Miracle-dz/UniFAR-FTUs huggingface dataset:
CXCR4 Is Down-Regulated in Cells Infected with the CD4-Independent X4 Human Immunodeficiency Virus Type 1 Isolate m7NDK

ABSTRACT Macrophages and T cells infected in vitro with CD4-dependent human immunodeficiency virus type 1 (HIV-1) isolates have reduced levels of CD4 protein, a phenomenon involved in retroviral interference. We have previously characterized the first CD4-independent HIV-1 X4 isolate m7NDK, which directly interacts with CXCR4 through its mutated gp120. We thus investigate CXCR4 expression in cells infected with this m7NDK CXCR4-dependent HIV-1 mutant. We present evidence of the down-regulation of CXCR4 membrane expression in CD4-positive or -negative cells chronically infected with the HIV-1 m7NDK, a phenomenon which is not observed in the CD4-dependent HIV-1 NDK parental strain. This down-regulation of CXCR4 was demonstrated by fluorescence-activated cell sorter analysis and was confirmed by the absence of CXCR4 functionality in m7NDK-infected cells, independently of the presence of CD4 protein. Furthermore, a drastic reduction of the intracellular level of CXCR4 protein was also observed. Reduced levels of CXCR4 mRNA transcripts were found in m7NDK-infected HeLa and CEM cells, reduced levels that could not be attributed to a reduced stability of CXCR4 mRNA. Down-regulation of CXCR4 on m7NDK-infected cells may thus be explained by transcriptional regulation.
Convergence of EM image reconstruction algorithms with Gibbs smoothing.

P.J. Green has defined an OSL (one-step late) algorithm that retains the E-step of the EM algorithm (for image reconstruction in emission tomography) but provides an approximate solution to the M-step. Further modifications of the OSL algorithm guarantee convergence to the unique maximum of the log posterior function. Convergence is proved under a specific set of sufficient conditions. Several of these conditions concern the potential function of the Gibb's prior, and a number of candidate potential functions are identified. Generalization of the OSL algorithm to transmission tomography is also considered.
Forms of Formative Assessment in Virtual Learning Environments

One of the challenges in the contemporary education is improving learner’s learning capability during the learning period through formative assessment in virtual learning environments. The formative assessment process requires learner to be active participants in the learning process by communicating and interacting with the instructor. The formative assessment process accommodates learner responses that give an opportunity to support the learner in learning through feedback. In a virtual learning environment, formative assessment can be significantly improved by the use of information systems. In this research we explore forms of formative assessment in virtual leaning environments with a specific focus on the design dimension. Our analysis improves the understanding of formative assessment and the design dimension specific to forms of formative assessment in virtual learning environments. Our work informs the design of online learning environments to improve the effectiveness of formative assessment.
Studies on peptides. CLI. Syntheses of cystine-peptides by oxidation of S-protected cysteine-peptides with thallium(III) trifluoroacetate.

Thallium (III) trifluoroacetate, a mild oxidant with a soft-acid character, was found to cleave various S-protecting groups of cysteine in trifluoroacetic acid, with spontaneous formation of cystine. Except for unmasked Trp and Met, other amino acids, including His and Tyr, remained intact in the presence of this oxidant. The usefulness of this oxidant for intramolecular disulfide bond-forming reactions was demonstrated by direct conversion of three model S-protected cysteine-peptides into cystine-peptides, i.e., oxytocin, urotensin II and human calcitonin generelated peptide.
Physical activity consultation for people with Type 2 diabetes. Evidence and guidelines

