Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation between Progressive Adsorption of Plasminogen to Blood Clots and Their Sensitivity to Lysis

Summary The binding of plasminogen to preformed human plasma clots immersed in citrated human plasma was measured and correlated with the sensitivity of these clots to lysis with recombinant tissuetype plasminogen activator (rt-PA), recombinant single-chain urokinase-type plasminogen activator (rscu-PA) or two chain urokinase-type plasminogen activator (tcu-PA, urokinase) When 0.15 ml plasma clots were compressed mechanically to about 1% of their original weight, and immersed in 0.15 ml plasma, 131I-labeled native plasminogen (Glu-plasminogen) adsorbed progressively from the plasma milieu onto the clot; binding was 3 ± l% (, - 10) after 1 h, 7 ± L% after 12h and 12 ± l% after 48 h. This was associated with an increased sensitivity of the clot to lysis; 50% clot lysis in 4 h was obtained with 65 ± 5 ng/ml (n= 3) rt-PA before and 30 ± 5 ng/ml (n = 3) after 48 h preincubation in plasma (p <p 0.01), with corresponding values of 660 ± 55 ng/ml (n = 3) and 280 125 ng/ml (n = 3) for rscu-PA, (p < 0.01), ind 800 ± 85 nglml (n = 3) and 270 ± 35 ngt ml (n = 3) for urokinase (p < 0.01). Additional binding of plasminogen and increased sensitivity to lysis were reduced or abolished when the clot was preincubated in plasminogendepteted or in t-PA-depleted plasma, of when 20 mM 6-aminohexanoic acid or 2,000 KIU/ml aprotinin were added. When 0.1- ml retracted whole blood clots were preincubated in 1- ml plasma, 50% clot lysis in 4h was obtained with 1,150 ± L60 ng/ml (n = 3) rt-PA before incubation and 55 ± 10 ng/ml (n = 3) after 48 h preincubation (p < 0.01), with corresponding values of 3,200 ± 430 ng/ml (n = 3) and 190 ± 30 ng/ml (n = 3) for rscu-PA (p < p0.01), and > 1,600 ng/ml and 220 ± 2A ng/ml (n = 3) for urokinase. These results show that preincubation of compressed plasma clots or retracted whole blood clots in plasma causes a progressive increase in both the binding of plasminogen and the sensitivity to lysis with plasminogen activators. Increased plasminogen binding may be the result of partial fibrindigestion.
Cwp2p, the plasma membrane receptor for Pichia membranifaciens killer toxin

PMKT is a channel‐forming killer toxin secreted by Pichia membranifaciens. To identify novel genes that mediate cellular resistance to PMKT we screened a collection of 288 deletion mutants. We found 29 open reading frames (ORFs) that, when deleted, confer resistance to PMKT. In addition, the deletion of 15 ORFs was observed to increase protoplast resistance, in agreement with the initial assumption that a plasma membrane receptor for PMKT exists. Whole cells and protoplasts of a cwp2Δ mutant were found to be completely resistant to PMKT and were unable to bind PMKT, indicating that Cwp2p interacts with it. A protein with a molecular mass of 11.7 kDa was purified from PMKT‐affinity columns. This protein was sequenced and identified as Cwp2p. Glycosylphosphatidylinositol (GPI) anchoring‐defective mutants were much less sensitive to PMKT, as were wild‐type protoplasts pretreated with phosphatidylinositol‐specific phospholipase C to remove GPI‐anchored proteins, indicating that the GPI‐anchored precursor of Cwp2p is also necessary for PMKT activity. Carboxyfluorescein‐entrapped liposomes containing a purified GFP–Cwp2p fusion protein in their membranes were much more sensitive to PMKT than protein‐free liposomes. Cwp2p and its GPI‐anchored precursor are proposed for the first time to be involved as PMKT secondary receptors.
The Effect of Etoricoxib on the Pharmacodynamics and Pharmacokinetics of Warfarin

The effects of etoricoxib on pharmacodynamic and pharmacokinetic parameters of warfarin were determined in healthy men and women. Subjects titrated with warfarin to an international normalized ratio for prothrombin time of 1.4 to 1.7 during a 28‐day prestudy period were randomly assigned in crossover fashion to be coadministered etoricoxib (120 mg) or matching placebo over two 21‐day continuous periods. On day 21, a 24‐hour pharmacokinetic profile of both S(−) and R(+) warfarin, as well as international normalized ratio values, were determined. Etoricoxib increased the international normalized ratio by 13% (90% confidence interval: 8%, 19%; P ≤.001). Etoricoxib had no effect on the pharmacokinetics of S(−) warfarin but led to a modest increase in the AUC24 h (∼10%) of R(+) warfarin. This increase in the international normalized ratio is not likely to be clinically important in most patients; however, the international normalized ratio of patients coadministered oral anticoagulants and etoricoxib should be closely monitored, particularly during initiation of therapy.
Magnetic-Field-Induced ELF Currents in a Human Body by the Use of a GSM Phone

