Miracle-dz/UniFAR-FTUs huggingface dataset:
Current equations estimating glomerular filtration rate in primary care: Comparison and determinants

Abstract Objective. The aims of this study were to compare estimated glomerular filtration rate (eGFR) by Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations, to assess the classification of chronic kidney disease (CKD) stages by both equations, and to identify factors associated with differences between both equations in patients with or at high risk of CKD managed in primary care. Material and methods. This was an observational study of 803 patients with CKD, long-standing, severe hypertension and diabetes exclusively managed in primary care. Bias and precision between the two equations used to calculate eGFR were quantified as proposed by Bland and Altman. Results. In 1534 eGFR calculations, mean eGFRMDRD was 0.8 ± 3.6 ml/min/1.73 m2 higher than eGFRCKD-EPI. Precision between the two equations was ±7.1 ml/min/1.73 m2. Classification of CKD stages by MDRD or CKD-EPI equations agreed in 93.3% of cases. Age above 70 years, eGFR below 60 and above 120 ml/min/1.73 m2 were associated with higher eGFRMDRD values; and age below 50 years and inadequately controlled hypertension with higher eGFRCKD-EPI values. Conclusions. Comparison of eGFR calculated by MDRD and CKD-EPI equations demonstrated no clinically relevant difference. In addition, CKD classification by both equations agreed highly. As both equations performed equally well, the simpler and more established MDRD equation should be preferred in patients with or at high risk of CKD managed in primary care. Patients' characteristics seem to account for previously reported differences in the performance of CKD-EPI and MDRD equations.
Evaluation of a model for maximizing interprofessional education in an acute hospital

Summary A one-year planning phase established a rolling programme of bi-monthly interprofessional clinical teaching workshops derived directly from patient experiences in an acute hospital. Pre-registration healthcare students from 8 professions spent an afternoon in the hospital training centre, randomly allocated to one of 6 – 8 small working groups. Using a problem-based methodology they analysed a ward case with patient consent, chosen to reflect the input of a wide range of health professionals. Students worked through a prepared workbook facilitated by a range of tutors from all disciplines. Each small group reported back on one aspect of team working to the entire cohort entering into debate and discussion with the support of clinical and academic tutors. Post course patient details were found on a website enabling students to progress their uni-professional knowledge, e.g., on anatomy, physiology, pharmacology etc. The questionnaire evaluation on over 126 students and 11 tutors identified that interprofessional competencies were understood and valued. Students related principles of team working and collaborative practice to their placement experiences of team work. Interactive learning enables further appreciation of professions roles and responsibilities and the importance of teamwork to optimize patient care (82.0 – 90.5%). The half-day learning model can be easily supported by busy clinical staff, led by hospital educators and accessed by students on hospital placements, at a mid-point in training, with learning supported by consenting in-patients or recent admissions prepared to share their experiences.
Fast Object Class Recognition

We propose a novel approach for object class recognition using scale invariant features and Gaussian Processes as our kernel-based classifier. We measure the performance of this approach in two stages: predicting the presence of a class of objects in images and localizing them. Our object class recognition method is comparable to other state-of-the-art approaches. Furthermore, we propose sophisticated numerical methods for reducing the computational cost of Gaussian Processes. Speed-ups are achieved using Krylov Subspace and Dual-Tree methods. We also reduced the storage requirement from O(M 2) to O(M). We trained and tested our algorithms on the PASCAL collection of images, which is a common database in this research area.
Implementing the Davis-Putnam Algorithm by Tries

The Davis-Putnam method is one of the major practical methods for the satiss-ability (SAT) problem of propositional logic. We show how to implement the Davis-Putnam method eeciently using the trie data structure for propositional clauses by presenting seven implementations of the method. We propose a new technique for implementing unit propagation whose complexity is sublinear to the number of occurrences of the variable in the input. We present the performance of our programs on some quasigroup problems. The eeciency of our programs allowed us to solve some open quasigroup problems.
An Empirical Evaluation of Pronoun Resolution and Clausal Structure