Physical activity is an important, but often underused, therapeutic strategy within diabetes care. To date, little is known about the best way to promote physical activity in diabetes care. Physical activity consultation is an intervention designed to promote physical activity behaviour change. This article provides guidelines on how to conduct a physical activity consultation with people who have Type 2 diabetes, and reviews the evidence surrounding the effectiveness of this intervention in this population. The trans‐theoretical model is the underlying theory of behaviour change for the physical activity consultation intervention. The review identifies research which supports the use of this model for understanding physical activity behaviour in people with Type 2 diabetes. The review outlines a number of modifiable variables associated with physical activity behaviour change in this population. How each of these variables is addressed within the guidelines for conducting a physical activity consultation is identified. Finally, limited but consistent research highlights the effectiveness of physical activity consultation for promoting physical activity in people with Type 2 diabetes.
An application of the finite differences method to a dynamical interface problem

A multiple-order-parameter model for Cu−Au system on a face cubic centered lattice was recently developed in the presence of anisotropy. In that model, three order parameters (non-conserved) and one concentration order parameter (conserved), which has been taken as a constant, were considered. Later on, the model has been extended, so that, concentration has been taken as a variable. It has been seen that two models were in a good agreement near critical temperature since the non-conserved order parameter behaves like a constant near critical temperature in both models. Thus, we extended the first model to a dynamical diffuse interface model near critical temperature. After writing the free energy of the system in terms of the order parameters, minimizing the energy with respect to the order parameters and Langevin equation yield the non-linear system of parabolic equations. The finite differences method was implemented to solve this non-linear system of parabolic equations. The forward difference discretization was applied for the first derivative of the solution with respect to time and centered difference discretization was applied for the second order derivative of the solution with respect to spatial variable. We obtained stability criteria and find the error bound. The orientation dependence profiles, variation of interfacial energy and the effect of the degree of the anisotropy on the width of the diffuse interface are simulated when the time evolves.
Use of carbonate extraction in analyzing moderately hydrophobic transmembrane proteins in the mitochondrial inner membrane

Resistance to sodium carbonate extraction is regarded as a canonical way to distinguish integral membrane proteins (MPs) from other membrane‐associated proteins. However, it has been observed that carbonate extraction releases some mitochondrial integral MPs. Here, by analyzing both artificially designed and native mitochondrial inner MPs containing transmembrane domains (TMDs) of different hydrophobicities, we show that carbonate treatment can release moderately hydrophobic TMDs from the mitochondrial inner membrane. These results suggest that resistance and sensitivity to carbonate extraction may be interpreted with caution when analyzing the nature of mitochondrial inner MPs.
Field‐of‐view limitations in parallel imaging

Parallel imaging is one of the most promising developments in recent years for the acceleration of MR acquisitions. One area of practical importance where different parallel imaging methods perform differently is the manner in which they deal with aliasing in the full‐FOV reconstructed image. It has been reported that sensitivity encoding (SENSE) reconstruction fails whenever the reconstructed FOV is smaller than the object being imaged. On the other hand, generalized autocalibrating partially parallel acquisition (GRAPPA) has been used successfully to reconstruct images with aliasing in the reconstructed FOV, as in conventional imaging. The disparate behavior of these methods can be easily demonstrated by a few simple illustrative examples. Additional in vivo examples using GRAPPA and modified SENSE (mSENSE) make this distinction clear. These experiments demonstrate that SENSE fails to reconstruct correct images when coil sensitivity maps are used that do not automatically account for the object size and therefore the aliasing in the reconstructed images. However, with the use of aliased high‐resolution coil sensitivity maps, accurate SENSE reconstructions can be generated. On the other hand, GRAPPA produces images with an aliasing appearance that is exactly as would be expected from normal nonaccelerated acquisitions. An understanding of these effects could potentially lead to fewer operator‐dependent errors, as well as a better understanding of the differences between the underlying reconstruction processes. Magn Reson Med 52:1118–1126, 2004. © 2004 Wiley‐Liss, Inc.
Transcription from efficient promoters can interfere with plasmid replication and diminish expression of plasmid specified genes.