A finite element method (FEM) with nonuniform mesh is employed for the calculation of extremely low frequency (ELF) currents induced in a human body by a global system for mobile communications (GSM) phone. The magnetic field of the phone is measured, and an equivalent source with magnetic dipoles is constructed for the numerical simulation. A cell of variable size is used in the simulation to accurately model the most important areas of the body model, namely areas close to the source and parts of the central nervous system. Three different mobile phone positions are considered: normal operation on the side of the head, breast pocket, and the small of the back where the spinal cord is close to the phone. Obtained results are compared with the guidelines of the International Commission on Non-Ionizing Radiation Protection (ICNIRP).
Head to head comparison of N-terminal proB-type natriuretic peptide and B-type natriuretic peptide in patients with / without left ventricular systolic dysfunction

Background: Human pro-B-type natriuretic peptide is cleaved into the active B-type natriuretic peptide (BNP) and the inactive fragment NTproBNP. It is unclear if, similar to BNP, NT-proBNP can be used as a marker of impaired left ventricular (LV) ejection fraction (EF). This study evaluated the analytical performance of both assays to detect LV systolic dysfunction. Methods: In 72 patients with various degrees of left ventricular systolic dysfunction (LVSD), blood analysis for BNP and NT-proBNP was performed prior to cardiac catheterization, using a point-of-care analyzer (Biosite) and a fully automated laboratory analyzer (Roche-Elecsys), respectively. The within-run and between-run imprecision for BNP and NT-proBNP was calculated. Results: Both markers were able to detect impaired LV EF with the largest area under the receiver-operating-characteristic curve for NTproBNP (NT-proBNP: 0.851 (0.747–0.924); BNP: 0.803 (0.692–0.887) 95% confidence interval; P = 0.07). A significant correlation was observed between BNP and NT-proBNP (r = 0.9; P < 0.0001). Estimating the within-run imprecision, the coefficient of variance for BNP was 3.14% (n = 20, mean 316 ng/L) to 3.32% (n = 20, mean 820 ng/L) and for NT-proBNP 0.9% (n = 20, mean 4390.8 ng/L) to 1.4% (n = 20, mean 225 ng/L). The between-run imprecision for NT-proBNP ranged between 2.1% (n = 20, mean 224.6 ng/L) and 2% (n = 20, mean 4391 ng/L). Optimal discriminator values for BNP and NT-proBNP were 139 ng/L and 358 ng/L, respectively. However, adjusting the BNP cut-off value to 54 ng/L improved the negative predictive value and sensitivity of the assay. Conclusion: Similar to BNP, NT-proBNP is a promising marker in identifying LVSD. Although both assays are reliable and have good analytical performance, their diagnostic cut-off value is dynamic and population-dependent. The slightly wider detection range and the more stable structure of NT-proBNP compared to the BNP assay suggest that NT-proBNP could play an additional role in the evaluation of patients with LV systolic dysfunction. © 2006 The Canadian Society of Clinical Chemists. All rights reserved.
Zebra finches exhibit speaker-independent phonetic perception of human speech

Humans readily distinguish spoken words that closely resemble each other in acoustic structure, irrespective of audible differences between individual voices or sex of the speakers. There is an ongoing debate about whether the ability to form phonetic categories that underlie such distinctions indicates the presence of uniquely evolved, speech-linked perceptual abilities, or is based on more general ones shared with other species. We demonstrate that zebra finches (Taeniopygia guttata) can discriminate and categorize monosyllabic words that differ in their vowel and transfer this categorization to the same words spoken by novel speakers independent of the sex of the voices. Our analysis indicates that the birds, like humans, use intrinsic and extrinsic speaker normalization to make the categorization. This finding shows that there is no need to invoke special mechanisms, evolved together with language, to explain this feature of speech perception.
First record of Ceratocystis fimbriata associated with shisham (Dalbergia sissoo) decline in Pakistan

