Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrast medium-induced nephrotoxicity risk assessment in adult inpatients: a comparison of serum creatinine level- and estimated glomerular filtration rate-based screening methods.

PURPOSE To compare serum creatinine (SCr) level- and estimated glomerular filtration rate (eGFR)-based screening methods for identifying adult inpatients at risk for contrast medium-induced nephrotoxicity (CIN). MATERIALS AND METHODS Institutional review board approval was obtained; informed consent was waived for this HIPAA-compliant retrospective study. Computed tomographic examinations performed during 10 years in adult inpatients with stable renal function were identified (n = 28 390). The proportion of inpatients meeting various eGFR (≥60, <60, <45, <30, 30-44, 45-59 mL/min/1.73 m(2)) and SCr (<1.5, ≥1.5, ≥1.6, ≥1.7, ≥1.8, ≥1.9, ≥2.0 mg/dL) thresholds were contrasted with each other and with published guidelines (≥2.0 mg/dL [SCr] and <45 mL/min/1.73 m(2) [eGFR]) using McNemar and binomial tests. RESULTS Most inpatients were considered low risk for CIN with commonly used thresholds: 92.6% (26 285 of 28 390) had SCr <1.5 mg/dL; 91.3% (25 922 of 28 390) had eGFR of ≥45 mL/min/1.73 m(2). Using SCr threshold of ≥1.5 mg/dL, identified inpatients had the following eGFRs: 19.6% (413 of 2105), 45-59 mL/min/1.73 m(2); 51.1% (1075 of 2105), 30-44 mL/min/1.73 m(2); 28.6% (603 of 2105), <30 mL/min/1.73 m(2); and 0.7% (14 of 2105), ≥60 mL/min/1.73 m(2) . Using SCr threshold of ≥2.0 mg/dL, identified inpatients had the following eGFRs: 100% (658 of 658), <45 mL/min/1.73 m(2); 74.6% (491 of 658), <30 mL/min/1.73 m(2). Threshold of SCr ≥2.0 mg/dL could not be used to identify eGFR <30 mL/min/1.73 m(2) in 0.4% (112 of 28 390) and <45 mL/min/1.73 m(2) in 6.4% (1810 of 28 390) of all inpatients. Using eGFR <45 mL/min/1.73 m(2) instead of SCr of ≥1.5 mg/dL would result in a significant but small increase in identified inpatients (8.7% [2468 of 28 390; 95% confidence interval: 8.4%, 9.0%] vs 7.4% [2105 of 28 390; 95% confidence interval: 7.1%, 7.7%]; P < .0001). CONCLUSION Screening using eGFR <45 mL/min/1.73 m(2) instead of common SCr thresholds would significantly increase the number of inpatients identified to be at risk for CIN but would reduce misidentification of a large number of inpatients at low risk according to eGFR criteria.
Proteome reference maps of the Lotus japonicus nodule and root

Legume symbiosis with rhizobia results in the formation of a specialized organ, the root nodule, where atmospheric dinitrogen is reduced to ammonia. In Lotus japonicus (Lotus), several genes involved in nodule development or nodule function have been defined using biochemistry, genetic approaches, and high‐throughput transcriptomics. We have employed proteomics to further understand nodule development. Two developmental stages representing nodules prior to nitrogen fixation (white) and mature nitrogen fixing nodules (red) were compared with roots. In addition, the proteome of a spontaneous nodule formation mutant (snf1) was determined. From nodules and roots, 780 and 790 protein spots from 2D gels were identified and approximately 45% of the corresponding unique gene accessions were common. Including a previous proteomics set from Lotus pod and seed, the common gene accessions were decreased to 7%. Interestingly, an indication of more pronounced PTMs in nodules than in roots was determined. Between the two nodule developmental stages, higher levels of pathogen‐related 10 proteins, HSPs, and proteins involved in redox processes were found in white nodules, suggesting a higher stress level at this developmental stage. In contrast, protein spots corresponding to nodulins such as leghemoglobin, asparagine synthetase, sucrose synthase, and glutamine synthetase were prevalent in red nodules. The distinct biochemical state of nodules was further highlighted by the conspicuous presence of several nitrilases, ascorbate metabolic enzymes, and putative rhizobial effectors.
Simple and Effective Parameter Tuning for Domain Adaptation of Statistical Machine Translation

