Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow acetone‐staining technique: A highly efficient procedure for the simultaneous analysis of DNA content, cell morphology, and immunophenotype by flow cytometry

The accurate determination of cell cycle, immunophenotypes and morphology at single‐cell level is not fully achieved by current flow cytometry protocols. Acetone, a coagulant fixative/permealizing agent, is widely used in static cytometry, but is impractical in flow cytometry because of its shrinking effect. We sought for conditions of acetone treatment that could permit the simultaneous analysis of physical parameters, surface and intracellular immunostaining, and DNA content. We evaluated different experimental conditions (concentration, duration of fixation, temperature, presence of proteins) to test the capacity of acetone fixation/permeabilization to preserve cell physical parameters (forward and side scatters, FSC, and SSC) and immunophenotyping while allowing stoichiometric DNA staining. The commonly used ethanol fixation technique was used as reference method. To detect phenotypes and DNA content simultaneously, we employed 7‐aminoactinomycin D (7‐AAD) as “intercalating” dye for DNA in spite of, or just for, its controversial ability in stoichiometric DNA staining. Cells were resting peripheral blood monucleated cells (PBMCs), T‐ and B‐cell blasts obtained by PBMCs stimulation, and the human cell lines Ramos and Shep. Acetone fixation, preserving both the recovery and the physical parameters of cells, is drastically influenced by temperature of treatment and is practicable only when the protocol is realized at 8°C. Under this condition, acetone maintains the immunophenotypic fluorescences (realized before or after the fixation) better than ethanol. Stoichiometric DNA staining of acetone processed cells, the variation coefficients (CV) of frequency distributions of G1/G0 and G2/M phases, the modes ratio of these distributions and doublets generation are at least comparable to those obtained with ethanol treatment. The assay developed in the present study, that we called flow acetone‐staining technique (FAST), accurately analyzes cell cycle, physical parameters and immunophenotypes in heterogenous cell populations, and thus provides a useful tool for cytomics. © 2008 International Society for Analytical Cytology.
A fast and accurate computational approach to protein ionization

We report a very fast and accurate physics‐based method to calculate pH‐dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm‐based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines electrostatic energy calculations based on the Generalized Born approximation with an iterative mobile clustering approach to calculate the equilibria of proton binding to multiple titration sites in protein molecules. The use of the GBIM (Generalized Born with Implicit Membrane) CHARMm module makes it possible to model not only water‐soluble proteins but membrane proteins as well. The method includes a novel algorithm for preliminary refinement of hydrogen coordinates. Another difference from existing approaches is that, instead of monopeptides, a set of relaxed pentapeptide structures are used as model compounds. Tests on a set of 24 proteins demonstrate the high accuracy of the method. On average, the RMSD between predicted and experimental pK values is close to 0.5 pK units on this data set, and the accuracy is achieved at very low computational cost. The pH‐dependent assignment of hydrogen atoms also shows very good agreement with protonation states and hydrogen‐bond network observed in neutron‐diffraction structures. The method is implemented as a computational protocol in Accelrys Discovery Studio and provides a fast and easy way to study the effect of pH on many important mechanisms such as enzyme catalysis, ligand binding, protein–protein interactions, and protein stability.
An intact Raf zinc finger is required for optimal binding to processed Ras and for ras-dependent Raf activation in situ

The function of the c-Raf-1 zinc finger domain in the activation of the Raf kinase was examined by the creation of variant zinc finger structures. Mutation of Raf Cys 165 and Cys 168 to Ser strongly inhibits the Ras-dependent activation of c-Raf-1 by epidermal growth factor (EGF). Deletion of the Raf zinc finger and replacement with a homologous zinc finger from protein kinase C gamma (PKC gamma) (to give gamma/Raf) also abrogates EGF-induced activation but enables a vigorous phorbol myristate acetate (PMA)-induced activation. PMA activation of gamma/Raf does not require endogenous Ras or PKCs and probably occurs through a PMA-induced recruitment of gamma/Raf to the plasma membrane. The impaired ability of EGF to activate the Raf zinc finger variants in situ is attributable, at least in part, to a major decrement in their binding to Ras-GTP; both Raf zinc finger variants exhibit decreased association with Ras (V12) in situ upon coexpression in COS cells, as well as diminished binding in vitro to immobilized, processed COS recombinant Ras(V12)-GTP. In contrast, Raf binding to unprocessed COS or prokaryotic recombinant Ras-GTP is unaffected by Raf zinc finger mutation. Thus, the Raf zinc finger contributes an important component to the overall binding to Ras-GTP in situ, through an interaction between the zinc finger and an epitope on Ras, distinct from the effector loop, that is present only on prenylated Ras.
Investigation of optimization-based reconstruction with an image-total-variation constraint in PET

