gebhart/patrepeval huggingface dataset:
Study of active controlled tocilizumab monotherapy for rheumatoid arthritis patients with an inadequate response to methotrexate (SATORI): significant reduction in disease activity and serum vascular endothelial growth factor by IL-6 receptor inhibition therapy (2008)

We investigated the clinical efficacy and safety of tocilizumab (a humanized anti-IL-6 receptor antibody) monotherapy in active rheumatoid arthritis (RA) patients with an inadequate response to low dose methotrexate (MTX). In a multicenter, double-blind, randomized, controlled trial, 125 patients were allocated to receive either tocilizumab 8 mg/kg every 4 weeks plus MTX placebo (tocilizumab group) or tocilizumab placebo plus MTX 8 mg/week (control group) for 24 weeks. The clinical responses were measured using the American College of Rheumatology (ACR) criteria and the Disease Activity Score in 28 joints. Serum vascular endothelial growth factor (VEGF) levels were also monitored. At week 24, 25.0% in the control group and 80.3% in the tocilizumab group achieved ACR20 response. The tocilizumab group showed superior ACR response criteria over control at all time points. Additionally, serum VEGF levels were significantly decreased by tocilizumab treatment. The overall incidences of adverse events (AEs) were 72 and 92% (serious AEs: 4.7 and 6.6%; serious infections: 1.6 and 3.3%) in the control and the tocilizumab groups, respectively. All serious adverse events improved by adequate treatment. Tocilizumab monotherapy was well tolerated and provided an excellent clinical benefit in active RA patients with an inadequate response to low dose MTX.
The generalized lapped biorthogonal transform (2002)

A lattice structure based on the singular value decomposition (SVD) is introduced. The lattice can be proven to use a minimal number of delay elements and to completely span a large class of M-channel linear phase perfect reconstruction filter banks (LPPRFB): all analysis and synthesis filters have the same FIR length of L=KM, sharing the same center of symmetry. The lattice also structurally enforces both linear phase and perfect reconstruction properties, is capable of providing fast and efficient implementation, and avoids the costly matrix inversion problem in the optimization process. From a block transform perspective, the new lattice represents a family of generalized lapped biorthogonal transforms (GLBT) with arbitrary integer overlapping factor K. The relaxation of the orthogonal constraint allows the GLBT to have significantly different analysis and synthesis basis functions which can then be tailored appropriately to fit a particular application. Several design examples are presented along with a high-performance GLBT-based progressive image coder to demonstrate the superiority of the new lapped transforms.
Electrospinning Nanofibers as Uniaxially Aligned Arrays and Layer‐by‐Layer Stacked Films (2004)

Abstract The conventional procedure for electrospinning has been modified to generate nanofibers as uniaxially aligned arrays over large areas. The key to the success of this method was the use of a collector composed of two conductive strips separated by an insulating gap of variable width. Directed by electrostatic interactions, the charged nanofibers were stretched to span across the gap and became uniaxially aligned arrays. Two types of gaps have been demonstrated: void gaps and gaps made of a highly insulating material. When a void gap was used, the nanofibers could readily be transferred onto the surfaces of other substrates for various applications. When an insulating substrate was involved, the electrodes could be patterned in various designs on the solid insulator. In both cases, the nanofibers could be conveniently stacked into multi‐layered architectures with controllable hierarchical structures. This new version of electrospinning has already been successfully applied to a range of different materials that include organic polymers, carbon, ceramics, and composites.
New insights into organic–inorganic hybrid perovskite CH3NH3PbI3nanoparticles. An experimental and theoretical study of doping in Pb2+sites with Sn2+, Sr2+, Cd2+and Ca2+ (2015)

