bluuebunny/crossref_metadata_2025 huggingface dataset:
Chronic ethanol feeding enhances miR-21 induction during liver regeneration while inhibiting proliferation in rats
Authors: Dippold Rachael P. , Vadigepalli Rajanikanth , Gonye Gregory E. , Hoek Jan B.
Published: July 2012

Liver regeneration is an important repair response to liver injury. Chronic ethanol consumption inhibits and delays liver regeneration in experimental animals. We studied the effects of chronic ethanol treatment on messenger RNA (mRNA) and microRNA (miRNA) expression profiles during the first 24 h after two-thirds partial hepatectomy (PHx) and found an increase in hepatic miR-21 expression in both ethanol-fed and pair-fed control rats after PHx. We demonstrate that the increase of miR-21 expression during liver regeneration is more robust in ethanol-fed rats. Peak miR-21 expression occurs at 24 h after PHx in both ethanol-fed and control rats, corresponding to the peak of hepatocyte S phase in control rats, but not in ethanol-exposed livers in which cell cycle is delayed. The induction of miR-21 24 h after PHx in control rats is not greater than the increase in expression of miR-21 due to sham surgery. However, in the ethanol-fed rat, miR-21 is induced to a greater extent by PHx than by sham surgery. To elucidate the implications of increased miR-21 expression during liver regeneration, we employed unbiased global target analysis using gene expression data compiled by our group. Our analyses suggest that miR-21 may play a greater role in regulating gene expression during regeneration in the ethanol-fed rat than in the control rat. Our analysis of potential targets of miR-21 suggests that miR-21 affects a broad range of target processes and may have a widespread regulatory role under conditions of suppressed liver regeneration in ethanol-treated animals.
Impact of β‐Turn Sequence on β‐Hairpin Dynamics Studied with Infrared‐Detected Temperature Jump
Authors: Popp Alexander , Wu Ling , Keiderling Timothy A. , Hauser Karin
Published: July 2012

Folding dynamics for β‐structure loss and disordered structure gain were studied in a model β‐hairpin peptide based on Cochran’s tryptophan zipper peptide Trpzip2, but with an altered Thr‐Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser‐induced temperature‐jump (T‐jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamic β‐hairpin stability as compared to the Asn‐Gly sequence used in Trpzip2 (TZ2‐NG). In this study, we found that the TG‐turn slows down the overall relaxation dynamics as compared to TZ2‐NG, which were studied at higher temperatures where the time constants show little difference between relaxation of the β‐strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2‐TG than was seen for TZ2‐NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lower kf, with less change of the unfolding rate, ku, assuming two state behavior at higher temperatures.
Developing Self-Regulation by Using Reflective Support in a Video-Digital Microteaching Environment
Authors: Kohen Zehavit , Kramarski Bracha
Published: July 2012

Recent research efforts have established that self-regulated learning (SRL) is necessary for teachers to attain successful professional development. Our study addresses two central questions: under what conditions in preservice teachers' education can SRL processes be enhanced to the optimum level, and how can we assess these processes? The participants of the study were ninety-seven preservice teachers, who were engaged in real-time teaching in a video-digital Microteaching environment. Each participant was randomly assigned to one of two groups: reflective support (RS) for SRL or no support (NS) for SRL. Participants in the RS group were explicitly exposed to SRL aspects and were directed to address these aspects in their reflective discussions of the teaching experience. The SRL process was measured as an online event during real-time teaching exercises, based on a coding scheme developed for this study to identify and assess the SRL skills by two major aspects: metacognition (planning, information management, monitoring, debugging, and evaluating) and motivation (interest and value, self-efficacy, and teaching anxiety). Results indicate that the RS group outperformed the NS group in all SRL measures. Implications for reflective support for SRL and event measures of real-time observations of preservice teachers' SRL are discussed.
Regulation of Adherens Junction Dynamics by Phosphorylation Switches
Authors: Bertocchi Cristina , Vaman Rao Megha , Zaidel-Bar Ronen
Published: July 2012