The copy number of plasmids containing the ColE1 replicon is affected by changes in the transcriptional activity within the plasmid if these changes lead to transcriptional readthrough into the replication region towards the promoter priming DNA replication. Such readthrough e.g., from the tet region in pBR322 not only causes overproduction of a peptide known to affect the copy number negatively but also appears to interfere negatively with the replication of the plasmid itself. The proper placement of efficient transcriptional terminators prevents such interference and permits the stable integration of strong promoters. Due to this termination effect, up to 9‐fold differences in plasmid copy number were observed, depending upon the particular growth conditions. The higher copy number is of course reflected by higher yields of plasmid‐specified gene products indicating the relevance of the above effects for studies of gene expression.
Nonlinear feedback excitation for system interrogation by bifurcation morphing

This paper demonstrates a novel system-interrogation method based on observing the morphing of bifurcations and the postbifurcation dynamics through both experimental and numerical methods. A sensing cantilever beam is built with lead-zirconate-titanate patches symmetrically bonded to both sides of its root A desired bifurcation in the dynamics of the beam can be induced by applying a nonlinear feedback excitation to the beam. The nonlinear feedback excitation requires the active measurement of the dynamics and a feedback loop, and it is generated by applying the voltage (resulting from a nonlinear feedback) to the piezoelectrode. Also, a finite element model is used to design the nonlinear feedback excitation and to predict the response of the sensing beam. Numerical simulations and experiments are performed and compared that demonstrate the effectiveness and high level of sensitivity of the novel approach to detect very small amounts of mass added at the tip of the beam.
Inclusion volume solid‐phase synthesis

Solid‐phase synthesis of peptides was carried out using only the volume of the solvent included in the swollen solid‐phase resin beads [inclusion volume synthesis]. This approach enables (i) the use of higher concentrations of activated amino acids, resulting in increased coupling rates, (ii) drastically decreased consumption of solvents, and (iii) the construction of multiple peptide synthesizers having virtually no reaction vessels.
Subjective cognitive complaints, neuropsychological performance, affective and behavioural symptoms in non‐demented patients

Subjective cognitive complaints (SCC) have been previously investigated to establish whether they are risk factors for dementia, but no clear‐cut conclusions have emerged. In this study non‐demented patients with SCC were studied and the neuropsychological findings, affective and behavioural aspects and parameters with the highest correct classifications in discriminating patients who had only SCC but no objective clinical and neuropsychological impairment, i.e. no cognitive impairment (NCI) patients and those with objective neuropsychological deficits, namely patients with mild cognitive (MCI) were analyzed.
Supporting End-users of Statistical Information: The Role of Statistical Metadata in the Statistical Knowledge Network

Metadata is integral to many processes in the Statistical Knowledge Network (SKN). Recent efforts such as the Semantic Web (Berners-Lee et al., 2001), the joint work of ISI and Columbia University (Ambite et al., 2002), and ours (Marchionini, et al., 2003) express the importance of metadata in supporting integration of information across multiple sources. This paper adds to those efforts by highlighting two aspects of using metadata to help users "find what they want and use what they find. " The first is to identify integration challenges that users experience and metadata to resolve them. The second is to establish an architecture that supports metadata acquisition and use throughout the SKN.
Inclusive Fitness in Finite Deme-structured and Stepping-stone Populations

Very little attention has been given in the literature to the interesting question of how to handle relatedness in finite populations. The main problem is that a finite population is never really iat equilibriumi in that it represents just one realization of an infinite assemblage of possible allelic distributions. A recent paper of Rousset and Billiard (manuscript) provides coefficients which, if used in inclusive fitness models under conditions of weak selection, give us a measure of average allele frequency change where the average is taken over all such realizations. Their coefficients are expressed in terms of identity in state, and an alternative formulation (Taylor and Day, manuscript) in terms of coefficients of consanguinity permits the calculation of relatedness in simple cases from pedigree analysis. Here we implement these calculations in a finite asexual haploid population with either a deme structure or a one-dimensional stepping-stone structure and verify our results with numerical simulations in small populations. Our simulations allow us to investigate the dependence of relatedness on allele frequency, and our results here agree qualitatively with those obtained by Rousset and Billiard. Finally, we examine a model of altruism in a deme-structured population to verify numerically that our relatedness coefficients provide a correct measure of allele frequency change.
Fabrication of 3D-magnetophotonic crystal with artificial opal template prepared by gravitational sedimentation