This paper presents the synthesis of the organic-inorganic hybrid perovskite, CH3NH3PbI3, doped in the Pb(2+) position with Sn(2+), Sr(2+), Cd(2+) and Ca(2+). The incorporation of the dopants into the crystalline structure was analysed, observing how the characteristics of the dopant affected properties such as the crystalline phase, emission and optical properties. XRD showed how doping with Sn(2+), Sr(2+) and Cd(2+) did not modify the normal tetragonal phase. When doping with Ca(2+), the cubic phase was obtained. Moreover, DR-UV-Vis spectroscopy showed how the band gap decreased with the dopants, the values following the trend Sr(2+) < Cd(2+) < Ca(2+) < CH3NH3PbI3 ≈ Sn(2+). The biggest decrease was generated by Sr(2+), which reduced the CH3NH3PbI3 value by 4.5%. In turn, cathodoluminescence (CL) measurements confirmed the band gap obtained. Periodic-DFT calculations were performed to understand the experimental structures. The DOS analysis confirmed the experimental results obtained using UV-Vis spectroscopy, with the values calculated following the trend Sn(2+) ≈ Pb(2+) > Cd(2+) > Sr(2+) for the tetragonal structure and Pb(2+) > Ca(2+) for the cubic phase. The electron localization function (ELF) analysis showed similar electron localizations for undoped and Sn(2+)-doped tetragonal structures, which were different from those doped with Sr(2+) and Cd(2+). Furthermore, when Cd(2+) was incorporated, the Cd-I interaction was strengthened. For Ca(2+) doping, the Ca-I interaction had a greater ionic nature than Cd-I. Finally, an analysis based on the non-covalent interaction (NCI) index is presented to determine the weak-type interactions of the CH3NH3 groups with the dopant and I atoms. To our knowledge, this kind of analysis with these hybrid systems has not been performed previously.
Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: A relic of early life? (2002)

In most Gram-positive bacteria, serine-46-phosphorylated HPr (P-Ser-HPr) controls the expression of numerous catabolic genes ( approximately 10% of their genome) by acting as catabolite corepressor. HPr kinase/phosphorylase (HprK/P), the bifunctional sensor enzyme for catabolite repression, phosphorylates HPr, a phosphocarrier protein of the sugar-transporting phosphoenolpyruvate/glycose phosphotransferase system, in the presence of ATP and fructose-1,6-bisphosphate but dephosphorylates P-Ser-HPr when phosphate prevails over ATP and fructose-1,6-bisphosphate. We demonstrate here that P-Ser-HPr dephosphorylation leads to the formation of HPr and pyrophosphate. HprK/P, which binds phosphate at the same site as the beta phosphate of ATP, probably uses the inorganic phosphate to carry out a nucleophilic attack on the phosphoryl bond in P-Ser-HPr. HprK/P is the first enzyme known to catalyze P-protein dephosphorylation via this phospho-phosphorolysis mechanism. This reaction is reversible, and at elevated pyrophosphate concentrations, HprK/P can use pyrophosphate to phosphorylate HPr. Growth of Bacillus subtilis on glucose increased intracellular pyrophosphate to concentrations ( approximately 6 mM), which in in vitro tests allowed efficient pyrophosphate-dependent HPr phosphorylation. To effectively dephosphorylate P-Ser-HPr when glucose is exhausted, the pyrophosphate concentration in the cells is lowered to 1 mM. In B. subtilis, this might be achieved by YvoE. This protein exhibits pyrophosphatase activity, and its gene is organized in an operon with hprK.
Some Effects of 2-Deaminopteroylglutamic Acid upon Bacterial Growth (1953)

SUMMARY: Four analogues of pteroic acid and one of pteroylglutamic acid were tested for their ability to stimulate growth of Streptococmfaecalis R in the absence of pteroic acid or to inhibit growth in its presence. The four analogues of pteroic acid were inactive in either respect, but 2-deamhopteroylglutamk acid was inhibitory. Inhibition of the or anism wasmost marked in the presence of pteroic acid, and became relatively more efficient as the concentrations of inhibitor and growth factor were increased. Inhibition was much less marked in the presence of rhizopterin or Leucovorin, the relative efficiency decreasing in comparable conditions. Pteroylglutamic acid had an intermediate position and showed a competitive relationship. Lactobacillus cmei was similarly inhibited when growth was supported by either pteroylglutamic acid or Leucovorin, but was less pronounced in the presence of the latter. On the other hand, the analogue could substitute for pteroylglutamic acid in stimulating the suboptimal growth supported by a mixture of thymine and a purine in the absence of added folic acid. Several other organisms whose growth is independent of exogenous folic acid were unaffected by the analogue.
Fibulin‐1 binds the amino‐terminal head of β‐amyloid precursor protein and modulates its physiological function (2001)