Adherens junctions connect the actin cytoskeleton of neighboring cells through transmembrane cadherin receptors and a network of adaptor proteins. The interactions between these adaptors and cadherin as well as the activity of actin regulators localized to adherens junctions are tightly controlled to facilitate cell junction assembly or disassembly in response to changes in external or internal forces and/or signaling. Phosphorylation of tyrosine, serine, or threonine residues acts as a switch on the majority of adherens junction proteins, turning “on” or “off” their interactions with other proteins and/or their enzymatic activity. Here, we provide an overview of the kinases and phosphatases regulating phosphorylation of adherens junction proteins and bring examples of phosphorylation events leading to the assembly or disassembly of adherens junctions, highlighting the important role of phosphorylation switches in regulating their dynamics.
Old and New Identities for Bernoulli Polynomials via Fourier Series
Authors: Navas Luis M. , Ruiz Francisco J. , Varona Juan L.
Published: July 2012

The Bernoulli polynomialsBkrestricted to[0,1)and extended by periodicity haventh sine and cosine Fourier coefficients of the formCk/nk. In general, the Fourier coefficients of any polynomial restricted to[0,1)are linear combinations of terms of the form1/nk. If we can make this linear combination explicit for a specific family of polynomials, then by uniqueness of Fourier series, we get a relation between the given family and the Bernoulli polynomials. Using this idea, we give new and simpler proofs of some known identities involving Bernoulli, Euler, and Legendre polynomials. The method can also be applied to certain families of Gegenbauer polynomials. As a result, we obtain new identities for Bernoulli polynomials and Bernoulli numbers.
Guanine: A Combined Study Using Vibrational Spectroscopy and Theoretical Methods
Authors: Lopes R. Pedro , Marques M. Paula M. , Valero Rosendo , Tomkinson John , de Carvalho Luís A. E. Batista
Published: July 2012

The present paper reports a conformational study of solid‐state anhydrous guanine, using vibrational spectroscopy techniques—infrared, Raman, and inelastic neutron scattering—coupled to quantum mechanical methods at the DFT level, both for the isolated molecule and the condensed state. In both cases, the 7H‐keto‐amino tautomer was found to be the prevalent form, contrary to aqueous solutions and hydrated polycrystalline guanine, where the 9H‐keto‐amino tautomer is the most favoured species. This paper is a significant contribution for the existing spectroscopic characterization of this purine base, by unambiguously assigning its vibrational spectra.
General Iterative Algorithms for Hierarchical Fixed Points Approach to Variational Inequalities
Authors: Wairojjana Nopparat , Kumam Poom
Published: July 2012

This paper deals with new methods for approximating a solution to the fixed point problem; find , where H is a Hilbert space, C is a closed convex subset of H, f is a ρ‐contraction from C into H, 0 < ρ < 1, A is a strongly positive linear‐bounded operator with coefficient , , T is a nonexpansive mapping on C, and PF(T) denotes the metric projection on the set of fixed point of T. Under a suitable different parameter, we obtain strong convergence theorems by using the projection method which solves the variational inequality for x ∈ F(T), where τ ∈ [0, ∞). Our results generalize and improve the corresponding results of Yao et al. (2010) and some authors. Furthermore, we give an example which supports our main theorem in the last part.
Interleukin-12p70 Expression by Dendritic Cells of HIV-1-Infected Patients Fails to Stimulategag-Specific Immune Responses
Authors: Van Gulck Ellen , Cools Nathalie , Atkinson Derek , Bracke Lotte , Vereecken Katleen , Vekemans Marc , Van Tendeloo Viggo F. I. , Berneman Zwi N. , Vanham Guido
Published: July 2012

A variety of immune-based therapies has been developed in order to boost or induce protective CD8+T cell responses in order to control HIV replication. Since dendritic cells (DCs) are professional antigen-presenting cells (APCs) with the unique capability to stimulate naïve T cells into effector T cells, their use for the induction of HIV-specific immune responses has been studied intensively. In the present study we investigated whether modulation of the activation state of DCs electroporated with consensus codon-optimized HxB2gagmRNA enhances their capacity to induce HIVgag-specific T cell responses. To this end, mature DCs were (i) co-electroporated with mRNA encoding interleukin (IL)-12p70 mRNA, or (ii) activated with a cytokine cocktail consisting of R848 and interferon (IFN)-γ. Our results confirm the ability of HxB2gag-expressing DCs to expand functional HIV-specific CD8+T cells. However, although most of the patients had detectablegag-specific CD8+T cell responses, no significant differences in the level of expansion of functional CD8+T cells could be demonstrated when comparing conventional or immune-modulated DCs expressing IL-12p70. This result which goes against expectation may lead to a re-evaluation of the need for IL-12 expression by DCs in order to improve T-cell responses in HIV-1-infected individuals.
Spectroscopic Study of the Interaction of DNA with the Linker Histone H1 from Starfish Sperm Reveals Mechanisms of the Formation of Supercondensed Sperm Chromatin
Authors: Chikhirzhina Elena , Starkova Tatyana , Kostyleva Elena , Polyanichko Alexander
Published: July 2012