Current state-of-the-art Statistical Machine Translation systems are based on log-linear models that combine a set of feature functions to score translation hypotheses during decoding. The models are parametrized by a vector of weights usually optimized on a set of sentences and their reference translations, called development data. In this paper, we explore a (common and industry relevant) scenario where a system trained and tuned on general domain data needs to be adapted to a specific domain for which no or only very limited in-domain bilingual data is available. It turns out that such systems can be adapted successfully by re-tuning model parameters using surprisingly small amounts of parallel in-domain data, by cross-tuning or no tuning at all. We show in detail how and why this is effective, compare the approaches and effort involved. We also study the effect of system hyperparameters (such as maximum phrase length and development data size) and their optimal values in this scenario.
Author ' s personal copy NERVE GROWTH FACTOR AND ITS RECEPTORS TrkA AND p 75 ARE UPREGULATED IN THE BRAIN OF mdx DYSTROPHIC MOUSE

Increased angiogenesis and an altered blood– brain barrier have been reported in the brain of dystrophindeficient mdx mouse, an experimental model of Duchenne muscular dystrophy. To further elucidate the mechanisms underlying angiogenesis in Duchenne muscular dystrophy, in this study we evaluated whether nerve growth factor (NGF) and nerve growth factor receptors (NGFRs) are involved, then correlated NGF-NGFRs expression with vascular endothelial growth factor (VEGF) and its receptor-2 (VEGFR-2) content and matrix metalloproteinases-2 and -9 (MMP-2 and -9) activity, by confocal laser microscopy and immunohistochemistry. Results showed that neurons, astrocytes and ependymal cells were strongly labeled by NGF in mdx brain, expressing NGFRs on glial and endothelial cells. In controls, NGF faintly labeled neurons and astrocytes, whereas endothelial cells were negative for NGFRs. Immunogold electron microscopy demonstrated NGFR gold particles on endothelial cells in mdx brain, while in controls few particles were recognizable only on glial end feet. Western blotting and real time polymerase chain reaction (RT-PCR) demonstrated a higher expression of NGF and NGFR mRNA and protein in mdx brain as compared to controls, and increase of VEGF-VEGFR-2 and active MMP-2 and -9 content. Overall, these data suggest that in the brain of mdx mice, an upregulation of the NGF-NGFRs system might be involved directly, or indirectly through the activation of VEGF-VEGFR-2 and MMP-2 and -9, in the angiogenic response taking place in this pathological condition. © 2009 IBRO. Published by Elsevier Ltd. All rights reserved.
Probing Peptide and Protein Insertion in a Biomimetic S-Layer Supported Lipid Membrane Platform

The most important aspect of synthetic lipid membrane architectures is their ability to study functional membrane-active peptides and membrane proteins in an environment close to nature. Here, we report on the generation and performance of a biomimetic platform, the S-layer supported lipid membrane (SsLM), to investigate the structural and electrical characteristics of the membrane-active peptide gramicidin and the transmembrane protein α-hemolysin in real-time using a quartz crystal microbalance with dissipation monitoring in combination with electrochemical impedance spectroscopy. A shift in membrane resistance is caused by the interaction of α-hemolysin and gramicidin with SsLMs, even if only an attachment onto, or functional channels through the lipid membrane, respectively, are formed. Moreover, the obtained results did not indicate the formation of functional α-hemolysin pores, but evidence for functional incorporation of gramicidin into this biomimetic architecture is provided.
An optimal value of multi-threshold in the bandwidth reservation scheme of integrated services over wireless networks

Provisioning of guaranteed Quality of Service (QoS) in next generation cellular networks has become a great challenge specially, when the wireless access networks have been used to deliver the multimedia services. Call Admission Control (CAC) is one of the most important components of Radio Resource Management (RRM) that affects the provided bandwidth utilization efficiency and QoS guarantees. In this paper, a multi-threshold bandwidth reservation scheme is proposed to provide an acceptable solution for the trade-off between new call blocking and handoff call dropping probabilities. The major objective of this paper is to find the optimal values of the bandwidth thresholds'. In addition, the total cost function and loss probabilities were adopted to fulfill the requirements of bandwidth management in wireless environments. The proposed scheme is modelled by deploying a two-dimensional Markov process to evaluate the system performance. Throughout this work, a detailed numerical investigation for the optimal thresholds is conducted.
Atoms and molecules in intense laser fields: gauge invariance of theory and models