We report results on fabrication of three-dimensional (3D)-magnetophotonic crystals (MPCs) based on artificial opals. The opal samples composed of amorphous SiO/sub 2/ spheres were prepared using gravitational sedimentation. Quantitative evaluation of opal structure was done by fitting the (111) photonic bandgap by a Gaussian function. Changes in depth and width of the (111) photonic bandgap were observed after polishing less-ordered bottom side of the as-grown opal samples. To create 3D-MPCs, terbium gallium garnet was synthesized in an opal matrix.
Type A factors as predictors of changes in the metabolic syndrome precursors in adolescents and young adults--a 3-year follow-up study.

The predictive associations of Type A factors with changes in some essential parameters of the cluster of disorders known as metabolic syndrome (Syndrome X) were studied during a 3-year follow-up period in 1,147 randomly selected healthy adolescents and young adults. Type A behavior was measured with the Hunter Wolf A-B Rating Scale. Physiological parameters studied were serum insulin, high-density and low-density lipoprotein cholesterol, triglycerides (TG), systolic and diastolic blood pressure, body-mass index (BMI), subscapular skinfold thickness (SSF), and centrality index. Among the Type A factors in boys and men, high baseline Aggression predicted an increase in the individual parameters of metabolic syndrome (i.e., insulin, TG, SSF, and BMI) as well as a global aggravation of the cluster of metabolic parameters. In girls and women, increases in Eagerness-Energy and Responsibility across the 3 years of follow-up predicted an increase in serum insulin and a decrease in SSF, respectively.
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Riboswitches are cis-acting elements that regulate gene expression by affecting transcriptional termination or translational initiation in response to binding of a metabolite. A typical riboswitch is made of an upstream aptamer domain and a downstream expression platform. Both domains participate in the folding and structural rearrangement in the absence or presence of its cognate metabolite. RNA polymerase pausing is a fundamental property of transcription that can influence RNA folding. Here we show that pausing plays an important role in the folding and conformational rearrangement of the Escherichia coli btuB riboswitch during transcription by the E. coli RNA polymerase. This riboswitch consists of an approximately 200 nucleotide, coenzyme B12 binding aptamer domain and an approximately 40 nucleotide expression platform that controls the ribosome access for translational initiation. We found that transcriptional pauses at strategic locations facilitate folding and structural rearrangement of the full-length riboswitch, but have minimal effect on the folding of the isolated aptamer domain. Pausing at these regulatory sites blocks the formation of alternate structures and plays a chaperoning role that couples folding of the aptamer domain and the expression platform. Pausing at strategic locations may be a general mechanism for coordinated folding and conformational rearrangements of riboswitch structures that underlie their response to environmental cues.
Intermediate cells in normal and malignant prostate epithelium express c‐MET: Implications for prostate cancer invasion

Analysis of keratin (K) expression discriminates luminal (K18) and intermediate (K5/18) cells in prostate carcinoma, while basal (K5/14) cells are absent. Intermediate cells have been proposed as targets of malignant transformation in prostate cancer and precursors of androgen‐independent tumor progression. We demonstrate localization of hepatocyte growth factor (HGF) receptor c‐MET in intermediate cells in both normal and malignant prostate epithelium.
Sexuality education: it can reduce unprotected intercourse.