The interaction of the linker histone H1Z from the sperm chromatin of starfish Asterias amurensis with DNA was studied by spectroscopic and thermodynamic approaches. It has been shown that at the physiological conditions the interaction of the H1Z with DNA results in more compact structures compared to complexes of DNA with somatic histone H1. The typical profile of the DNA melting curves reveals two peaks attributed to the bound and unbound DNA. It has been shown that H1Z from starfish sperm stabilizes DNA to a greater extent compared to the somatic H1. It is possible that the presence of the additional α—helical segments within the C‐terminal part of the H1Z typical for the linker histones from echinoderm sperm facilitates the protein‐protein interactions which in turn stimulate cooperative binding of the histones to DNA, resulting in the formation of the supercompact sperm chromatin.
Evaluation of Biochemical Changes in Skin‐Derived Mesenchymal Stem Cells during In Vitro Neurodifferentiation by FT‐IR Analysis
Authors: Parfejevs V. , Gavare M. , Cappiello L. , Grube M. , Muceniece R. , Riekstina U.
Published: July 2012

Recently FT‐IR analysis has been employed to study changes in molecular signatures during embryonic stem cell differentiation. We were interested to find out whether FT‐IR spectroscopy could be applied to analyze changes in human skin mesenchymal stem cell (S‐MSC) biochemical profile during in vitro neurodifferentiation. S‐MSCs were propagated in serum‐free medium with EGF and FGF‐2 during six weeks. Neural progenitor cell line ReNcell CX (Millipore) was used as a reference cell line. Samples were collected each week and analyzed for neural marker nestin, tubulin βIII, GFAP, and CD271 expression. FT‐IR analysis was carried out using microplate reader HTS‐XT (Bruker, Germany). Despite the immunophenotype similarity, FT‐IR spectroscopy revealed distinct profiles for S‐MSC culture and ReNcell CX cells. FT‐IR spectra analyses showed changes of protein and lipid concentration during neurodifferentiation and different carbohydrate composition in ReNcell CX and S‐MSCs. It was possible to discriminate between S‐MSC cultures at different time points during neurodifferentiation. The results of this study demonstrate that FT‐IR spectroscopy is more sensitive than conventional immunophenotyping analysis and it has a great potential for the monitoring of the stem cell differentiation status.
The Global Behavior of a Periodic Epidemic Model with Travel between Patches
Authors: Wen Luosheng , Long Bin , Liang Xin , Zeng Fengling
Published: July 2012

We establish an SIS (susceptible‐infected‐susceptible) epidemic model, in which the travel between patches and the periodic transmission rate are considered. As an example, the global behavior of the model with two patches is investigated. We present the expression of basic reproduction ratio R0 and two theorems on the global behavior: if R0 < 1 the disease‐free periodic solution is globally asymptotically stable and if R0 > 1, then it is unstable; if R0 > 1, the disease is uniform persistence. Finally, two numerical examples are given to clarify the theoretical results.
Robust Filtering for Linear Equality Constrained Systems
Authors: Wen Chuanbo , Cai Yunze , Xu Xiaoming
Published: July 2012

This paper deals with the robust filtering problem for linear discrete‐time constrained systems. The purpose is the design of a linear filter such that the resulting error system is bounded. An orthogonal factorization is used to decompose the original robust filtering problem into stochastic and deterministic parts, which are then solved separately. Finally, a numerical example is presented to demonstrate the applicability of the proposed method.
Can We Make Time for Physical Activity? Simulating Effects of Daily Physical Activity on Mortality
Authors: Rowe Geoff , Tremblay Mark S. , Manuel Douglas G.
Published: July 2012