Genetic studies have implicated amyloid precursor protein (APP) in the pathogenesis of Alzheimer's disease. While accumulating lines of evidence indicate that APP has various functions in cells, little is known about the proteins that modulate its biological activity. Toward this end, we employed a two-hybrid system to identify potential interacting factors. We now report that fibulin-1, which contains repetitive Ca(2+)-binding EGF-like elements, binds to APP at its amino-terminal growth factor-like domain, the region that is responsible for its neurotrophic activities. Fibulin-1 expression in the brain is confined to neurons, and is not expressed significantly by astrocytes or microglia. Direct binding of fibulin-1 to the secreted form of APP (sAPP) was demonstrated with a pull-down assay using fragments of both fibulin-1 fused with glutathione-S transferase and sAPP, produced in bacteria and yeast, respectively. The fibulin-1/sAPP heteromer was shown to form in the conditioned medium of transfected COS-7 cells. Furthermore, fibulin-1 blocks sAPP-mediated proliferation of primary cultured rat neural stem cells. These results suggest that fibulin-1 may play a significant role in modulating the neurotrophic activities of APP.
Quantitative Analysis of Nucleic Acids - the Last Few Years of Progress (2004)

DNA and RNA quantifications are widely used in biological and biomedical research. In the last ten years, many technologies have been developed to enable automated and high-throughput analyses. In this review, we first give a brief overview of how DNA and RNA quantifications are carried out. Then, five technologies (microarrays, SAGE, differential display, real time PCR and real competitive PCR) are introduced, with an emphasis on how these technologies can be applied and what their limitations are. The technologies are also evaluated in terms of a few key aspects of nucleic acids quantification such as accuracy, sensitivity, specificity, cost and throughput.
Comparison between Parainfluenza Virus Type 2 and Simian Virus 5: Monoclonal Antibodies Reveal Major Antigenic Differences (1988)

Marked differences in the apparent Mrs of the HN, NP and F proteins of simian virus 5 (SV5) and parainfluenza virus type 2 (PF-2) were revealed by SDS-PAGE. To examine the antigenic relationships between SV5, PF-2 and other paramyxoviruses, monoclonal antibodies (MAbs) specific to PF-2 were isolated. These antibodies had specificities for the HN, NP and P proteins and together with 54 MAbs to SV5 were tested for their ability to react with SV5, PF-2, PF-3, mumps and measles virus proteins. Most of these MAbs (55 out of 60) reacted with homologous virus only. However, five reacted with both SV5 and PF-2. These antibodies had reactivities to the NP, M and P proteins. Furthermore, one of the antibodies with reactivity to the P protein also reacted with mumps virus. Although none of the 21 MAbs with specificities for the HN protein of either SV5 or PF-2 cross-reacted with heterologous virus, some antigenic similarities between the HN protein of SV5 and PF-2 could be detected. This was demonstrated by raising a series of polyclonal antisera to purified preparations of SV5 or PF-2 HN proteins in BALB/c mice, and testing for their ability to neutralize both SV5 and PF-2 and also to immunoprecipitate the HN proteins of these viruses. Surprisingly, while low levels of cross-neutralizing antibody could be detected in some sera (e.g. neutralization of SV5 1:1600 and of PF-2 1:80), other sera with similar neutralization titres against homologous virus failed to neutralize heterologous virus. Furthermore, only a minority of the anti-HN antisera showed any immune-precipitating activity against the heterologous HN protein.
Mammalian Septins Nomenclature (2002)

