-time prototype setup, i.e. in the Berlin LTE-Advance Testbed.
Growth factor levels in the platelet-rich plasma produced by 2 different methods: curasan-type PRP kit versus PCCS PRP system. (2002)

PRP contains growth factors in high concentrations. Precise predictions of growth factor levels based on the thrombocyte counts of whole blood or PRP appeared limited. There are different sources for growth factors (platelets, leukocytes, plasma).
Rafts defined: a report on the Keystone symposium on lipid rafts and cell function (2006)

The recent Keystone Symposium on Lipid Rafts and Cell Function (March 23-28, 2006 in Steamboat Springs, CO) brought together biophysicists, biochemists, and cell biologists to discuss the structure and function of lipid rafts. What emerged from the meeting was a consensus definition of a membrane raft: "Membrane rafts are small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions." This definition helps to clarify current thinking in a field that has been plagued by the heterogeneous and sometimes ephemeral nature of its subject.
Unified theory regarding A/P and M/L balance in quiet stance (1996)

1. Control of posture in quiet stance has been quantified by center of pressure (COP) changes in the anterior-posterior (A/P) and medial-lateral (M/L) directions from a single force platform. Recording from a single force platform, researchers are unable to recognize two separate mechanisms that become evident when two force platforms are used. Depending on the stance position taken, many combinations of an ankle mechanism and a hip (load/unload) mechanism are evident. In side-by-side stance, A/P balance is totally under ankle (plantar/dorsiflexor) control, whereas M/L balance is under hip (abductor/adductor) control. In tandem stance, the A/P balance is dominated by the hip mechanism, with mixed and small or sometimes negligible contributions by the ankle plantar/dorsiflexors: for M/L balance, the reverse is evident; ankle invertors/evertors dominate, with mixed and small contribution from the hip load/unload mechanism. In an intermediate 45 degrees stance position, both ankle and hip mechanisms contribute to the net balance control in totally different ways. In the M/L direction the two strategies reinforce, whereas in the A/P direction the ankle mechanism must overcome and cancel most of the inappropriate contribution by the hip load/unload mechanism. A spatial plot of the separate mechanisms reveals the fact that the random-looking COP scatter plot is nothing more than a spatial and temporal summation of two separate spatial plots. A straight line joining the individual COPs under each foot is the load/unload line controlled by the hip mechanism. At right angles to this load/unload line in the side-by-side and tandem positions is the independent control line by the ankle muscles. In an intermediate standing position, the separate control lines exist, but now the ankle control is not orthogonal to the load/unload line; rather, it acts at an angle of approximately 60 degrees. The direction of these ankle control and load/unload lines also allows us to pinpoint the muscle groups responsible at the ankle and hip in any of the stance positions.
Performance modeling and prediction for scientific Java applications (2006)

With the expansion of the Internet, the grid has become an attractive platform for scientific computing. Java, with a platform-independent execution model and built-in support for distributed computing is an inviting choice for implementation of applications intended for grid execution. Recent work has shown that an accurate performance model combined with a load-balancing scheduling strategy can significantly improve the performance of distributed applications on a heterogeneous computing platform, such as the grid. However, current performance modeling techniques are not suitable for Java applications, as the virtual machine execution model presents several difficulties: 1) a significant amount of time is spent on compilation at the beginning of the execution, 2) the virtual machine continuously profiles and recompiles the code during the execution, 3) garbage collection can have unpredictable effects on memory hierarchy, 4) some applications can spend more time garbage collecting than computing for certain heap sizes and 5) small variations in virtual machine implementation can have a large impact on the application's behavior. In this paper, we present a practical profile-based strategy for performance modeling of Java scientific applications intended for execution on the grid. We introduce two novel concepts for the Java execution model: point of predictability (PoP) and point of unpredictability (PoU). PoP accounts for the volatile nature of the effects of the virtual machine on execution time for small problem sizes. PoU accounts for the effects of garbage collection on certain applications that have a memory footprint that approaches the total heap size. We present an algorithm for determining PoP and PoU for Java applications, given the hardware platform, virtual machine and heap size. We also present a code-instrumentation-based mechanism for building the algorithm complexity model for a given application. We introduce a technique for calibrating this model that is able to accurately predict the execution time of Java programs for problem sizes between PoP and PoU. Our preliminary experiments show that techniques can achieve load balancing with more than 90% average CPU utilization.
Interactive clipping techniques for texture-based volume visualization and volume shading (2003)