Background. The link between physical activity and health outcomes is well established, yet levels of physical activity remain low. This study quantifies effects on mortality of the substitution of low activity episodes by higher activity alternatives using time-use data. Methods. Sample time profiles are representative of the Canadian population (n=19,597). Activity time and mortality are linked using metabolic equivalents(METs). Mortality risk is determined by peak daily METs and hours spent sedentary. The impact of altering activity patterns is assessed using simulated life expectancy. Results. If all leisure screen time was replaced with an equal amount of time spent going for a walk, an increase in life expectancy of about 2.5 years (95% CI, 1.4 to 3.8) would be expected. No other activity category would have as large as an effect. Conclusions. Reducing leisure screen time has a large effect, because seniors particularly have a large potential for mortality reduction and watch more television than other age groups. The general problem of inactivity cannot be solved simply by reallocating time to more active pursuits, because daily activity patterns can be heterogeneous or fragmented and activities may be nondiscretionary (e.g., work or childcare).
Effects of a Pseudophysiological Environment on the Elastic and Viscoelastic Properties of Collagen Gels
Authors: Meghezi Sébastien , Couet Frédéric , Chevallier Pascale , Mantovani Diego
Published: July 2012

Vascular tissue engineering focuses on the replacement of diseased small-diameter blood vessels with a diameter less than 6 mm for which adequate substitutes still do not exist. One approach to vascular tissue engineering is to culture vascular cells on a scaffold in a bioreactor. The bioreactor establishes pseudophysiological conditions for culture (medium culture, 37°C, mechanical stimulation). Collagen gels are widely used as scaffolds for tissue regeneration due to their biological properties; however, they exhibit low mechanical properties. Mechanical characterization of these scaffolds requires establishing the conditions of testing in regard to the conditions set in the bioreactor. The effects of different parameters used during mechanical testing on the collagen gels were evaluated in terms of mechanical and viscoelastic properties. Thus, a factorial experiment was adopted, and three relevant factors were considered: temperature (23°C or 37°C), hydration (aqueous saline solution or air), and mechanical preconditioning (with or without). Statistical analyses showed significant effects of these factors on the mechanical properties which were assessed by tensile tests as well as stress relaxation tests. The last tests provide a more consistent understanding of the gels' viscoelastic properties. Therefore, performing mechanical analyses on hydrogels requires setting an adequate environment in terms of temperature and aqueous saline solution as well as choosing the adequate test.
Phosphorus Compartmentalization on the Cellular Level of Douglas Fir Root as Affected by Mn Toxicity: A Synchrotron‐Based FTIR Approach
Authors: Dučić Tanja , Thieme Jürgen , Polle Andrea
Published: July 2012

We investigated distribution of phosphorus under manganese toxicity in different tissues of 10 μm thin‐root cross‐section of Douglas fir (DF) (Pseudotsuga menziesii) seedlings by using synchrotron‐based Fourier transform infrared microscopy (SR‐FTIR) as a chemically sensitive imaging method. Manganese is an essential micronutrient in all organisms but may become toxic when present in excess. We found previously that DF variety glauca (DFG) and variety menziesii (DFM) differed in phosphorus uptake, subcellular localization, transport and tissue allocation, as an effect of manganese toxicity. To address the role of P in seedling tolerance under Mn toxicity, we determined P allocation in different root tissues. In DFG, but not in DFV, the P concentration was kept at a constant level even under Mn toxicity. Earlier X‐ray microanalysis showed Mn accumulation in epidermal and cortical cells of both varieties after Mn treatment, suggesting that the root endodermis was a barrier for Mn to protect the vascular system and shoot from high Mn, with possible role of P ameliorations. Here, we discuss the potential role of P in Mn compartmentalization and toxicity tolerance in two different varieties.
Study of Cellular Uptake of Modified Oligonucleotides by Using Time‐Resolved Microspectrofluorimetry and Florescence Imaging
Authors: Praus P. , Kočišová E. , Mojzeš P. , Štěpánek J. , Sureau F.
Published: July 2012