This paper presents an automated empirical evaluation of the relationship between clausal structure and pronominal reference. Past work has theorized that incorporating discourse structure can constrain the search space in the resolution of pronouns since discourse segments, and thus potential antecedents, can be made inaccessible as the discourse progresses and the focus changes. However, very little empirical work has been done to evaluate these claims. In this study, we develop an automated system and use a corpus annotated for RST and coreference to test whether basic formulations of these claims hold. In particular, we develop and evaluate two pronoun resolution algorithms that incorporate clausal and discourse structure. The first is based on Grosz and Sidner’s theory of discourse structure and the second is based on Cristea et al.’s Veins Theory. Our results show that incorporating basic clausal structure does not improve performance.
Identification of an Abbreviated Test Battery for Detection of HIV-Associated Neurocognitive Impairment in an Early-Managed HIV-Infected Cohort

Background HIV-associated neurocognitive disorders (HAND) remain prevalent despite improved antiretroviral treatment (ART), and it is essential to have a sensitive and specific HAND screening tool. Methods Participants were 200 HIV-infected US military beneficiaries, managed early in the course of HIV infection, had few comorbidities, and had open access to ART. Participants completed a comprehensive, seven-domain (16-test), neuropsychological battery (∼120 min); neurocognitive impairment (NCI) was determined using a standardized score derived from demographically adjusted T-scores (global deficit score ≥0.5). Restricting the estimated administration time of the screening battery to < = 20 minutes, we examined the sensitivity and specificity of detecting NCI for all possible combinations of 2-, 3-, and 4- tests from the comprehensive battery. Results Participants were relatively healthy (median CD4 count: 546 cells/mm3) with 64% receiving ART. Prevalence of NCI was low (19%). The best 2-test screener included the Stroop Color Test and the Hopkins Verbal Learning Test-Revised (11 min; sensitivity = 73%; specificity = 83%); the best 3-test screener included the above measures plus the Paced Auditory Serial Addition Test (PASAT; 16 min; sensitivity = 86%; specificity = 75%). The addition of Action Fluency to the above three tests improved specificity (18 min; sensitivity = 86%; specificity = 87%). Conclusions Combinations of widely accepted neuropsychological tests with brief implementation time demonstrated good sensitivity and specificity compared to a time intensive neuropsychological test battery. Tests of verbal learning, attention/working memory, and processing speed are particularly useful in detecting NCI. Utilizing validated, easy to administer, traditional neuropsychological tests with established normative data may represent an excellent approach to screening for NCI in HIV.
Observability properties of a semi-discrete 1d wave equation derived from a mixed finite element method on nonuniform meshes

The goal of this article is to analyze the observability properties for a space semi-discrete approximation scheme derived from a mixed finite element method of the 1d wave equation on nonuni- form meshes. More precisely, we prove that observability properties hold uniformly with respect to the mesh-size under some assumptions, which, roughly, measures the lack of uniformity of the meshes, thus extending the work (Castro and Micu, Numer. Math. 102 (2006) 413-462) to nonuniform meshes. Our results are based on a precise description of the spectrum of the discrete approximation schemes on nonuniform meshes, and the use of Ingham's inequality. We also mention applications to the boundary null controllability of the 1d wave equation, and to stabilization properties for the 1d wave equation. We finally present some applications for the corresponding fully discrete schemes, based on recent articles by the author.
Systematic genomic and translational efficiency studies of uveal melanoma

To further our understanding of the somatic genetic basis of uveal melanoma, we sequenced the protein-coding regions of 52 primary tumors and 3 liver metastases together with paired normal DNA. Known recurrent mutations were identified in GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. The role of mutated EIF1AX was tested using loss of function approaches including viability and translational efficiency assays. Knockdown of both wild type and mutant EIF1AX was lethal to uveal melanoma cells. We probed the function of N-terminal tail EIF1AX mutations by performing RNA sequencing of polysome-associated transcripts in cells expressing endogenous wild type or mutant EIF1AX. Ribosome occupancy of the global translational apparatus was sensitive to suppression of wild type but not mutant EIF1AX. Together, these studies suggest that cells expressing mutant EIF1AX may exhibit aberrant translational regulation, which may provide clonal selective advantage in the subset of uveal melanoma that harbors this mutation.
The pochoir stencil compiler

