gebhart/patrepeval huggingface dataset:
'The honeymoon phase' in children with type 1 diabetes mellitus: frequency, duration, and influential factors (2006)

Background: The honeymoon period (i.e., partial remission) of type 1 diabetes mellitus is characterized by reduced insulin requirements while good glycemic control is maintained. The clinical significance is the potential possibility for pharmacological intervention during this period to either slow down or arrest the ongoing destruction of the remaining beta-cells. Methods: A group of 103 diabetic children, younger than 12 yr of age, were prospectively studied to assess the frequency, duration, and factors that may affect partial remission. At the time of admission, patients were characterized by age, gender, symptom duration, diabetic ketoacidosis (DKA), and blood sugar level at admission. The honeymoon period was defined as a period with insulin requirements of less than 0.5 U/kg/day and hemoglobin A1c (HbA1c) level of less or equal to 6%. Results: Partial remission occurred in 71, being complete in three. The length of time until remission was 28.6 ± 12.3 (mean ± SD) days. The duration of remission was 7.2 ± 4.8 months. Remission rates were higher in those patients older than 5 yr compared with those between 3 and 5 yr of age. DKA at presentation and long duration of symptoms were associated with lower duration of remission (p < 0.001 and p < 0.001, respectively). Children in whom remission occurred had significantly lower blood glucose levels and higher pH at presentation (p < 0.001 and p < 0.001, respectively). Conclusions: Young age and severe disease at presentation are associated with decreased residual beta-cells function that is reflected by a lower incidence of partial remission. These observations are important to consider in the research regarding therapies that will have the potential goal to induce prolonged and/or complete remission at disease onset or shortly thereafter.
Complete spatiotemporal characterization and optical transfer matrix inversion of a 420 mode fiber (2016)

The ability to measure a scattering medium's optical transfer matrix, the mapping between any spatial input and output, has enabled applications such as imaging to be performed through media which would otherwise be opaque due to scattering. However, the scattering of light occurs not just in space, but also in time. We complete the characterization of scatter by extending optical transfer matrix methods into the time domain, allowing any spatiotemporal input state at one end to be mapped directly to its corresponding spatiotemporal output state. We have measured the optical transfer function of a multimode fiber in its entirety; it consists of 420 modes in/out at 32768 wavelengths, the most detailed complete characterization of multimode waveguide light propagation to date, to the best of our knowledge. We then demonstrate the ability to generate any spatial/polarization state at the output of the fiber at any wavelength, as well as predict the temporal response of any spatial/polarization input state.
FAM83 family oncogenes are broadly involved in human cancers: an integrative multi‐omics approach (2017)

The development of novel targeted therapies for cancer treatment requires identification of reliable targets. FAM83 ('family with sequence similarity 83') family members A, B, and D were shown recently to have oncogenic potential. However, the overall oncogenic abilities of FAM83 family genes remain largely unknown. Here, we used a systematic and integrative genomics approach to investigate oncogenic properties of the entire FAM83 family members. We assessed transcriptional expression patterns of eight FAM83 family genes (FAM83A-H) across tumor types, the relationship between their expression and changes in DNA copy number, and the association with patient survival. By comparing the gene expression levels of FAM83 family members in cancers from 17 different tumor types with those in their corresponding normal tissues, we identified consistent upregulation of FAM83D and FAM83H across the majority of tumor types, which is largely driven by increased DNA copy number. Importantly, we found also that a higher expression level of a signature of FAM83 family members was associated with poor prognosis in a number of human cancers. In breast cancer, we found that alterations in FAM83 family genes correlated significantly with TP53 mutation, whereas significant, but inverse correlation was observed with PIK3CA and CDH1 (E-cadherin) mutations. We also identified that expression levels of 55 proteins were significantly associated with alterations in FAM83 family genes including a decrease in GATA3, ESR1, and PGR proteins in tumors with alterations in FAM83. Our results provide strong evidence for a critical role of FAM83 family genes in tumor development, with possible relevance for therapeutic target development.
A Correlation of Freejet Data (1972)