Fluorescence microimaging and homodyne phase‐resolved confocal microspectrofluorimetry were used to monitor the transport of antisense oligonucleotide into cancer MCF7 cells and the subsequent intracellular distribution. Phosphorothioate analog of 15‐mer oligoadenylate (dA15) labeled by ATTO 425 was complexed with 5,10,15,20‐tetrakis (1‐methyl‐4‐pyridyl) porphyrin (H2TMPyP4) as an uptake‐mediating agent. Fluorescence lifetime data within a broad spectral range have revealed properties of both components inside the cell. H2TMPyP4 lifetime inside the cell is not influenced in this malignant cell line, while the lifetime of modified oligonucleotide was found to be slightly shortened.
Polyphenol-Rich Fraction of Brown AlgaEcklonia cavaCollected from Gijang, Korea, Reduces Obesity and Glucose Levels in High-Fat Diet-Induced Obese Mice
Authors: Park Eun Young , Kim Eung Hwi , Kim Mi Hwi , Seo Young Wan , Lee Jung Im , Jun Hee Sook
Published: July 2012

Ecklonia cava (E. cava)is a brown alga that has beneficial effects in models of type 1 and type 2 diabetes. However, the effects ofE. cavaextracts on diet-induced obesity and type 2 diabetes have not been specifically examined. We investigated the effects ofE. cavaon body weight, fat content, and hyperglycemia in high-fat diet- (HFD) induced obese mice and sought the mechanisms involved. C57BL/6 male mice were fed a HFD (60% fat) diet or normal chow. After 3 weeks, the HFD diet group was given extracts (200 mg/kg) ofE. cavaharvested from Jeju (CA) or Gijang (G-CA), Korea or PBS by oral intubation for 8 weeks. Body weights were measured weekly. Blood glucose and glucose tolerance were measured at 7 weeks, and fat pad content and mRNA expression of adipogenic genes and inflammatory cytokines were measured after 8 weeks of treatment. G-CA was effective in reducing body weight gain, body fat, and hyperglycemia and improving glucose tolerance as compared with PBS-HFD mice. The mRNA expression of adipogenic genes was increased, and mRNA expression of inflammatory cytokines and macrophage marker gene was decreased in G-CA-treated obese mice. We suggest that G-CA reduces obesity and glucose levels by anti-inflammatory actions and improvement of lipid metabolism.
Spectroscopic (FT‐IR, Raman, NMR) and DFT Quantum Chemical Studies on Phenoxyacetic Acid and Its Sodium Salt
Authors: Samsonowicz M. , Regulska E. , Lewandowski W.
Published: July 2012

FT‐IR, Raman, and NMR spectra of phenoxyacetic acid and its sodium salt were recorded and analyzed. Optimized geometrical structures of studied compounds were calculated by B3LYP/6‐311++G** method. The atomic charges were calculated by Mulliken, NPA (natural population analysis), APT (atomic polar tensor), MK (Merz‐Singh‐Kollman method), and ChelpG (charges from electrostatic potentials using grid‐based method) methods. Geometric as well as magnetic aromaticity indices, dipole moments, and energies were also calculated. The theoretical wavenumbers and intensities of IR spectra as well as chemical shifts in  1H and  13C NMR spectra were obtained. The calculated parameters were compared with experimental characteristics of these molecules.
Theoretical and Experimental Studies on Alkali Metal Phenoxyacetates
Authors: Regulska E. , Samsonowicz M. , Świsłocka R. , Lewandowski W.
Published: July 2012

Optimized geometrical structures of alkali metal phenoxyacetates were obtained using B3LYP/6‐311++G** method. Geometric and magnetic aromaticity indices, dipole moments, and energies were calculated. Atomic charges on the atoms of phenoxyacetic acid molecule and its alkali metal salts were calculated by Mulliken, APT (atomic polar tensor), NPA (natural population analysis), MK (Merz‐Singh‐Kollman method), and ChelpG (charges from electrostatic potentials using grid‐based method) methods. The theoretical wavenumbers and intensities of IR as well as chemical shifts in NMR spectra were obtained and compared with experimental data. The effect of alkali metals on molecular structure of phenoxyacetic acid appears in the shift of selected bands along the series of alkali metal salts. The correlations between chosen bands and some metal parameters, such as electronegativity, ionization energy, and atomic, and ionic radius, have been noticed.
Background Estimation of Biomedical Raman Spectra Using a Geometric Approach
Authors: Kourkoumelis Nikolaos , Polymeros Alexandros , Tzaphlidou Margaret
Published: July 2012