Interest remains in reconstruction-algorithm research and development for possible improvement of image quality in current PET imaging and for enabling innovative PET systems to enhance existing, and facilitate new, preclinical and clinical applications. Optimization-based image reconstruction has been demonstrated in recent years of potential utility for CT imaging applications. In this work, we investigate tailoring the optimization-based techniques to image reconstruction for PET systems with standard and non-standard scan configurations. Specifically, given an image-total-variation (TV) constraint, we investigated how the selection of different data divergences and associated parameters impacts the optimization-based reconstruction of PET images. The reconstruction robustness was explored also with respect to different data conditions and activity up-takes of practical relevance. A study was conducted particularly for image reconstruction from data collected by use of a PET configuration with sparsely populated detectors. Overall, the study demonstrates the robustness of the TV-constrained, optimization-based reconstruction for considerably different data conditions in PET imaging, as well as its potential to enable PET configurations with reduced numbers of detectors. Insights gained in the study may be exploited for developing algorithms for PET-image reconstruction and for enabling PET-configuration design of practical usefulness in preclinical and clinical applications.
Identification of pathogen-specific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain

Escherichia coli is a diverse bacterial species that comprises commensal nonpathogenic strains such as E. coli K-12 and pathogenic strains that cause a variety of diseases in different host species. Avian pathogenic E. coli strain χ7122 (O78:K80:H9) was used in a chicken infection model to identify bacterial genes that are expressed in infected tissues. By using the cDNA selection method of selective capture of transcribed sequences and enrichment for the isolation of pathogen-specific (non-E. coli K-12) transcripts, pathogen-specific cDNAs were identified. Pathogen-specific transcripts corresponded to putative adhesins, lipopolysaccharide core synthesis, iron-responsive, plasmid- and phage-encoded genes, and genes of unknown function. Specific deletion of the aerobactin siderophore system and E. coli iro locus, which were identified by selective capture of transcribed sequences, demonstrated that these pathogen-specific systems contribute to the virulence of strain χ7122. Consecutive blocking to enrich for selection of pathogen-specific genes did not completely eliminate the presence of transcripts that corresponded to sequences also present in E. coli K-12. These E. coli conserved genes are likely to be highly expressed in vivo and contribute to growth or virulence. Overall, the approach we have used simultaneously provided a means to identify novel pathogen-specific genes expressed in vivo and insight regarding the global gene expression and physiology of a pathogenic E. coli strain in a natural animal host during the infectious process.
State-Space Reconstruction and Spatio-Temporal Prediction of Lattice Dynamical Systems

This paper addresses the problems of state space reconstruction and spatio-temporal prediction for lattice dynamical systems. It is shown that the state space of any finite lattice dynamical system can be embedded into a reconstruction space for almost every, in the sense of prevalence, smooth measurement mapping as long as the dimension of the reconstruction space is larger than twice the size of the lattice. Based on this result, an input-output spatio-temporal dynamical relation for each site within the lattice is derived and used for spatio-temporal prediction of the system. In the case of infinite lattice dynamical systems, an approach based on constructing local lattice dynamical systems is proposed. It is shown that the finite dimensional results can be directly applied to the local modelling and spatio-temporal prediction for infinite lattice dynamical systems. Two numerical examples are provided to demonstrate the proposed theory and approach
Resting vagal activity in schizophrenia: Meta-analysis of heart rate variability as a potential endophenotype