1.73 0.47591 0.47597 0.54778 0.54776 0.28897 0.28893 3.46 1.77701 1.77706 0.92169 0.91267 0.10679 0.10678 5.19 3.48062 3.48064 0.99367 0.99565 0.01159 0.01157 The running mill time was about 1.2 sec, compared to 4.3 sec (to get the same accuracy) by using finite difference approach.
Long-Term Follow-Up of Cytokines and Soluble Cytokine Receptors in Peripheral Blood of Patients with Juvenile Rheumatoid Arthritis (1999)

Plasma levels of interleukin-1beta (IL-1beta), IL-2, soluble IL-2 receptor (sIL-2R), IL-6, IL-8, tumor necrosis factor-alpha (TNF-alpha), and the p60 soluble TNF receptor (sTNFR) were repeatedly determined by enzyme-linked immunosorbent assays (ELISA) in 35 patients with different subtypes of juvenile rheumatoid arthritis (JRA) during an observation period of up to 36 months. The data were related to conventional inflammatory parameters and disease activity. Patients with systemic disease showed the most pronounced elevations of plasma cytokines, followed by polyarticular and pauciarticular JRA. Soluble receptors sIL-2R and sTNFR were consistently elevated in patients of all JRA subtypes and indicated disease activity even in patients with normal C-reactive protein (CRP). In contrast, the determination of IL-1beta, IL-2, IL-8, and TNF-alpha revealed strikingly different individual profiles in patients of the same clinical subtype of JRA and irrespective of disease activity. It is concluded that the determination of sIL-2R and sTNFR may be relevant for monitoring JRA, as they indicate disease activity also in cases with unaltered conventional inflammatory parameters. The different individual cytokine profiles of patients within identical subtypes of disease suggest JRA to be even more heterogeneous than hitherto assumed. The data should be considered in attempts to develop anticytokine strategies in the therapy of JRA.
In vivo effects of interleukin‐11 and stem cell factor in combination with erythropoietin in the regulation of erythropoiesis (1995)

In this study we evaluated the in vivo effects of interleukin-11 (IL-11) and stem cell factor (SCF), in combination with erythropoietin (EPO) on murine erythropoiesis. Mice were treated for 7 d with IL-11. SCF and EPO, each at three dose levels. In total, 27 different dose combinations were tested. IL-11 as well as SCF could only marginally stimulate erythroid progenitor cell numbers, but IL-11 in combination with SCF was able to increase BFU-E and CFU-E numbers 4-fold, in the absence of exogenous EPO. This resulted in an increased reticulocyte count. In contrast with the stimulatory effect on immature erythroid cell stages, IL-11 treatment induced a mild anaemia, which probably resulted from a plasma volume expansion. The additional treatment with EPO resulted in strong synergistic effects on CFU-E numbers. The combination of high-dose IL-11 and high-dose SCF was able to increase the overall efficiency of EPO-induced erythroid amplification, which was reflected by a left-shift of the in vivo EPO dose-response curve. The stimulating effects of IL-11 and SCF were further demonstrated when the effects on the reticulocyte count of a single high-dose EPO injection were assessed in normal and SCF+IL-11 treated mice. Whereas a single EPO dose increased the reticulocyte count by a factor of 3, IL-11 + SCF pretreatment increased this to a factor of 7. This study shows that in vivo SCF and IL-11 are important modulators of red blood cell production. First, these factors probably increase the input from the stem cell compartment into the erythroid lineage, where subsequently EPO is required for further amplification. Additionally, however, IL-11 and SCF increase the overall efficiency of EPO-induced amplification, probably due to a stimulatory effect on late-stage erythroid cells and to a redistribution of cells from marrow to spleen.
HINT1 inhibits β‐catenin/TCF4, USF2 and NFκB activity in human hepatoma cells (2008)