Gauge invariance was discovered in the development of classical electromagnetism and was required when the latter was formulated in terms of the scalar and vector potentials. It is now considered to be a fundamental principle of nature, stating that different forms of these potentials yield the same physical description: they describe the same electromagnetic field as long as they are related to each other by gauge transformations. Gauge invariance can also be included into the quantum description of matter interacting with an electromagnetic field by assuming that the wavefunction transforms under a given local unitary transformation. The result of this procedure is a quantum theory describing the coupling of electrons, nuclei and photons. Therefore, it is a very important concept: it is used in almost every field of physics and it has been generalized to describe electroweak and strong interactions in the standard model of particles. A review of quantum mechanical gauge invariance and general unitary transformations is presented for atoms and molecules in interaction with intense short laser pulses, spanning the perturbative to highly nonlinear non-perturbative interaction regimes. Various unitary transformations for a single spinless particle time-dependent Schrödinger equation (TDSE) are shown to correspond to different time-dependent Hamiltonians and wavefunctions. Accuracy of approximation methods involved in solutions of TDSEs such as perturbation theory and popular numerical methods depend on gauge or representation choices which can be more convenient due to faster convergence criteria. We focus on three main representations: length and velocity gauges, in addition to the acceleration form which is not a gauge, to describe perturbative and non-perturbative radiative interactions. Numerical schemes for solving TDSEs in different representations are also discussed. A final brief discussion of these issues for the relativistic time-dependent Dirac equation for future super-intense laser field problems is presented.
Are Plants Able to Utilize Nitrogen Released from Thawing Permafrost? Implications for Carbon Cycling and Feedback with the Climate System

ARE PLANTS ABLE TO UTILIZE NITROGEN RELEASED FROM THAWING PERMAFROST? IMPLICATIONS FOR CARBON CYCLING AND FEEDBACK WITH THE CLIMATE SYSTEM by Lucas Jacob Albano Advisor: University of Guelph, 2018 Dr. Merritt Turetsky Climate warming in high-latitude regions triggers widespread permafrost thaw, releasing massive amounts of carbon and nitrogen that were previously frozen in soil organic matter, through increased microbial activity. Climate warming has motivated extensive research on permafrost carbon release; however, fewer studies have addressed whether plants can access new nitrogen sources, potentially increasing primary productivity. Two research questions were explored using Carex aquatilis in sites experiencing thaw and thermokarst in interior Alaska: 1) does C. aquatilis ammonium uptake vary with depth and time-since-thaw; 2) does variation in C. aquatilis growth characteristics and ammonium uptake correlate with aboveground primary production? An ammonium uptake experiment was conducted on C. aquatilis roots, determining that deep roots took up equal if not greater amounts of ammonium than shallow roots. I also found that rooting depth was positively correlated with aboveground biomass, providing a plausible mechanism for increased N uptake post-thaw to impact aboveground plant productivity.
Gravitational Collapse of Filamentary Magnetized Molecular Clouds

We develop models for the self-similar collapse of magnetized isothermal cylinders. We find solutions for the case of a fluid with a constant toroidal flux-to-mass ratio (Γϕ = constant) and the case of a fluid with a constant gas to magnetic pressure ratio (β = constant). In both cases, we find that a low magnetization results in density profiles that behave as ρ ∝ r-4 at large radii, and at high magnetization we find density profiles that behave as ρ ∝ r-2. This density behavior is the same as for hydrostatic filamentary structures, suggesting that density measurements alone cannot distinguish between hydrostatic and collapsing filaments—velocity measurements are required. Our solutions show that the self-similar radial velocity behaves as vr ∝ r during the collapse phase, and that unlike collapsing self-similar spheres, there is no subsequent accretion (i.e., expansion-wave) phase. We also examine the fragmentation properties of these cylinders and find that in both cases, the presence of a toroidal field acts to strengthen the cylinder against fragmentation. Finally, the collapse timescales in our models are shorter than the fragmentation timescales. Thus, we anticipate that highly collapsed filaments can form before they are broken into pieces by gravitational fragmentation.
Multiple-frequency tomography of the upper mantle beneath the African/Iberian collision zone