Ceratocystis fimbriata has been associated with decline disorders of several fruit and forest trees. In 2006 this pathogen was isolated for the first time from declining mango trees in Pakistan. It has also recently been isolated from samples of declining shisham trees and pathogenicity tests have confirmed that it is indeed responsible for the decline disorders observed on shisham tress in Pakistan. This is the first record of C. fimbriata in association with shisham decline and the first time it is demonstrated to be the etiological agent of this important disease.
Prognostic signatures of breast cancer: Perou's molecular subtypes and Schmidt's metagenes

The search for biomarkers predicting metastasis-free survival or overall survival identified two key factors, namely estrogen receptor expression (Osborne et al., 1980) and the degree of proliferation (Gentili et al., 1981). However, a coherent picture did not emerge until the advent of gene array technology (Sorlie et al., 2001; Perou et al., 2000; Rouzier et al., 2005; review: Schmidt et al., 2009a). Several groups have identified sets of genes that are associated with increased risk of metastasis (van’t Veer et al., 2002; Wang et al., 2005; van de Vijver et al., 2002; Foekens et al., 2006). It has become clear that these genes mostly represent proliferation, estrogen receptor alpha (ESR1) and immune cell associated genes (Paik et al., 2004; Sotiriou et al., 2006; Oh et al., 2006; Fan et al., 2006; Desmedt et al., 2007; Schmidt et al., 2008). Two basic discoveries have particularly contributed to the current knowledge on how gene expression relates to prognosis:
Simulating the effect of capillary flux on the soil water balance in a stochastic ecohydrological framework

Groundwater uptake can play a major role in the survival of vegetation in semiarid areas, but this has not yet been included in an earlier developed ecohydrological stochastic framework. In this paper we provide a piecewise linear equation which includes capillary fluxes from shallow groundwater in the loss function of the ecohydrological stochastic model. The results indicate that this model is able to simulate the capillary fluxes, and the model also reflects the impact of the fluxes on the soil moisture balance. In addition, the results are analytically tractable and allow calculation of the probability density functions of soil water saturation and water stress for different groundwater depths below the root zone.
Human breast cancer susceptibility to paclitaxel therapy is independent of Bcl-2 expression.

In laboratory studies, ectopic overexpression of the antiapoptotic protein Bcl-2 has been shown to result in resistance to the cytotoxic effects of many chemotherapeutic drugs. Furthermore, posttranslational modification of moderately expressed endogenous Bcl-2 has been correlated with susceptibility to paclitaxel treatment in vitro. To determine whether tumor expression of Bcl-2 protein correlates with response and ultimate outcome in vivo, we quantified Bcl-2 expression by immunohistochemical analysis of archived biopsy specimens from metastatic breast cancer patients treated with single-agent paclitaxel. The statistical association between the degree of Bcl-2 expression, objective tumor response, and clinical outcome was then determined. In patients (n = 39) whose tumors had low (< or = 10% cells positive) Bcl-2 levels by immunohistochemical analysis, the overall response (complete response + partial response) rate was 21% versus an overall response rate of 22% in patients (n = 36) with high (>10% cells positive) Bcl-2 expression (P = 0.92). In patients with low Bcl-2 expression, the median time to progression was 126 days [95% confidence interval (CI), 63-160 days]. This was not significantly different than the 105 days for patients with high tumor Bcl-2 expression (95% CI, 84-214 days). The median survival time from initiation of paclitaxel therapy for patients with low Bcl-2 expression was 663 days (95% CI, 456-1119 days) and was not significantly different than the 450 days (95% CI, 239-1058 days) observed for patients with high Bcl-2 expression. In conclusion, we found that in metastatic breast cancer, there is no significant association between tumor Bcl-2 expression and response to paclitaxel, median time to progression, or survival, suggesting that the main mechanism of paclitaxelinduced cytotoxicity in breast tumors is independent of Bcl-2 expression.
The kuru infectious agent is a unique geographic isolate distinct from Creutzfeldt–Jakob disease and scrapie agents