We propose clipping methods that are capable of using complex geometries for volume clipping. The clipping tests exploit per-fragment operations on the graphics hardware to achieve high frame rates. In combination with texture-based volume rendering, these techniques enable the user to interactively select and explore regions of the data set. We present depth-based clipping techniques that analyze the depth structure of the boundary representation of the clip geometry to decide which parts of the volume have to be clipped. In another approach, a voxelized clip object is used to identify the clipped regions. Furthermore, the combination of volume clipping and volume shading is considered. An optical model is introduced to merge aspects of surface-based and volume-based illumination in order to achieve a consistent shading of the clipping surface. It is demonstrated how this model can be efficiently incorporated in the aforementioned clipping techniques.
Biomedical applications of high gradient magnetic separation: progress towards therapeutic haeomofiltration (2015)

High gradient magnetic separation is a well-established technology in the mineral processing industry, and has been used for decades in the bioprocessing industry. Less well known is the increasing role that high gradient magnetic separation is playing in biomedical applications, for both diagnostic and therapeutic purposes. We review here the state of the art in this emerging field, with a focus on therapeutic haemofiltration, the key enabling technologies relating to the functionalisation of magnetic nanoparticles with target-specific binding agents, and the development of extra-corporeal circuits to enable the in situ filtering of human blood.
Production of Transgenic Mice with Yeast Artificial Chromosomes (2003)

The stable introduction of recombinant DNA into the germline of mammals is one of the major technological advances in biology and has greatly facilitated the study of gene function in development and disease,as well as the development of biotherapeutics. Landmark experiments conducted in the early 1980s established the feasibility and reproducibility of stably introducing DNA by microinjection into the male pronucleus of single-cell mouse embryos (, , , , ).The utilization of transgenic mice now represents a major strategy for the examination of genetic and biologic questions in vivo,both in basic research and industry.
Interleukin 6isexpressed inhighlevels inpsoriatic skinand stimulates proliferation ofcultured humankeratinocytes (1989)

Psoriasis isacommonpapulosquamous skin disease. Thehistopathology ischaracterized byepidermal hyperplasia andinflammation. Recent studies suggest that keratinocyte proliferation andinflammation inpsoriasis are manifestations ofthesameunderlying pathological process. Interleukin 6(IL-6), acytokine that isamajor mediator ofthe host response totissue injury andinfection, isproduced byboth keratinocytes andleukocytes inculture. IL-6expression was studied inpsoriatic plaques byimmunoperoxidase staining withtwodifferent polyclonal anti-recombinant IL-6antisera andbyinsitu nucleic acidhybridization withIL-6cRNA probes. Epidermal anddermal cells inactive psoriatic plaques from35psoriasis patients stained heavily forIL-6 ascompared withnonlesional skinandwithplaques after treatment with antimetabolic andantiinflammatory agents. Absorption ofthe anti-recombinant IL-6antisera withpurified fibroblast- derived IL-6orwithrecombinant IL-6, butnotbovine serum albumin, removed theimmunostaining. Increased levels of IL-6weredetected intheplasma ofpatients withactive psoriasis (mean 3ng/ml) byusing twodifferent bioassays. IL-6 production byproliferating keratinocytes wassuggested by 11-6-specific immunostaining incultured normal andpsoriatic keratinocytes andbythedetection ofmRNAspecific forIL-6 inpsoriatic epidermis byinsitu hybridization. IL-6 stimulated theproliferation ofcultured, normal humankeratinocytes as assessed bytwodifferent assays. Thus,IL-6could directly contribute totheepidermal hyperplasia seen inpsoriatic epi- thelium aswell asaffect thefunction ofdermal inflammatory
Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies (2016)