A stencil computation repeatedly updates each point of a d-dimensional grid as a function of itself and its near neighbors. Parallel cache-efficient stencil algorithms based on "trapezoidal decompositions" are known, but most programmers find them difficult to write. The Pochoir stencil compiler allows a programmer to write a simple specification of a stencil in a domain-specific stencil language embedded in C++ which the Pochoir compiler then translates into high-performing Cilk code that employs an efficient parallel cache-oblivious algorithm. Pochoir supports general d-dimensional stencils and handles both periodic and aperiodic boundary conditions in one unified algorithm. The Pochoir system provides a C++ template library that allows the user's stencil specification to be executed directly in C++ without the Pochoir compiler (albeit more slowly), which simplifies user debugging and greatly simplified the implementation of the Pochoir compiler itself. A host of stencil benchmarks run on a modern multicore machine demonstrates that Pochoir outperforms standard parallelloop implementations, typically running 2-10 times faster. The algorithm behind Pochoir improves on prior cache-efficient algorithms on multidimensional grids by making "hyperspace" cuts, which yield asymptotically more parallelism for the same cache efficiency.
Scalable Anonymous Group Communication in the Anytrust Model

Anonymous communication capabilities are useful and desirable, but practical onion routing approaches are vulnerable to traffic analysisand DoS attacks—especially againsta powerful adversary, such as a repressive government or compromised ISP. To fill this gap we introduce D3, the first practical anonymous group communication system offering anonymity and disruption resistance against strong traffic analysis and collusion attacks, with scalability to hundreds of group members and quick response to churn. D3 builds on a trust model we call anytrust. Anytrust is a decentralized client/server network model, in which each of many clients—representing group members—trust only that at least one of a smaller but diverse set of “servers” or “super-peers” behaves honestly, but clients need not know which server to trust. By combining and adapting verifiable shuffle and DC-nets techniques to anytrust, D3 achieves short shuffle latencies and efficient tree-based DC-nets ciphertext combining, while guaranteeing message anonymity and integrity, transmission proportionality among group members, and adaptability to both network/node failures and active disruption. Experiments with a working prototype demonstrate that D3 is practical at scales infeasible in prior systems offering comparable security.
Antibody-Directed Phototherapy (ADP)

Photodynamic therapy (PDT) is a clinically-approved but rather under-exploited treatment modality for cancer and pre-cancerous superficial lesions. It utilises a cold laser or LED to activate a photochemical reaction between a light activated drug (photosensitiser-drug) and oxygen to generate cytotoxic oxygen species. These free radical species damage cellular components leading to cell death. Despite its benefits, the complexity, limited potency and side effects of PDT have led to poor general usage. However, the research area is very active with an increasing understanding of PDT-related cell biology, photophysics and significant progress in molecular targeting of disease. Monoclonal antibody therapy is maturing and the next wave of antibody therapies includes antibody-drug conjugates (ADCs), which promise to be more potent and curable. These developments could lift antibody-directed phototherapy (ADP) to success. ADP promises to increase specificity and potency and improve drug pharmacokinetics, thus delivering better PDT drugs whilst retaining its other benefits. Whole antibody conjugates with first generation ADP-drugs displayed problems with aggregation, poor pharmacokinetics and loss of immuno-reactivity. However, these early ADP-drugs still showed improved selectivity and potency. Improved PS-drug chemistry and a variety of conjugation strategies have led to improved ADP-drugs with retained antibody and PS-drug function. More recently, recombinant antibody fragments have been used to deliver ADP-drugs with superior drug loading, more favourable pharmacokinetics, enhanced potency and target cell selectivity. These improvements offer a promise of better quality PDT drugs.
Determination of the extracellular lipases of Pseudomonas fluorescens spp. in skim milk with the β-naphthyl caprylate assay