Human sporadic Creutzfeldt–Jakob disease (sCJD), endemic sheep scrapie, and epidemic bovine spongiform encephalopathy (BSE) are caused by a related group of infectious agents. The new U.K. BSE agent spread to many species, including humans, and clarifying the origin, specificity, virulence, and diversity of these agents is critical, particularly because infected humans do not develop disease for many years. As with viruses, transmissible spongiform encephalopathy (TSE) agents can adapt to new species and become more virulent yet maintain fundamentally unique and stable identities. To make agent differences manifest, one must keep the host genotype constant. Many TSE agents have revealed their independent identities in normal mice. We transmitted primate kuru, a TSE once epidemic in New Guinea, to mice expressing normal and ≈8-fold higher levels of murine prion protein (PrP). High levels of murine PrP did not prevent infection but instead shortened incubation time, as would be expected for a viral receptor. Sporadic CJD and BSE agents and representative scrapie agents were clearly different from kuru in incubation time, brain neuropathology, and lymphoreticular involvement. Many TSE agents can infect monotypic cultured GT1 cells, and unlike sporadic CJD isolates, kuru rapidly and stably infected these cells. The geographic independence of the kuru agent provides additional reasons to explore causal environmental pathogens in these infectious neurodegenerative diseases.
A UDP-HexNAc:Polyprenol-P GalNAc-1-P Transferase (WecP) Representing a New Subgroup of the Enzyme Family

ABSTRACT The Aeromonas hydrophila AH-3 WecP represents a new class of UDP-HexNAc:polyprenol-P HexNAc-1-P transferases. These enzymes use a membrane-associated polyprenol phosphate acceptor (undecaprenyl phosphate [Und-P]) and a cytoplasmic UDP-d-N-acetylhexosamine sugar nucleotide as the donor substrate. Until now, all the WecA enzymes tested were able to transfer UDP-GlcNAc to the Und-P. In this study, we present in vitro and in vivo proofs that A. hydrophila AH-3 WecP transfers GalNAc to Und-P and is unable to transfer GlcNAc to the same enzyme substrate. The molecular topology of WecP is more similar to that of WbaP (UDP-Gal polyprenol-P transferase) than to that of WecA (UDP-GlcNAc polyprenol-P transferase). WecP is the first UDP-HexNAc:polyprenol-P GalNAc-1-P transferase described.
Hurricane initialization using airborne doppler radar data for WRF [presentation]

Landfalling hurricanes are one of the most dangerous disasters. Accurate prediction of their track and intensity are crucial for the protection of life and property. Although progress has been made in track forecasting during the past decade, intensity forecasting remains unsatisfactory. An acknowledged deficiency in all hurricane-forecast systems, including the most advanced Weather Research and Forecasting (WRF) model, is an improper initialization of the hurricane and its surrounding environment (Davis et al. 2007). Clearly, an improved vortex initialization, using advanced data assimilation techniques, would augment the skill of short-term forecasts (< 2 days) of the critical rain and wind features of tropical cyclones as they approach land.
Coherence loss by sample dynamics and heterogeneity in x-ray laser diffraction

In its most common implementations, single particle imaging with x-ray free-electron lasers (XFELs) assumes the perfect coherence of the diffracted x-rays. However, XFEL imaging is destructive and exhibits a reduction of coherence due to sample dynamics (radiation damage). Sample heterogeneity also manifests as effective loss of coherence in averaged data, which is increasingly encountered in the development of 3D XFEL imaging techniques. Here we review coherence loss in XFEL imaging experiments, which has focused primarily on femtosecond electronic dynamics. We present extensions of coherence theory to XFEL crystallography, ion diffusion, the Coulomb explosion of a single particle and to heterogeneity using a spherical model. In each case, we provide illustrative simulations of the effects of coherence loss and discuss when these effects will need to be taken into account.
Text S1: Quantification and images analysis of microscopy and of ABM simulation data

Removal of temporarily immotile cells: Analysis of the cell trajectories revealed several instances in which the fluorescent cells stop moving for extended periods of time (> 5 min). These data were removed from the trajectories. This was accomplished by identifying those cells for which the instant cell speed was < 0.2 μm/min (less than 5% of the average speed) for continuous time intervals of 5 min or longer and excluding these intervals from the motility statistics.
Gossip Based Prediction Market Simulation

In this paper I present a software tool for simulating a dynamic parimutuel market (DPM) based on an underlying model for the spread of information through a community. I use a standard gossip model for the information flow through the community. Typically these models are used to model network congestion, but I have taken a more literal interpretation of the “gossip”. The typical scenario for this simulation involves a rumor that spreads through the community; the rumor gives some information about the content of the DPM auction. When an individual hears the rumor, he will place a bet in the DPM in response to the content of the rumor. The prices of the assets in the DPM change according to the selected price function. The simulation tracks both the change in prices of the assets and the spread of the information through the community. At the end, the simulation ranks each of the individuals in order of influence on the community using a PageRank type metric. In the first section, I present a terse theoretical background on the primary components of the simulation: gossip models, DPM’s, and PageRank. Following the theory, I give detailed documentation of the simulation including where to access it and how to use it. In the third section, I give some typical experiments the simulation can perform. And in the final section, I give some preliminary conclusions and ideas for future work and development of the simulation.
Guidelines by an AD HOC European Committee for Elective Chronic Peritoneal Dialysis in Pediatric Patients