Background Cardiac vagal tone, indexed by heart rate variability (HRV), is a proxy for the functional integrity of feedback mechanisms integrating central and peripheral physiology. Aims To quantify differences in HRV in individuals with schizophrenia compared with healthy controls. Method Databases were systematically searched for studies eligible for inclusion. Random effect meta-analyses of standardised mean differences were calculated for vagal activity indicated by high-frequency HRV and the root mean square of successive R–R interval differences (RMSSD). Results Thirty-four studies were included. Significant main effects were found for high-frequency HRV (P = 0.0008; Hedges' g =–0.98, 95% CI −1.56 to −0.41, k = 29) and RMSSD (P<0.0001; g =–0.91, 95% CI −1.19 to −0.62, k = 24), indicating lower vagal activity in individuals with schizophrenia than in healthy controls. Considerable heterogeneity was evident but effects were robust in subsequent sensitivity analyses. Conclusions Given the association between low HRV, threat processing, emotion regulation and executive functioning, reduced vagal tone may be an endophenotype for the development of psychotic symptoms.
Monitoring of cornea elastic properties changes during UV-A/riboflavin-induced corneal collagen cross-linking using supersonic shear wave imaging: a pilot study.

PURPOSE Keratoconus disease or post-LASIK corneal ectasia are increasingly treated using UV-A/riboflavin-induced corneal collagen cross-linking (CXL). However, this treatment suffers from a lack of techniques to provide an assessment in real-time of the CXL effects. Here, we investigated the potential interest of corneal elasticity as a biomarker of the efficacy of this treatment. METHODS For this purpose, supersonic shear wave imaging (SSI) was performed both ex vivo and in vivo on porcine eyes before and after CXL. Based on ultrasonic scanners providing ultrafast frame rates (~30 kHz), the SSI technique generates and tracks the propagation of shear waves in tissues. It provides two- and three-dimensional (2-D and 3-D) quantitative maps of the corneal elasticity. RESULTS After CXL, quantitative maps of corneal stiffness clearly depicted the cross-linked area with a typical 200-μm lateral resolution. The CXL resulted in a 56% ± 15% increase of the shear wave speed for corneas treated in vivo (n = 4). CONCLUSIONS The in vivo CXL experiments performed on pigs demonstrated that the quantitative estimation of local stiffness and the 2-D elastic maps of the corneal surface provide an efficient way to monitor the local efficacy of corneal cross-linking.
Development of methods for body composition studies

This review is focused on experimental methods for determination of the composition of the human body, its organs and tissues. It summarizes the development and current status of fat determinations from body density, total body water determinations through the dilution technique, whole and partial body potassium measurements for body cell mass estimates, in vivo neutron activation analysis for body protein measurements, dual-energy absorptiometry (DEXA), computed tomography (CT) and magnetic resonance imaging (MRI, fMRI) and spectroscopy (MRS) for body composition studies on tissue and organ levels, as well as single- and multiple-frequency bioimpedance (BIA) and anthropometry as simple easily available methods. Methods for trace element analysis in vivo are also described. Using this wide range of measurement methods, together with gradually improved body composition models, it is now possible to quantify a number of body components and follow their changes in health and disease.
In Vivo Suppression of Heat Shock Protein (HSP)27 and HSP70 Accelerates DMBA-Induced Skin Carcinogenesis by Inducing Antigenic Unresponsiveness to the Initiating Carcinogenic Chemical

Heat shock proteins (HSPs) are constitutively expressed in murine skin. HSP27 is present in the epidermis, and HSP70 can be found in both the epidermis and dermis. The purpose of this study was to investigate the role of these proteins in cutaneous chemical carcinogenesis and to determine whether their effects on cell-mediated immune function were a contributing factor. In vivo inhibition of HSP27 and HSP70 produced a reduction in the T cell–mediated immune response to 7,12-dimethylbenz(a)anthracene (DMBA) and benzo(a)pyrene in C3H/HeN mice and resulted in a state of Ag-specific tolerance. When mice were pretreated with anti-HSP27 and anti-HSP70 Abs in vivo prior to subjecting them to a standard two-stage DMBA/12-O-tetradecanoylphorbol-13-acetate cutaneous carcinogenesis protocol, the percentage of mice with tumors was much greater (p < 0.05) in anti-HSP27– and HSP70–pretreated animals compared with mice pretreated with control Ab. Similar results were obtained when the data were evaluated as the cumulative number of tumors per group. Mice pretreated with HSP27 and HSP70 Abs developed more H-ras mutations and fewer DMBA-specific cytotoxic T lymphocytes. These findings indicate that in mice HSP27 and HSP70 play a key role in the induction of cell-mediated immunity to carcinogenic polyaromatic hydrocarbons. Bolstering the immune response to carcinogenic polyaromatic hydrocarbons may be an effective method for prevention of the tumors that they produce.
Development and psychometric testing of the Bakas Caregiving Outcomes Scale.