Raman spectroscopy grows into an essential tool for biomedical applications. Nevertheless, the weak Raman signal associated mainly with biological samples is often obscured by a broad background signal due to the intrinsic fluorescence of the organic molecules present, making further analysis unfeasible. A computational geometry method based on the definition of convex hull is described to estimate the background from Raman spectra of samples with biological interest. The method is semiautomated requiring sample‐dependent user intervention. It does not depend, however, on curve fitting, requires no information about background distribution or source, and keeps the original spectral data intact.
Simulation and Domain Identification of Sea Ice Thermodynamic System
Authors: Tan Bing , Lu Peng , Li Zhijun , Feng Enmin , Wang Juan
Published: July 2012

Based on the measured data and characteristics of sea ice temperature distribution in space and time, this study is intended to consider a parabolic partial differential equation of the thermodynamic field of sea ice (coupled by snow, ice, and sea water layers) with a time‐dependent domain and its parameter identification problem. An optimal model with state constraints is presented with the thicknesses of snow and sea ice as parametric variables and the deviation between the calculated and measured sea ice temperatures as the performance criterion. The unique existence of the weak solution of the thermodynamic system is proved. The properties of the identification problem and the existence of the optimal parameter are discussed, and the one‐order necessary condition is derived. Finally, based on the nonoverlapping domain decomposition method and semi‐implicit difference scheme, an optimization algorithm is proposed for the numerical simulation. Results show that the simulated temperature of sea ice fit well with the measured data, and the better fit is corresponding to the deeper sea ice.
Mathematical Analysis of Inclusion Removal from Liquid Steel by Gas Bubbling in a Casting Tundish
Authors: Arcos-Gutierrez H. , Barreto J. de J. , Garcia-Hernandez S. , Ramos-Banderas A.
Published: July 2012

The mechanism of inclusion removal from liquid steel by gas bubbling and bubble attachment in the tundish is complex due to the great number of variables involved, and it is even more difficult to study because of the turbulent flow conditions. The main objective of this work is to analyze and improve the understanding of the alumina inclusion removal rate by bubble attachment and by gas bubbling fluid dynamics effects. The results show that the inclusion collection probability mainly depends on the attachment mechanism by collision. This parameter was determined by calculating the induction time, which is shorter when the rupture time and the formation time of a stable three phases contact (particle/liquid/gas) are ignored than when it is fully considered, affecting the attachment probability. In addition, to achieve acceptable inclusion removal, a smaller bubble diameter is required, such as 1 mm. This consideration is almost impossible to achieve during tundish operation; a more realistic bubble diameter around 10 mm is employed, resulting in a very inefficient inclusion removal process by bubble attachment. Nevertheless, in a real casting tundish the inclusion removal rate employing argon bubbling is efficient; is mainly due to the fluid flow pattern changes rather than bubble attachment. Consequently, it is imperative to consider the summation of both removal mechanisms to compute a better approximation of this important operation.
Raman Spectroscopy of Bacterial Species and Strains Cultivated under Reproducible Conditions
Authors: Almarashi Jamal F. M. , Kapel Natalia , Wilkinson Thomas S. , Telle Helmut H.
Published: July 2012

Rapid and reproducible discrimination between bacterial pathogens is a clear goal in microbiological laboratories when processing infected clinical samples. In this study Raman spectra were taken from at least 30 colonies of four strains of bacteria including Staphylococcus epidermidis (1457 and 9142) and Escherichia coli (K12 and Top 10) using the Renishaw in Via Raman microscope system. Analysis based on principal components suggests that even strain differentiation (e.g., 1457 versus 9142 or K12 versus Top10) is possible.
A Fixed Point Result for Boyd-Wong Cyclic Contractions in Partial Metric Spaces
Authors: Aydi Hassen , Karapinar Erdal
Published: July 2012