Correspondence to: A.R. Watson, Children & Young People’s Kidney Unit, Nottingham City Hospital, Hucknall Road, Nottingham NG5 1PB United Kingdom. watpaed@aol . com Received 15 August 2000; accepted 12 January 2001. a A. Edefonti, Clinica Pediatrica C and D de Marchi, University of Milan, Italy; M. Fischbach, Hôpital de Hautepierre, Strasbourg, France; G. Klaus, University of Marburg, Marburg, Germany; K. Ronnholm, University of Helsinki, Helsinki, Finland; C. Schröder, Wilhelmina Kinderziekenhuis, Utrecht, The Netherlands; E. Simkova, University Hospital Motol, Prague, Czech Republic; D. Stefanidis, A&P Kyriakou Children’s Hospital, Athens, Greece; A. Zurowska, Medical University of Gdansk, Gdansk, Poland; J. Vande Walle, University Hospital, Ghent, Belgium; F. Schaefer, University Hospital, Heidelberg, Germany; A. Alonso, Hospital Infantil La Paz, Madrid, Spain; V. Strazdins, University Hospital, Riga, Latvia. Chronic peritoneal dialysis (CPD) is the dialysis modality of choice in many European countries (1). It has enabled children of all ages, from neonates to young adults, to be successfully treated while awaiting the ultimate goal of renal transplantation. Since end-stage renal failure (ESRF) is comparatively rare in children, their care needs to be concentrated in designated tertiary-care centers. This is essential if children are to benefit from the support of an experienced multidisciplinary team. The European Paediatric Peritoneal Dialysis Working Group was established in 1999 by pediatric nephrologists with a major interest in peritoneal dialysis (PD). Currently, the group has representatives from 12 European countries. One of the functions of the group is to establish expert guidance in important clinical areas associated with PD, in conjunction with other members of the multidisciplinary team. The relatively small number of pediatric patients has resulted in few controlled comparative studies in CPD, but there are increasing numbers of reports of clinical experience based on cooperative work via registries. These guidelines were initiated and discussed at three meetings of the group and developed through eight drafts by email discussion with the principle authors, one of whom is a senior pediatric renal nurse (CG). They are opinion based, incorporating the cumulative clinical experience of the group members and relevant literature. These guidelines emphasize the importance of preparation of the child and family, the attention to detail to secure peritoneal access, and the importance of postinsertion catheter and exit-site care. Preparation for home PD should follow a proper training program, and the need for continuing support to the child and family at home is stressed.
Monoclonal Antibody Specific for TIRC7 Induces Donor‐specific Anergy and Prevents Rejection of Cardiac Allografts in Mice

T cell immune response c‐DNA (TIRC7) is up‐regulated during the early stages of T‐cell activation in response to alloantigens. In this study, we analyzed the effects of newly developed monoclonal antibodies (mAb) against TIRC7 in acute cardiac allograft rejection. Fully vascularized heterotopic allogeneic heart transplantation was performed in mice across a full‐mismatch barrier (C57Bl/10 into CBA). Recipients received seven injections (day 0–7) of a novel anti‐TIRC7 mAb or remained untreated. Graft survival, histology and ex vivo lymphocyte functions were tested. Targeting of TIRC7 with an anti‐TIRC7 mAb diminishes lymphocyte infiltration into grafts resulting in delay of morphological graft damage and prolongation of allograft survival. The lymphocytes from anti‐TIRC7 mAb‐treated animals exhibit hypo‐responsiveness without evidence of lymphocyte depletion against the donor allo‐antigens. Proliferation and expression of interferon‐γ (IFN‐γ) and tumor necrosis factor‐α (TNF‐α) were down‐regulated while interleukin‐4 (IL‐4) and IL‐10 expression were spared. Moreover, anti‐TIRC7 mAb enhanced up‐regulation of CTLA‐4 expression but suppressed up‐regulation of CD25 on stimulated lymphocytes in vitro and in vivo. Ligation of TIRC7 has important effects on the regulation of co‐stimulatory signaling pathways associated with suppressing of T‐cell activation. Targeting of TIRC7 may therefore provide a novel therapeutic approach for modulating T cell immune responses during organ transplantation.