During the Cenozoic, the geodynamics of the western Mediterranean domain has been characterized by a complex history of subduction of Mesozoic oceanic lithosphere. The final stage of these processes is proposed to have led to the development of the Calabria and Gibraltar arcs, whose formation is still under debate. In this study, we take advantage of the dense broad-band station networks now available in the Alboran Sea region, to develop a high-resolution 3-D tomographic P velocity model of the upper mantle beneath the African/Iberian collision zone that will better constraint the past dynamics of this zone. The model is based on 13200 teleseismic arrival times recorded between 2008 and 2012 at 279 stations for which cross-correlation delays are measured with a new technique in different frequency bands centred between 0.03 and 1.0 Hz, and for the first time interpreted using multiple frequency tomography. Our model shows, beneath the Alboran Sea, a strong (4 per cent) fast vertically dipping anomaly observed to at least 650 km depth. The arched shape of this anomaly, and its extent at depth, are coherent with a lithospheric slab, thus favouring the hypothesis of a westward consumption of the Ligurian ocean slab by roll-back during Cenozoic. In addition to this fast anomaly in the deep upper mantle, high intensity slow anomalies are widespread in the lithosphere and asthenosphere beneath Morocco and southern Spain. These anomalies are correlated at the surface with the position of the Rif and Atlas orogens and with Cenozoic volcanic fields. We thus confirm the presence, beneath Morocco, of an anomalous (hot? ) upper mantle, but without clear indication for a lateral spreading of the Canary plume to the east.
Chemoprevention by perillyl alcohol coupled with viral gene therapy reduces pancreatic cancer pathogenesis

Pancreatic cancer is one of the deadliest of cancers. Even with aggressive therapy, the 5-year survival rate is <5%, mandating development of more effective treatments. Melanoma differentiation–associated gene-7/interleukin-24 (mda-7/IL-24) shows potent antitumor activity against most cancers displaying safety with significant clinical efficacy. However, pancreatic cancer cells display inherent resistance to mda-7/IL-24 that is the result of a “protein translational block” of mda-7/IL-24 mRNA in these tumor cells. We now show that a dietary supplement perillyl alcohol (POH) has significant chemopreventive effects for pancreatic cancer and, when coupled with adenovirus-mediated mda-7/IL-24 gene therapy (Ad.mda-7), effectively eliminates s.c. and i.p. xenografts of human pancreatic cancer cells in nude mice, promoting enhanced survival. The combination of POH and Ad.mda-7 efficiently abrogates the mda-7/IL-24 protein translational block, resulting in MDA-7/IL-24 protein production and growth suppression. Of direct translational relevance, clinically achievable concentrations of POH with Ad.mda-7, both of which have been found safe and without toxic effects in human trials, were used. This novel and innovative approach combining a dietary agent and a virally delivered therapeutic cytokine provides a means of both preventing and treating human pancreatic cancer with significant clinical translational potential. [Mol Cancer Ther 2008;7(7):2042–50]
Inhibition of Src Kinases Combined with CD40 Ligand Blockade Prolongs Murine Cardiac Allograft Survival

Background. Members of the Src family of tyrosine kinases (SFKs) are requisite signaling molecules activated by multiple receptors during immune responses. Their expression and catalytic activity has not been characterized in allograft rejection in vivo. Methods. We measured expression and catalytic activity of SFKs in MHC- mismatched murine cardiac allografts. We also examined the effects of a Src inhibitor (CGP77675) with or without anti-CD154 mAb on graft survival, histology, and expression and catalytic activity of SFKs within the grafts. Results. In acutely rejecting allografts from untreated controls, total activity of Hck and Lyn increased 10-fold, predominantly reflecting increases in the amount of protein. Total activity of Lck increased only fourfold, reflecting small changes in both the amount of protein and specific activity. One dose of anti-CD154 plus CGP77675 markedly diminished cellular infiltration, but survival was only moderately prolonged despite inhibition of all SFKs in the rejected grafts. Two doses of anti-CD154 plus CGP77675 allowed permanent graft acceptance in 60% of recipients even after discontinuation of the inhibitor. Both rejected and long surviving grafts showed increased activity of all SFKs. Recipients that rejected their grafts showed serum alloantibody production, and grafts rejected during treatment demonstrated deposition of complement indicating the contribution of antibody to rejection. Conclusions. The myeloid and B cell Src family kinases, Hck and Lyn, rather than the T cell Src kinase Lck, show the greatest increase in expression and total activity in rejecting allografts. Both rejected and long-surviving grafts show significant increases in SFK expression and acitivity.
Prediction of Pharmacokinetics and Penetration of Moxifloxacin in Human with Intra-Abdominal Infection Based on Extrapolated PBPK Model