In this study we explored the relevance of Hint, a novel tumor suppressor gene, to human hepatoma. The human hepatoma cell lines Hep3B and HepG2 express very low levels of the HINT1 protein but the Huh7 cells express a relatively high level. In Hep3B and HepG2 cells, but not in Huh7 cells, the promoter region of Hint1 is partially methylated and treatment with 5-azadcdeoxycytidine increased expression of the HINT1 protein and Hint1 mRNA in Hep3B and HepG2 cells. Increased expression of HINT1 in HepG2 cells markedly inhibited their growth. It also inhibited the transcriptional activities of beta-catenin/TCF4, and USF2, and inhibited the expression of endogenous cyclin D1 and TGFbeta2. Furthermore, HINT1 co-immunoprecipitated with USF2 in extracts of Hep2 cells. HINT1 also inhibited NFkappaB transcription factor reporter activity and inhibited translocation of the endogenous p65 protein to the nucleus of HepG2 cells. Therefore, decreased expression of the Hint1 gene through epigenetic silencing may play a role in enhancing the growth of a subset of human hepatoma by increasing the expression of genes controlled by the transcription factors beta-catenin, USF2, and NFkappaB.
X-ray-Excited Optical Luminescence (XEOL) and X-ray Absorption Fine Structures (XAFS) Studies of Gold(I) Complexes with Diphosphine and Bipyridine Ligands (2007)

Synchrotron techniques, X-ray-excited optical luminescence (XEOL) combined with X-ray absorption fine structures (XAFS), have been used to study the electronic structure and optical properties of a series of luminescent gold(I) complexes with diphosphine and bipyridine ligands using tunable X-rays (in the regions of the C and P K-edges and the Au L3-edge) and UV from synchrotron light sources. The effects of gold-ligand and aurophilic interactions on the luminescence from these gold(I) complexes have been investigated. It is found that the luminescence from these complexes is phosphorescence, primarily due to the decay of the Au (5d) --> PR3 (pi*), metal to ligand charge transfer (MLCT) excitation as well as contributions from the conjugated pi-system in the bipyridine ligands via the gold-nitrogen bond. The large Au 5d spin-orbit coupling enhances the intersystem crossing. The elongation of the hydrocarbon chain of the diphosphine ligand does not greatly affect the spectral features of the luminescence from the gold(I) complexes. However, the intensity of the luminescence was reduced significantly when the bipyridine ligand was replaced with 1,2-bis(4-pyridylamido)benzene. The aurophilic interaction, as investigated by EXAFS at the Au L3-edge, is shown to be only one of the factors that contribute to the luminescence of the complexes.
In-Network Quality Optimization for Adaptive Video Streaming Services (2014)

HTTP adaptive streaming (HAS) services allow the quality of streaming video to be automatically adapted by the client application in face of network and device dynamics. Due to their advantages compared to traditional techniques, HAS-based protocols are widely used for over-the-top (OTT) video streaming. However, they are yet to be adopted in managed environments, such as ISP networks. A major obstacle is the purely client-driven design of current HAS approaches, which leads to excessive quality oscillations, suboptimal behavior, and the inability to enforce management policies. Moreover, the provider has no control over the quality that is provided, which is essential when offering a managed service. This article tackles these challenges and facilitates the adoption of HAS in managed networks. Specifically, several centralized and distributed algorithms and heuristics are proposed that allow nodes inside the network to steer the HAS client's quality selection process. The algorithms are able to enforce management policies by limiting the set of available qualities for specific clients. Additionally, simulation results show that by coordinating the quality selection process across multiple clients, the proposed algorithms significantly reduce quality oscillations by a factor of five and increase the average delivered video quality by at least 14%.
Design, Synthesis, and Biological Evaluation of Coumarin Derivatives Tethered to an Edrophonium‐like Fragment as Highly Potent and Selective Dual Binding Site Acetylcholinesterase Inhibitors (2010)

A large series of substituted coumarins linked through an appropriate spacer to 3-hydroxy-N,N-dimethylanilino or 3-hydroxy-N,N,N-trialkylbenzaminium moieties were synthesized and evaluated as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. The highest AChE inhibitory potency in the 3-hydroxy-N,N-dimethylanilino series was observed with a 6,7-dimethoxy-3-substituted coumarin derivative, which, along with an outstanding affinity (IC(50)=0.236 nM) exhibits excellent AChE/BChE selectivity (SI>300 000). Most of the synthesized 3-hydroxy-N,N,N-trialkylbenzaminium salts display an AChE affinity in the sub-nanomolar to picomolar range along with excellent AChE/BChE selectivities (SI values up to 138 333). The combined use of docking and molecular dynamics simulations permitted us to shed light on the observed structure-affinity and structure-selectivity relationships, to detect two possible alternative binding modes, and to assess the critical role of pi-pi stacking interactions in the AChE peripheral binding site.
A PCR-based strategy to generate integrative targeting alleles with large regions of homology (2002)