SUMMARY A method based on the hydrolysis of β-naphthyl caprylate (β-NC) has been developed for quantitating extracellular lipase from Pseudomonas fluorescens. The assay was extremely sensitive to skim milk (SM); as little as 0·02 ml raw SM in a 2·0 ml reaction mixture resulted in an apparent loss of 50% of the lipase activity. Activity improved 3-fold when trypsin (50 μg/ml) was included in the reaction mixture. When super-simplex optimization was used to determine the optimum levels of β-NC, Na taurocholate (NaTC), SM/lipase mixture and trypsin for maximum activity, NaTC was found to be unnecessary for activity. Subsequent addition of 15 mM-NaTC resulted in 80% loss of activity. On the other hand, NaTC was required for native lipase activity in the presence of SM. Native lipase was completely inhibited by heating at 70 °C for 2 min, while B52 lipase retained 75% of its activity under the same conditions. The assay was able to detect lipase produced by Ps. fluorescens B52 in SM at 5 °C when the cell density exceeded 108 colony forming units/ml. The presence of butterfat (3°5%) in the SM assay inhibited B52 lipase by 97%. The β-NC assay gave results comparable to the tributyrin agar diffusion assay using cell-free extracts of ten strains of common dairy psychrotrophs. The results suggest that the β-NC assay may be useful for determining lipase activity in raw SM.
Spatiotemporal dynamics of guanosine 3′,5′-cyclic monophosphate revealed by a genetically encoded, fluorescent indicator

To investigate the dynamics of guanosine 3′,5′-cyclic monophosphate (cGMP) in single living cells, we constructed genetically encoded, fluorescent cGMP indicators by bracketing cGMP-dependent protein kinase (cGPK), minus residues 1–77, between cyan and yellow mutants of green fluorescent protein. cGMP decreased fluorescence resonance energy transfer (FRET) and increased the ratio of cyan to yellow emissions by up to 1.5-fold with apparent dissociation constants of ≈2 μM and >100:1 selectivity for cGMP over cAMP. To eliminate constitutive kinase activity, Thr516 of cGPK was mutated to Ala. Emission ratio imaging of the indicators transfected into rat fetal lung fibroblast (RFL)-6 showed cGMP transients resulting from activation of soluble and particulate guanylyl cyclase, respectively, by nitric oxide (NO) and C-type natriuretic peptide (CNP). Whereas all naive cells tested responded to CNP, only 68% responded to NO. Both sets of signals showed large and variable (0.5–4 min) latencies. The phosphodiesterase (PDE) inhibitor 3-isobutyl-1-methylxanthine (IBMX) did not elevate cGMP on its own but consistently amplified responses to NO or CNP, suggesting that basal activity of guanylate cyclase is very low and emphasizing the importance of PDEs in cGMP recycling. A fraction of RFL cells showed slowly propagating tides of cGMP spreading across the cell in response to delocalized application of NO. Biolistically transfected Purkinje neurons showed cGMP responses to parallel fiber activity and NO donors, confirming that single-cell increases in cGMP occur under conditions appropriate to cause synaptic plasticity.
Forensic Conception: DNA typing of FTA Spotted Samples -

Article history: Received on: 23/06/2014 Revised on: 26/07/2014 Accepted on: 10/08/2014 Available online: 27/08/2014 Forensic labs globally face the same problem growing need to process a greater number and wider variety of samples for DNA analysis.DNA purification step has been thought to be essential for typing of STR DNA. However, this process is time-consuming, and there is a risk of unexpected cross-contamination during purification. There is a need, for each sample type, to develop new methodology that is not only faster but also more reliable than past procedures. FTA technologies provides use most reliable method for DNA extraction.FTA is a chemical treatment of paper, unique to Whatman Bioscience, and is used for the stabilization and storage of biological samples. The FTA matrix is chemically treated with proprietary reagents that lyse cells upon contact. FTA cards protect nucleic acids from nucleases, oxidation, UV damage and microbial and fungal attack. In forensic laboratory there is a need of such a method by which DNA can be extracted by simple method in less time. Here, the method is modified for semen and saliva samples for extraction of DNA on FTA classic cards for forensic use. All the samples were collected only on FTA Classic cards. After DNA extraction, amplification of DNA was carried out then the amplified DNA was placed into DNA sequencer for STR profiling. STR peaks were obtained from the all biological samples such as Blood, Saliva and Semen in our study thus there is no need of other kits available for collection of samples. On the basis of results, it is considered that modified procedure using an FTA card can be applicable to routine work.
Effectiveness of Calcium Deficiency in Nanosized Hydroxyapatite for Removal of Fe(II), Cu(II), Ni(II) and Cr(VI) Ions from Aqueous Solutions