BACKGROUND Family caregivers of stroke survivors experience more depression, emotional problems, social inactivity, and general ill-health than noncaregiving individuals. While a number of instruments measure these variables in family caregivers, they are often too global, indicating the need for a situation-specific instrument measuring life changes resulting from providing care. OBJECTIVES To develop and psychometrically test the Bakas Caregiving Outcomes Scale (BCOS) measuring changes in family caregiving outcomes in the stroke population. METHOD 48 items were developed, with 27 being judged as content valid by a panel of five experts. Psychometric testing with two convenience samples of family caregivers of stroke survivors (ns = 92, 104) was conducted using item analysis, Cronbach's alpha, factor analysis, and hierarchical multiple regression. RESULTS Item analysis in sample no. 1 resulted in a 12-item scale with alpha = . 90. The scale was further shortened to a 10-item scale in sample no. 2 with alpha = . 77. Unidimensionality was supported by factor analysis in both samples. Using hierarchical multiple regression, 63% of the variance of the 12-item BCOS in sample no. 1, and 45% of the variance of the 10-item BCOS in sample no. 2 was accounted for by the constructs in the conceptual model. Criterion-related validity was supported in both samples by significant correlations with the LIFE-3 and a criterion variable with the same response format as the BCOS. Significant BCOS correlations with the SF-36 Health Survey subscales in sample no. 2 provided further evidence of criterion-related validity. CONCLUSION The 10-item BCOS is a brief, easy to administer instrument that has evidence of reliability and validity in family caregivers of stroke survivors. The 10-item BCOS could serve as a valuable measure in research, as well as an assessment tool to identify family caregivers in need of intervention.
Modulated model predictive control of permanent magnet synchronous motor

In this paper a modulated model predictive control (MMPC) scheme for permanent magnet synchronous motor is proposed. The proposed strategy combines field orientation control with modulated model predictive control. It not only ensures the quick response of the system and low torque ripple of PMSM, but also obtains a fixed switching frequency. Eventually, simulation results validate the perfect performance of the proposed method.
Multiplex polymerase chain reaction for the detection of high-risk-human papillomavirus types in formalin-fixed paraffin-embedded cervical tissues

Detecting high-risk-human papillomavirus (HPV) types has become an integral part of the cervical cancer screening programmes. This study aimed to develop a multiplex polymerase chain reaction (PCR) for identification of HPV types 16 and 18 along with the beta globin gene in formalin-fixed and paraffin-embedded cervical biopsy specimens. A total of 59 samples from patients with cervical abnormalities were tested. HPV 16 positivity was 50% in cervical cancers and 52.9% in cervical intraepithelial neoplasia. Our multiplex PCR protocol can be used as a simple and cost-effective tool for high-risk-HPV detection in cervical cancer screening programmes.
Use of Nasopancreatic Drainage for Severe Post-endoscopic Retrograde Cholangiopancreatography Pancreatitis: A Case Series

Five patients complaining of severe pain due to severe post-endoscopic retrograde cholangiopancreatography pancreatitis (PEP) underwent nasopancreatic drainage (NPD) placement. Pain relief was achieved on the second, fourth, and fifth day in three, one, and one patients, respectively. Four patients underwent pancreatic juice culture; all were positive. Our results suggest that NPD can relieve severe PEP with severe pain. Bacteria-induced protease-activated receptor-2 activation may be associated with PEP.
Effects of ertiprotafib on hepatic cytochrome P450 and peroxisomal enzymes in rats and dogs, and in rat and human primary hepatocytes