Cryptococcus neoformans is an opportunistic fungal pathogen with a defined sexual cycle for which genetic and molecular techniques are well developed. The entire genome sequence of one C. neoformans strain is nearing completion. The efficient use of this sequence is dependent upon the development of methods to perform more rapid genetic analysis including gene-disruption techniques. A modified PCR overlap technique to generate targeting constructs for gene disruption that contain large regions of gene homology is described. This technique was used to disrupt or delete more than a dozen genes with efficiencies comparable to those previously reported using cloning technology to generate targeting constructs. Moreover, it is shown that disruptions can be made using this technique in a variety of strain backgrounds, including the pathogenic serotype A isolate H99 and recently characterized stable diploid strains. In combination with the availability of the complete genomic sequence, this gene-disruption technique should pave the way for higher throughput genetic analysis of this important pathogenic fungus.
Cytokines and their receptors as biomarkers of systemic lupus erythematosus (2008)

Systemic lupus erythematosus is the most clinically diverse autoimmune disease. Owing to its heterogeneous presentation, clinical management of systemic lupus erythematosus remains as one of the greatest challenges. Therefore, there is a great need to assess disease activity accurately. Biomarkers can be objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes or pharmacologic responses to a therapeutic intervention, and may also predict the risk of the disease, confirm diagnosis, monitor disease activity and provide prognostic information. Cytokines play an important and diverse role in the immune dysregulation in systemic lupus erythematosus. Measuring serum levels of soluble IL-2 receptor, IL-6, IL-10, soluble TNF receptor and IFN-alpha/IFN-induced genes may be promising biomarkers of disease activity in systemic lupus erythematosus.
Exploiting instruction level parallelism in processors by caching scheduled groups (1997)

Modern processors employ a large amount of hardware to dynamically detect parallelism in single-threaded programs and maintain the sequential semantics implied by these programs. The complexity of some of this hardware diminishes the gains due to parallelism because of longer clock period or increased pipeline latency of the machine.In this paper we propose a processor implementation which dynamically schedules groups of instructions while executing them on a fast simple engine and caches them for repeated execution on a fast VLIW-type engine. Our experiments show that scheduling groups spanning several basic blocks and caching these scheduled groups results in significant performance gain over fill buffer approaches for a standard VLIW cache.This concept, which we call DIF (Dynamic Instruction Formatting), unifies and extends principles underlying several schemes being proposed today to reduce superscalar processor complexity. This paper examines various issues in designing such a processor and presents results of experiments using trace-driven simulation of SPECint95 benchmark programs.
In vitro fermentability of dextran, oligodextran and maltodextrin by human gut bacteria (2000)

Anaerobic batch culture fermenters were used for a preliminary screening of the in vitro utilization by human gut microflora of dextran and novel oligodextrans (I, II and III) produced in the University of Reading (UK). Glucose and fructooligosaccharides (FOS) were used as reference carbohydrates. As expected, FOS acted as a good prebiotic in that it selectively increased numbers of bifidobacteria in the early stages of the fermentation. Dextran and oligodextrans each resulted in an enrichment of bifidobacteria in the batch cultures, with high levels of persistence up to 48 h. They also produced elevated levels of butyrate ranging from 5 to 14.85 mmol/l. To more effectively simulate conditions that prevail in different regions of the large intestine, a three-stage continuous culture cascade system was used to study further the fermentation of dextran, a low-molecular-mass oligodextran (IV) and maltodextrin. Oligodextran IV was shown to be the best substrate for bifidobacteria and lactobacilli with steady-state populations of bifidobacteria and lactobacilli being higher in all three vessels of the gut model than the respective populations resulting from dextran and maltodextrin. A maximum difference of 1.9 log was observed in vessel 1 for both bifidobacteria and lactobacilli in the case of dextran fermentation, with 1.4 log and 0.8 log in vessel 3 were the maximum differences for bifidobacteria and lactobacilli when maltodextrin was used as the carbohydrate source. Moreover, dextran and oligodextran appeared to stimulate butyrate production, with a maximum production up to 25.39 mmol/l in vessel 3 when fermenting dextran, followed by 21.70 mmol/l in the case of oligodextran IV and only 12.64 mmol/l in the case of maltodextrin.
Steric effects in the dynamics of electrolytes at large applied voltages. II. Modified Poisson-Nernst-Planck equations (2007)