False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by a fixed effect and random effect Mixed Linear Model (MLM) that incorporates population structure and kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci Linear Mixed Model (MLMM), incorporates multiple markers simultaneously as covariates in a stepwise MLM to partially remove the confounding between testing markers and kinship. To completely eliminate the confounding, we divided MLMM into two parts: Fixed Effect Model (FEM) and a Random Effect Model (REM) and use them iteratively. FEM contains testing markers, one at a time, and multiple associated markers as covariates to control false positives. To avoid model over-fitting problem in FEM, the associated markers are estimated in REM by using them to define kinship. The P values of testing markers and the associated markers are unified at each iteration. We named the new method as Fixed and random model Circulating Probability Unification (FarmCPU). Both real and simulated data analyses demonstrated that FarmCPU improves statistical power compared to current methods. Additional benefits include an efficient computing time that is linear to both number of individuals and number of markers. Now, a dataset with half million individuals and half million markers can be analyzed within three days.
Size‐Complementary Rotaxane Cross‐Linking for the Stabilization and Degradation of a Supramolecular Network (2011)

Break it down: Gels formed from rotaxane cross-linkers with end groups that are size-complementary to the macrocyclic cavity of wheel components (see picture) were prepared. The network structure was maintained in polar organic solvents or in the presence of a base to prevent hydrogen bonding. Anion exchange enabled the selective and efficient de-cross-linking of the gels.
Pharmacological properties of the enhanced-affinity glucocorticoid fluticasone furoate in vitro and in an in vivo model of respiratory inflammatory disease (2007)

Fluticasone furoate (FF) is a novel enhanced-affinity glucocorticoid that has been developed as topical therapy for allergic rhinitis. The pharmacological properties of FF have been investigated using a number of in vitro experimental systems. FF demonstrated very potent glucocorticoid activity in several key pathways downstream of the glucocorticoid receptor (GR) as follows: the transrepression nuclear factor-kappaB (NF-kappaB) pathway, the transactivation glucocorticoid response element pathway, and inhibition of the proinflammatory cytokine tumor necrosis factor-alpha. Furthermore, FF showed the greatest potency compared with other glucocorticoids for preserving epithelial integrity and reducing epithelial permeability in response to protease- and mechanical-induced cell damage. FF showed a 30- to >330,000-fold selectivity for GR-mediated inhibition of NF-kappaB vs. the other steroid hormone receptors, substantially better than a number of other clinically used glucocorticoids. In studies examining the respiratory tissue binding properties of glucocorticoids, FF had the largest cellular accumulation and slowest rate of efflux compared with other clinically used glucocorticoids, consistent with greater tissue retention. The in vivo anti-inflammatory activity of FF was assessed in the Brown Norway rat ovalbumin-induced lung eosinophilial model of allergic lung inflammation. At a dose of only 30 microg, FF achieved almost total inhibition of eosinophil influx in the lung, an inhibition that was greater than that seen with the same dose of fluticasone propionate. In conclusion, the potent and selective pharmacological profile of FF described here could deliver an effective, safe, and sustained topical treatment of respiratory inflammatory diseases such as allergic rhinitis and asthma.
Growth impairment resulting from expression of influenza virus M2 protein in Saccharomyces cerevisiae: identification of a novel inhibitor of influenza virus (1995)

The gene encoding M2, the ion channel-forming protein of influenza virus A, was expressed under the control of an inducible promoter in Saccharomyces cerevisiae. By using single and multicopy plasmids containing GAL promoter-M2 fusions, a correlation was observed between plasmid copy number and growth in medium inducing M2 expression. Cells expressing M2 from multicopy plasmids have reduced growth rates, suggesting that high levels of M2 are toxic to growth. The addition of amantadine, a compound known to block the ion channel activity of certain M2 alleles, restores the growth rates to wild-type levels in cells expressing an amantadine-susceptible allele of M2 but not an amantadine-resistant allele of M2, suggesting that M2 expression in S. cerevisiae results in the formation of functional M2 ion channels. Measurements of extracellular acidification by microphysiometry suggest that proton efflux in M2-expressing cells is altered and that the addition of amantadine permits the reestablishment of the proton gradient. The growth impairment phenotype resulting from M2 expression was used to develop a high-capacity screening assay which identified a novel inhibitor possessing an antiviral profile similar to that of amantadine.
Toxicity of Organosilicone Adjuvants and Selected Pesticides to the Asian Citrus Psyllid (Hemiptera: Psyllidae) and Its Parasitoid Tamarixia radiata (Hymenoptera: Eulophidae) (2008)