In this work, nanosized calcium deficient hydroxyapatite (nCDHA) was synthesized by the precipitation method, and then utilized as an adsorbent for removal of Fe (II), Cu (II), Ni (II) and Cr (VI) ions from aqueous solutions after characterizing it by various techniques as scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDX) and BET method. A possible structure of synthesized nCDHA was proposed. The adsorption study indicated that the adsorption equilibrium is well fitted with Langmuir isotherm model with the maximum adsorption capacities followed the order of Fe (II) > Cu (II) > Ni (II) > Cr (VI) with the values of 137.23, 128.02, 83.19 and 2.92 mg/g, respectively. The ion-exchange mechanism was dominant for the adsorption of metal ions onto nCDHA at initial metal concentrations lower than 0.01 mol/L. Along with the ion-exchange mechanism, there was an additional precipitation occurred on the surface of nCDHA in the case of Fe (II) and Cu (II) at initial concentrations higher than 0.01 mol/L.
The Use of a High-Speed 12-Bit A/D Converter for Digital Sampling of Communication Signal Carriers

Abstract : The use of an A/D converter is considered for digital sampling of modulated waveforms obtained from an antenna. Demodulation is assumed to occur following the digital sampling process, either by using a high speed digital processor or by using a more conventional receiver following reconstruction of the analog waveform by a D/A converter. Since many communication carriers are not conditioned for jam-resistance by coding and spectrum-spreading techniques, a large instantaneous linear dynamic range is necessary to permit the detection and modulation of a small desired signal in the presence of a strong inband interfering signal. Consequently, our interest lies in A/D converters having a large number of quantization bits - a condition that is necessary for large linear dynamic range. The effects of A/D device parameters such as quantization resolution (number of bits), sampling rate, and aperture uncertainty are discussed. A 12-bit A/D converter having an aperture uncertainty of 25 psec and a maximum sampling rate of 5 MHz was used to experimentally determine the magnitude of the spurious-free dynamic range that could be obtained with present off-the-shelf technology. A larger number of quantization bits would have resulted in unacceptably slow speed and an unacceptably low maximum frequency limitation. A smaller number of bits would have yielded a smaller spurious-free dynamic range. Since we did not have a digital processing facility to analyze the A/D directly, a D/A converter, deglitcher (sample-and-hold), and a high quality spectrum analyzer were used to evaluate the A/D performance. Consequently, the results reported are characteristic of the composite A/D-D/A- deglitcher system rather than the A/D alone.
Anidulafungin in Treatment of Experimental Invasive Infection by Candida parapsilosis: In Vitro Activity, (1→3)-β-d-Glucan and Mannan Serum Levels, Histopathological Findings, and In Vivo Efficacy

ABSTRACT We have evaluated the in vitro activity of anidulafungin (AFG) against 31 strains of Candida parapsilosis sensu stricto by using broth microdilution, disk diffusion, and minimal fungicidal concentration (MFC) determination procedures. The two first methods showed a high level of activity of the drug, while MFCs were 1 to 5 dilutions higher than their corresponding MICs. To assess if MICs were predictive of in vivo outcomes, six strains representing different AFG MICs (0.12 to 2 μg/ml) were tested in a murine model of disseminated infection treated with different doses of the drug (1, 5, or 10 mg/kg of body weight). AFG was able to prolong the survival of mice infected with all the strains tested but was able to reduce the tissue burden of those mice infected only with the strains that showed the lowest MIC (0.12 μg/ml).