A fixed point theorem involving Boyd-Wong-type cyclic contractions in partial metric spaces is proved. We also provide examples to support the concepts and results presented herein.
Can a Gleason 6 or Less Microfocus of Prostate Cancer in One Biopsy and Prostate-Specific Antigen Level <10 ng/mL Be Defined as the Archetype of Low-Risk Prostate Disease?
Authors: Taverna Gianluigi , Benecchi Luigi , Grizzi Fabio , Seveso Mauro , Giusti Guido , Piccinelli Alessandro , Benetti Alessio , Colombo Piergiuseppe , Minuti Francesco , Graziotti Pierpaolo
Published: July 2012

Prostate cancer (PC) remains a cause of death worldwide. Here we investigate whether a single microfocus of PC at the biopsy (graded as Gleason 6 or less, ≤5% occupancy) and the PSA <10 ng/mL can define the archetype of low-risk prostate disease. 4500 consecutive patients were enrolled. Among them, 134 patients with a single micro-focus of PC were followed up, and the parameters influencing the biochemical relapse (BR) were analysed. Out of 134 patients, 94 had clinically significant disease, specifically in 74.26% of the patients with PSA <10 ng/mL. Positive surgical margins and the extracapsular invasion were found in 29.1% and 51.4% patients, respectively. BR was observed in 29.6% of the patients. Cox regression evidenced a correlation between the BR and Gleason grade at the retropubic radical prostatectomy (RRP), capsular invasion, and the presence of positive surgical margins. Multivariate regression analysis showed a statistically significant correlation between the presence of surgical margins at the RRP and BR. Considering a single micro-focus of PC at the biopsy and PSA serum level <10 ng/mL, clinically significant disease was found in 74.26% patients and only positive surgical margins are useful for predicting the BR.
Spectroscopic Determination of pKa Constants of MADS Box Segments
Authors: Řezáčová Barbora , Coïc Yves-Marie , Zentz Christian , Turpin Pierre-Yves , Štěpánek Josef
Published: July 2012

We have introduced a new promising approach for the determination of pKa constants of oligopeptide intrinsic fluorophores and spectral components referring to their differently charged states. The method is based on the factor analysis of multiwavelength spectroscopic pH titration data. As an illustration, we present its application on the study of short segments of the MADS box, which is a highly conserved sequence of a so‐called family of transcription factors, by techniques of UV absorption and fluorescence spectroscopies. Investigated oligopeptides contain no tryptophan but one tyrosine serving as an intrinsic fluorophore and absorber. The results indicate both good sensitivity and spectroscopic selectivity of our method, which thus may be considered as a complementary technique to conventional electrochemical methods.
The Effect of Bacterial Adhesion on Grafted Chains Revealed by the Non‐Invasive Sum Frequency Generation Spectroscopy
Authors: Bulard Emilie , Fontaine-Aupart Marie-Pierre , Dubost Henri , Zheng Wanquan , Herry Jean-Marie , Bellon-Fontaine Marie-Noëlle , Briandet Romain , Bourguignon Bernard
Published: July 2012

In biomedical and food industry, surface colonization by bacteria is harmful: it leads to biofilm formation, a microbial consortia more resistant to antibiotics than planktonic bacteria. In order to design materials able to limit the biofilm formation, the effect of bacteria on materials has to be well characterized. In this work, a well‐defined surface composed of a self‐assembled monolayer (SAM) of octadecanethiol (ODT) onto a gold surface is probed in situ. The SAM conformation is obtained using the femtosecond vibrational sum frequency generation (SFG) spectroscopy. This technique provides selectively the molecular vibrational signature of the interface. The behaviour of the ODT SAM is studied in different environments: in air, in water, and upon exposure to hydrophilic or hydrophobic Lactococcus lactis bacteria. Modelling the experimental SFG spectra reveals a measurable change of the SAM conformation which depends on the environment, especially on the hydrophilic‐hydrophobic character.
Characterization of Type I and IV Collagens by Raman Microspectroscopy: Identification of Spectral Markers of the Dermo‐Epidermal Junction
Authors: Nguyen T. T. , Gobinet C. , Feru J. , -Pasco S. Brassart , Manfait M. , Piot O.
Published: July 2012