Sex education and venereal disease of sexually transmitted disease (STD) education has been around for some time. A review of major approaches implemented in the past 20 years and their evaluations is provided and discussed in terms of successful programs and the theoretical basis of 3 program types which have demonstrated effectiveness in changing adolescent behavior. Effective programs recognize that there are no "magic solutions. " Some programs are effective in delaying the beginning of intercourse, or increasing protection against pregnancy or STDs, or reducing the number of sexual partners. Abstinence and condoms prevent pregnancy and STD including AIDS/HIV infection. Programs should integrate AIDS, STD, and pregnancy reduction into a single more comprehensive unit. Group norm development and social skill development in responding to peer pressure need to be developed in very practical ways; i.e., what to say to your partner when contraception is unavailable and desire is strong. Programs need to encourage both delay and refraining from intercourse and also to encourage contraceptive usage which is appropriate to the age. Programs should be comprehensive and should include schoolwide peer programs, group discussions, individual counseling, media or theater events, and lends with community reproductive health services. Sexuality education curriculums fall into three broad groups: knowledge-based which stress risks and consequences of pregnancy; a continuation of factual knowledge which includes values and skills development in decision-making and communication; and reactionary abstinence-only programs. New approaches are based on a health belief model and use elements of social learning theory. Through discussions and role playing teenagers awareness of the probability of becoming pregnant, and of the personal benefits of delayed sexual activity and consistent effective contraceptive use is enhanced. The Schenke and Gilchrist curriculum based on social learning theory is reviewed in detail because its use led to evidence of behavioral change.
Impaired dopamine release and synaptic plasticity in the striatum of PINK1-deficient mice

Parkinson's disease (PD) is characterized by the selective vulnerability of the nigrostriatal dopaminergic circuit. Recently, loss-of-function mutations in the PTEN-induced kinase 1 (PINK1) gene have been linked to early-onset PD. How PINK1 deficiency causes dopaminergic dysfunction and degeneration in PD patients is unknown. Here, we investigate the physiological role of PINK1 in the nigrostriatal dopaminergic circuit through the generation and multidisciplinary analysis of PINK1−/− mutant mice. We found that numbers of dopaminergic neurons and levels of striatal dopamine (DA) and DA receptors are unchanged in PINK1−/− mice. Amperometric recordings, however, revealed decreases in evoked DA release in striatal slices and reductions in the quantal size and release frequency of catecholamine in dissociated chromaffin cells. Intracellular recordings of striatal medium spiny neurons, the major dopaminergic target, showed specific impairments of corticostriatal long-term potentiation and long-term depression in PINK1−/− mice. Consistent with a decrease in evoked DA release, these striatal plasticity impairments could be rescued by either DA receptor agonists or agents that increase DA release, such as amphetamine or l-dopa. These results reveal a critical role for PINK1 in DA release and striatal synaptic plasticity in the nigrostriatal circuit and suggest that altered dopaminergic physiology may be a pathogenic precursor to nigrostriatal degeneration.
Urea biosensor utilizing graphene-MoS2 and Kretschmann-based SPR

In this paper, a Kretschmann-based surface plasmon resonance (SPR) biosensor based on a combination of two dimensional (2D) nanomaterial and graphene is presented. The Kretschmann configuration is well known as one of the most effectively used technique for plasmon excitation. It leads to improvement in the efficiency of an urea biosensor due to high adsorption. In this work, we investigated the effect of 2D materials such as molybdenum disulfide (MoS2) with a fine layer of graphene deposited on a plasmonic material, gold (Au), and a oxide material, aluminium oxide (Al2O3), into the configuration. Simulation is based on finite-difference time-domain (FDTD) method for analysis. The performance of SPR biosensor can be monitored by analyzing the sensitivity and minimum reflectance (Rmin) of the SPR curves. The measurements are observed at 670 nm and 785 nm for urea detection. The molarity and refractive index (RI) is varied from 0.625 gm/dl to 10 gm/dl and RI of 1.335 to 1.347 for the sensing layer. The results show that there is 20% increase in the sensitivity of the urea biosensor with the addition of MoS2 and graphene at optical wavelength of 670 nm. This indicates that the proposed SPR biosensor is capable of increasing the sensitivity of urea detection using an easy and label-free method.