There are 10 known mammalian septin genes, some of which produce multiple splice variants. The current nomenclature for the genes and gene products is very confusing, with several different names having been given to the same gene product and distinct names given to splice variants of the same gene. Moreover, some names are based on those of yeast or Drosophila septins that are not the closest homologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature system, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes will be named SEPT1-SEPT10 and Sept1-Sept10, respectively. Splice variants will be designated by an underscore followed by a lowercase "v" and a number, e.g., SEPT4_v1.
Chemical reactivity of matched cytosine and thymine bases near mismatched and unmatched bases in a heteroduplex between DNA strands with multiple differences (1989)

The chemical reactivity of matched T and C bases to osmium tetroxide and hydroxylamine near mismatched and unmatched bases in a heteroduplex between two strands of DNA with multiple differences was examined. Data was available for matched bases one or two positions away from 24 mismatches. Reactive bases were found near 16 of the mismatches and were usually one or two bases away. This reactivity is consistent with structural studies indicating perturbation of the duplex around mismatches and will allow another mode of study of the effect of mismatches. The reactivity of these bases was found not to be strongly correlated with mismatch type or GC basepair content of the basepairs around the mismatches. Extra reactivity may have been promoted by the presence of either T or C in the mismatch allowing increased reactivity of nearby T or C. The utility of the phenomenon for the detection of mutations is discussed. Unmatched bases in the heteroduplex also gives rise to reactive matched bases nearby.
Visual servoing for automatic and uncalibrated percutaneous procedures (2000)

Visual servoing is well established in the field of industrial robotics, when using CCD cameras. This paper describes one of the first medical implementations of uncalibrated visual servoing. To our knowledge, this is the first time that visual servoing is done using x-ray fluoroscopy. In this paper we present a new image based approach for semi-automatically guidance of a needle or surgical tool during percutaneous procedures and is based on a series of granted and pending US patent applications. It is a simple and accurate method which requires no prior calibration or registration. Therefore, no additional sensors, no stererotactic frame and no additional calibration phantom is needed. Our techniques provides accurate 3D alignment of the tool with respect to an anatomic target and estimates the required insertion depth. We implemented and verified this method with three different medical robots at the Computer Integrated Surgery (CIS) Lab at the Johns Hopkins University. First tests were performed using a CCD-camera and a mobile uniplanar x-ray fluoroscope as imaging modality. We used small metal balls of 4 mm in diameter as target points. These targets were placed 60 to 70 mm deep inside a test-phantom. Our method led to correct insertions with mean deviation of 0.20 mm with CCD camera and mean deviation of about 1.5 mm in clinical surrounding with an old x-ray imaging system, where the images were not of best quality. These promising results present this method as a serious alternative to other needle placement techniques, which require cumbersome and time consuming calibration procedures.
Radiation-induced formation of 8-hydroxy-2'-deoxyguanosine and its prevention by scavengers (1994)

Reactive oxygen species (ROS) induce 8-hydroxy-2'-deoxyguanosine (8-OHdG) formation, which has been proposed as a key biomarker relevant to carcinogenesis. 8-OHdG has been induced in a number of different ways, most often without knowledge of the specific type and amount of ROS generated. We have measured 8-OHdG formation in calf thymus DNA exposed to ionizing radiation under conditions generating either hydroxyl radicals (OH.), superoxide anions (O2-) or both. Additionally, we investigated the relationship between the scavenger effect of the drug 5-aminosalicylic acid (5-ASA) and increasing OH. exposure toward 8-OHdG formation. The effect of this drug was compared to those of the physiological scavengers ascorbate and reduced glutathione (GSH). We found that OH. generated 8-OHdG in a dose-dependent manner, whereas O2- did not cause 8-OHdG formation. 5-ASA, ascorbate and GSH all acted as hydroxyl radical scavengers, although with different concentration-effect curves, emphasizing the importance of using relevant pharmaco-/physiological concentrations in studies focusing on therapeutic applications of scavengers. The scavenger effect of 5-ASA at concentrations > or = 0.1 mM was similar at 30 and 100 Gy radiation, i.e. within a wide range of OH. exposure, which is useful information considering clinical applications where the exact amount of ROS formed is unknown. Both 5-ASA and ascorbate at low concentrations (< or = 0.1 mM) were less efficient in preventing 8-OHdG formation from X-ray generated OH. than was shown in a previous comparable study using light as the source of ROS. This differentiation probably reflects variations in both number and type of ROS formed in the two systems.
Cytokine Function:A Study in Biologic Diversity (1996)