The aim of this study is to develop a physiologically based pharmacokinetic (PBPK) model in intra-abdominal infected rats, and extrapolate it to human to predict moxifloxacin pharmacokinetics profiles in various tissues in intra-abdominal infected human. 12 male rats with intra-abdominal infections, induced by Escherichia coli, received a single dose of 40 mg/kg body weight of moxifloxacin. Blood plasma was collected at 5, 10, 20, 30, 60, 120, 240, 480, 1440 min after drug injection. A PBPK model was developed in rats and extrapolated to human using GastroPlus software. The predictions were assessed by comparing predictions and observations. In the plasma concentration versus time profile of moxifloxcinin rats, Cmax was 11.151 µg/mL at 5 min after the intravenous injection and t1/2 was 2.936 h. Plasma concentration and kinetics in human were predicted and compared with observed datas. Moxifloxacin penetrated and accumulated with high concentrations in redmarrow, lung, skin, heart, liver, kidney, spleen, muscle tissues in human with intra-abdominal infection. The predicted tissue to plasma concentration ratios in abdominal viscera were between 1.1 and 2.2. When rat plasma concentrations were known, extrapolation of a PBPK model was a method to predict drug pharmacokinetics and penetration in human. Moxifloxacin has a good penetration into liver, kidney, spleen, as well as other tissues in intra-abdominal infected human. Close monitoring are necessary when using moxifloxacin due to its high concentration distribution. This pathological model extrapolation may provide reference to the PK/PD study of antibacterial agents.
Extended Locality Preserving Discriminant Analysis for Face Recognition

In this paper, an extended locality preserving discriminant analysis (ELPDA) method is proposed. To address the disadvantages of original locality preserving discriminant analysis (LPDA), a new locality preserving between-class scatter, which is characterized by samples and the corresponding k out-class nearest neighbors, is defined. Moreover, the small sample size problem is also avoided by solving a new optimization function. Experimental results on AR and FERET subsets illustrate the effectiveness of the proposed method for face recognition.
Computational modelling of evaporative cooling as a climate change adaptation measure at the spatial scale of buildings and streets

Knowledge of the pressure distribution on building walls is important for the evaluation of wind loads and natural ventilation. Wind-induced pressure distributions are influenced by a wide range of factors including approach-flow conditions, urban surroundings and building geometry. Computational Fluid Dynamics (CFD) can be a valuable tool for determining mean wind pressure coefficients on building facades. However, while many CFD studies of mean wind pressure on buildings have been performed in the past, the vast majority of these studies focused on simple building geometries without facade details such as balconies. These details however can drastically influence the flow pattern and the overall pressure distribution on the facade. This paper presents a systematic evaluation of 3D steady Reynolds-Averaged Navier-Stokes (RANS) CFD for predicting mean wind pressure distributions on windward and leeward surfaces of a medium-rise building with and without balconies. The evaluation is based on a gridsensitivity analysis and on validation with wind-tunnel measurements. It is shown that building balconies can lead to very strong changes in wind pressure distribution, because they introduce multiple areas of flow separation and recirculation across the facade. The results show that steady RANS, in spite of its limitations, can accurately reproduce the mean wind pressure distribution across the windward facade of the building. The average deviations from the wind-tunnel measurements are 12% and 10% for the building with and without balconies, respectively. In addition, also the important impact of the reference static pressure and the turbulence model are demonstrated.