In situations involving large potentials or surface charges, the Poisson-Boltzman (PB) equation has shortcomings because it neglects ion-ion interactions and steric effects. This has been widely recognized by the electrochemistry community, leading to the development of various alternative models resulting in different sets "modified PB equations," which have had at least qualitative success in predicting equilibrium ion distributions. On the other hand, the literature is scarce in terms of descriptions of concentration dynamics in these regimes. Here, adapting strategies developed to modify the PB equation, we propose a simple modification of the widely used Poisson-Nernst-Planck (PNP) equations for ionic transport, which at least qualitatively accounts for steric effects. We analyze numerical solutions of these modified PNP equations on the model problem of the charging of a simple electrolyte cell, and compare the outcome to that of the standard PNP equations. Finally, we repeat the asymptotic analysis of Bazant, Thornton, and Ajdari [Phys. Rev. E 70, 021506 (2004)] for this new system of equations to further document the interest and limits of validity of the simpler equivalent electrical circuit models introduced in Part I [Kilic, Bazant, and Ajdari, Phys. Rev. E 75, 021502 (2007)] for such problems.
NLRP3 inflammasome and its inhibitors: a review (2015)

Inflammasomes are newly recognized, vital players in innate immunity. The best characterized is the NLRP3 inflammasome, so-called because the NLRP3 protein in the complex belongs to the family of nucleotide-binding and oligomerization domain-like receptors (NLRs) and is also known as "pyrin domain-containing protein 3". The NLRP3 inflammasome is associated with onset and progression of various diseases, including metabolic disorders, multiple sclerosis, inflammatory bowel disease, cryopyrin-associated periodic fever syndrome, as well as other auto-immune and auto-inflammatory diseases. Several NLRP3 inflammasome inhibitors have been described, some of which show promise in the clinic. The present review will describe the structure and mechanisms of activation of the NLRP3 inflammasome, its association with various auto-immune and auto-inflammatory diseases, and the state of research into NLRP3 inflammasome inhibitors.
An Introduction to Computational Fluid Dynamics: The Finite Volume Method (1995)

*Introduction. *Conservation Laws of Fluid Motion and Boundary Conditions. *Turbulence and its Modelling. *The Finite Volume Method for Diffusion Problems. *The Finite Volume Method for Convection-Diffusion Problems. *Solution Algorithms for Pressure-Velocity Coupling in Steady Flows. *Solution of Discretised Equations. *The Finite Volume Method for Unsteady Flows. *Implementation of Boundary Conditions. *Advanced topics and applications. Appendices. References. Index.
Mapping of the monoclonal antibody W6/32: sensitivity to the amino terminus of β2‐microglobulin (1998)

The monoclonal antibody W6/32 is one of the most commonly used pan-HLA-ABC antibodies in studying human MHC I structure and function. We have discovered that the reactivity of W6/32 is absolutely sensitive to the amino terminus of human beta2-microglobulin (hbeta2m). Bacterially expressed recombinant forms of hbeta2m that have been extensively used in structural and biochemical studies of MHC I molecules often have an additional methionine at their amino terminus. Cell surface MHC I molecules reconstituted with allele-specific peptides and recombinant hbeta2m are reactive with various HLA-specific mAbs, but not W6/32. In contrast, cell surface HLA molecules reconstituted with peptide and native hbeta2m, which has no amino terminal methionine, are recognized by W6/32 as well as other HLA-specific mAbs. Thus, the specificity of W6/32 includes the amino terminus of hbeta2m.