Ertiprotafib (ERTI) significantly increased liver weights in male and female rats, and moderately increased liver weights in male dogs after treatment for 28 days. The present study tested the hypotheses that the organ weight increases were associated with peroxisome proliferation in rats and induction of hepatic enzymes in rats and dogs, and would have limited impacts on humans. At a dosage of 200 mg kg–1 day–1, CYP4A was induced by tenfold in male rats and 2.4-fold in female rats. In male rats, CYP2B was induced by 1.2-fold and CYP3A was induced by 1.7-fold. Palmitoyl CoA oxidase was induced by 5.1-fold in male rats and 2.9-fold in female rats; carnitine acetyltransferase was induced by 10.4-fold in male rats and 5.2-fold in female rats. CYP3A, CYP4A and peroxisomal enzymes were not induced in dogs at 150/200 mg kg–1 day–1. ERTI at 50 µM markedly induced the mRNA level of CYP4A by up to fivefold in rat hepatocytes, but not in human primary hepatocytes. In conclusion, the liver weight increases observed in rats treated with ERTI appears to be due to rodent-specific peroxisome proliferation and the substantial induction of CYP4A1. ERTI is not a potent P450 inducer in dogs or in human hepatocytes. Therefore, ERTI is not expected to exert any significant effects on hepatic drug-metabolizing enzymes in humans.
Speed and current Model Predictive Control of an IPM synchronous motor drive

Predictive control indicates a wide family of advanced control techniques that in last decade have been investigated in several studies and researches in the electrical drive field. This paper considers one of them, named Model Predictive Control (MPC). There are many advantages and interesting aspects in the use of this control technique compared to more traditional techniques that are usually employed in electrical drives. The typical cascade structure of FOC algorithms, for instance, can be avoided by implementing a single controller that manages both speed and currents. The innovation proposed within this paper is the application of Model Predictive Control to an IPM synchronous motor drive. Herein, special attention is given to the system's non-linearities and how the controller can be modified to realize flux-weakening and other control strategies. After a detailed description of the strategy that has been implemented, in the last part of the paper most important results obtained by simulations and by testing on a real drive are shown and discussed.
A Note on the Stability of Chens Lindahl Mechanism

There are no general theoretical results on the stability of the Lindahl mechanism introduced by Chen (2002). We show that despite not tting the requirements of the Milgrom and Roberts 1990 stability results for supermodular games, if the Chen mechanism induces a supermodular game, then the best reply map will be a contraction. This gives us a easy to identify su¢ cient condition for dynamic stability of equilibrium. 1 Introduction Mechanisms that induce supermodular games with a unique equilibrium have tended to be very successful in the lab.1 Milgrom and Roberts (1990), hereafter MR, have shown if a supermodular game has: rst, strategy spaces which are complete lattices; and second, a unique equilibrium; then its equilibrium is stable under a variety of learning behavior such as myopic best reply and ctitious play. Motivated by the aforementioned experimental studies as well as the MR result, Chen (2002) proposed a parametric family of Lindahl mechanisms (i.e., mechanisms that Nash implement Lindahl allocations) which, under some conditions of the mechanism parameters, induced a supermodular game with a unique equilibrium. Citing MR, she concluded Department of Economics, University of Arizona. mvanesse@email.arizona. edu. 1See Chen and Tang(1998), Healy (2004), or Chen and Gazzale (2004).
The simian malarias: zoonoses, anthroponoses, or both?

Abstract It now appears that Plasmodium cynomolgi, Plasmodium knowlesi, Plasmodium inui, and Plasmodium schwetzi are true zoonoses, although the latter, as Plasmodium ovale, may be an anthroponosis as well. Plasmodium malariae and Plasmodium rodhaini are generally accepted as being synonymous; if this is true, and it probably is, then this African quartan parasite is either one, i.e., a zoonosis or an anthroponosis, depending on which group of primates gave it origin. Certain African-Asian forms, Plasmodium gonderi for example, appear to be neither. The Central and South American primate malarias pose a different problem, for it is held that these malarias appeared only after 1492 when man, carrying P. malariae and Plasmodium vivax invaded this area from Europe. Consequently, each infection appeared in the monkeys as an anthroponosis. If this is true, synonymy is inevitable. If, on the other hand, Plasmodium brasilianum is a valid species, it acts as a zoonosis. There is reasonable doubt that Plasmodium simium acts in the same capacity.