The acute toxicity of the adjuvants Silwet L-77 and Kinetic, alone and in combination with petroleum oil and copper hydroxide, to the Asian citrus psyllid Diaphorina citri Kuwayama was evaluated in screenhouse bioassays. In addition, the acute and residual toxicity of Silwet L-77 and Kinetic, alone and in combination with petroleum oil, copper hydroxide, imidacloprid, and abamectin, to the parasitoid Tamarixia radiata (Waterston) were evaluated under laboratory conditions. In screenhouse trials, Silwet L-77 (0.05%) was more insecticidal than Kinetic (0.05%) and increased the toxicity of both petroleum oil and copper hydroxide to D. citri. Petroleum oil at reduced rates (0.5 and 1%) in combination with Silwet L-77 or Kinetic was less effective in reducing D. citri populations than petroleum oil at 2% in combination with these adjuvants. Petroleum oil at 2% plus Silwet L-77 was the most toxic combination to D. citri eggs, young (first- and second- instars) and mature nymphs (third- to fifth-instars), and adults (81, 83, 74, and 55% mortality, respectively). Copper hydroxide was only toxic to young nymphs when combined with Silwet L-77 (64.9% mortality). Under laboratory conditions, survival of T. radiata was reduced by the residual effects of imidacloprid (>95% mortality) and by the acute toxicity of abamectin (>91% mortality). Silwet L-77 and Kinetic alone, and petroleum oil and copper hydroxide alone or in combination with these adjuvants, had low residual and acute toxicity to the parasitoid and appear to be compatible with the biological control of D. citri by T. radiata. The results of this study suggest that Silwet L-77 may be used in a citrus IPM program in combination with petroleum oil or copper hydroxide to increase psyllid control while spraying to suppress other insect pests or plant diseases. Field trials should be conducted to evaluate the effectiveness of these products against D. citri and their impact on T. radiata populations.
Wall-Associated Kinases Are Expressed throughout Plant Development and Are Required for Cell Expansion (2001)

The mechanism by which events in the angiosperm cell wall are communicated to the cytoplasm is not well characterized. A family of five Arabidopsis wall-associated kinases (WAKs) have the potential to provide a physical and signaling continuum between the cell wall and the cytoplasm. The WAKs have an active cytoplasmic protein kinase domain, span the plasma membrane, and contain an N terminus that binds the cell wall. We show here that WAKs are expressed at organ junctions, in shoot and root apical meristems, in expanding leaves, and in response to wall disturbances. Leaves expressing an antisense WAK gene have reduced WAK protein levels and exhibit a loss of cell expansion. WAKs are covalently bound to pectin in the cell wall, providing evidence that the binding of a structural carbohydrate by a receptor-like kinase may have significance in the control of cell expansion.
Convenient screening for hemoglobin variants by using the Diamat HPLC system (1990)

Hemolysates from 102 different patients previously assessed for the presence of hemoglobin variants by cellulose acetate electrophoresis were reanalyzed with the Diamat, a microprocessor-controlled step-gradient HPLC technique designed to determine glycohemoglobin (Hgb A1c). This pool contained 81 abnormal specimens, each with one of seven different variant abnormalities. In all cases the HPLC technique correctly detected the presence or absence of a variant. The common S trait gave a large peak immediately after Hgb A, and the SS and SC variants gave clearly abnormal patterns, caused in part by the absence of Hgb A. The pattern from EE variants was distinguished by the appearance of the glycated fraction Hgb E1c, which is eluted at 4.7 instead of 4.2 min, whereas the AE pattern had two glycated peaks. Hemoglobins F, "fast", S, and C were discerned by the presence of a major peak at 3, 5.2, 6.5, and 7.5 min, respectively. The findings suggest that the Diamat is a convenient tool to detect and help diagnose variants in a screening pool.