Cytokines are a group of hormone-like polypeptide mediators that play a variety of regulatory roles in both host defense and normal and abnormal homeostatic mechanisms. They may he produced by diverse cell types and exert their function on a variety of cells. Their effects (which may be suppressive or enhancing) are on cellular proliferation, differentiation, activation, and motility. In addition, cytokines can exert cytodestructive effects on infectious agents or tumor cells, either directly or by activating cells with cytodestructive potential. Any given cytokine may have many different biologic effects. However, two different cytokines may have similar or identical activities. Cytokines may be classified on the basis of their cell of origin, their spectrum of activity, the category of activity they influence, the cells that are their targets, or on specific features of their ligand-receptor interaction. The mode of action of many of the cytokines involves typical signal transduction events such as protein phosphorylation, and to date there is only limited understanding of the mechanisms that lead to one activity over another when a specific cytokine is involved in a specific biologic reaction. Nevertheless, elucidation of their role in other pathologic processes has provided insight into autoimmune and allergic diseases, as well as a variety of systemic disorders. Because of their broad spectrum of activity, cytokines have been used in a variety of therapeutic settings involving both infectious diseases and neoplasia. As the number of known cytokines continues to grow, it will be increasingly difficult for the non-"cytokinologist" to follow the exponentially expanding literature. Hopefully, this brief review will provide an overview that can serve as a framework for the understanding of this important area of biology and pathology.
Measurement of Wall Shearing Stress in the Boundary Layer by Means of an Evaporating Liquid Film (1956)

A mass transfer method for measurement of local wall shear stress in laminar and turbulent flow is presented. A thin film of a suitable fluid is coated on the model surface and evaporation rate determined from film thickness measurements using light interference fringes. Application of the method to wall stress measurements in flat plate flow is presented and shows good correlation with theory. In the present state of development, the technique may be used for determining the shear stress distribution over a surface relative to the value at some reference station. The absolute magnitude of the shear stress at the reference station must be found by another method. In this respect the mass transfer method is similar to the interferometric method of measuring density distributions in high-speed flows.
Empirically-based re-design of a hypertext encyclopedia (1993)

This paper reports on the processes used and guidelines discovered in re-designing the user interface of the hypertext encyclopedia, HyperHolmes. The re-design was based on the outcomes of a previous experiment and was evaluated experimentally. Results showed that the new system resulted in superior performance and somewhat different styles of navigation compared to the old system and to paper. The study provides empirical support for design guidelines relating to tiled windows, navigation tools, graphics and hierarchical navigation.
Status of vaccine research and development of vaccines for herpes simplex virus (2016)

Herpes simplex virus type-1 (HSV-1) and -2 (HSV-2) are highly prevalent global pathogens which commonly cause recurrent oral and genital ulcerations. Less common but more serious complications include meningitis, encephalitis, neonatal infection, and keratitis. HSV-2 infection is a significant driver of the HIV epidemic, increasing the risk of HIV acquisition 3 fold. As current control strategies for genital HSV-2 infection, including antiviral therapy and condom use, are only partially effective, vaccines will be required to reduce infection. Both preventive and therapeutic vaccines for HSV-2 are being pursued and are in various stages of development. We will provide an overview of efforts to develop HSV-2 vaccines, including a discussion of the clinical need for an HSV vaccine, and status of research and development with an emphasis on recent insights from trials of vaccine candidates in clinical testing. In addition, we will touch upon aspects of HSV vaccine development relevant to low and middle income countries.