Type I and IV collagens are important constituents of the skin. Type I collagen is found in all dermal layers in high proportion, while type IV collagen is localized in the basement membrane of the dermo‐epidermal junction (DEJ). These proteins are strongly altered during aging or cancer progression. Although they possess amino acid compositions which, are close, they present also important structural differences inducing specific physicochemical properties. Raman spectroscopy is based on a nondestructive interaction of the light with the matter. This technique permits to probe the intrinsic molecular composition of the samples without staining or particular preparation. The aim of our research is to study the correlation between the molecular conformations of type I and IV collagens and their Raman features. We showed that signals specific of each protein can be revealed and that they translate structural differences between the two collagens. From this collagens spectral characterization, the analysis of skin sections also permitted to identify spectral markers of dermis, epidermis, and epidermis/dermis interface. These preliminary results represent basic data for further studies, particularly to probe skin molecular alterations induced by chronologic aging.
Finite‐Time H∞ Filtering for Linear Continuous Time‐Varying Systems with Uncertain Observations
Authors: Zhao Huihong , Zhang Chenghui
Published: July 2012

This paper is concerned with the finite‐time H∞ filtering problem for linear continuous time‐varying systems with uncertain observations and ℒ2‐norm bounded noise. The design of finite‐time H∞ filter is equivalent to the problem that a certain indefinite quadratic form has a minimum and the filter is such that the minimum is positive. The quadratic form is related to a Krein state‐space model according to the Krein space linear estimation theory. By using the projection theory in Krein space, the finite‐time H∞ filtering problem is solved. A numerical example is given to illustrate the performance of the H∞ filter.
THz and IR Spectroscopy of Molecular Systems That Simulate Function‐Related Structural Changes of Proteins
Authors: Brandt N. N. , Chikishev A. Yu. , Mankova A. A. , Nazarov M. M. , Sakodynskaya I. K. , Shkurinov A. P.
Published: July 2012

The activity of enzymes in organic solvents substantially increases in the presence of crown ethers. Tris(hydroxymethyl)aminomethane (tris) is chosen as a model compound to simulate the interaction of surface amino groups of proteins with crown ether. The methods of FTIR and time‐domain THz spectroscopy are used to study the interaction of tris with 18‐crown‐6. The THz spectra of the complexes are measured for the first time.
Factors Important to the Prioritization and Development of Successful Topical Microbicides for HIV-1
Authors: Buckheit Karen W. , Buckheit Robert W.
Published: July 2012

Significant advancements in topical microbicide development have occurred since the prevention strategy was first described as a means to inhibit the sexual transmission of HIV-1. The lack of clinical efficacy of the first generation microbicide products has focused development attention on specific antiretroviral agents, and these agents have proven partially successful in human clinical trials. With greater understanding of vaginal and rectal virus infection, replication, and dissemination, better microbicide products and delivery strategies should result in products with enhanced potency. However, a variety of development gaps exist which relate to product dosing, formulation and delivery, and pharmacokinetics and pharmacodynamics which must be better understood in order to prioritize microbicide products for clinical development. In vitro, ex vivo, and in vivo models must be optimized with regard to these development gaps in order to put the right product at the right place, at the right time, and at the right concentration for effective inhibition of virus transmission. As the microbicide field continues to evolve, we must harness the knowledge gained from unsuccessful and successful clinical trials and development programs to continuously enhance our preclinical development algorithms.
A New Method for D2O/H2O Exchange in Infrared Spectroscopy of Proteins
Authors: Malferrari Marco , Venturoli Giovanni , Francia Francesco , Mezzetti Alberto
Published: July 2012

In this paper, we describe a new method to obtain D2O/H2O exchange in photosynthetic reaction centres from Rhodobacter sphaeroides. The method is characterized by: (i) a very high efficiency of the isotopic replacement; (ii) an extremely low amount of D2O needed; (iii) the short time required for dehydration and D2O rehydration; (iv) the possibility of controlling concomitantly the hydration state of the sample. The proposed method can be applied to other proteins.
Postdiverticular Stasis—Introduction of a New Etiology for Small Intestine Obstruction: A Case Series
Authors: Mousavi Seyed Abdollah , Karami Hassan
Published: July 2012

Introduction. Intestinal obstruction in the setting of Meckel’s diverticulum in young age and with orange and meat bezoar is a rare, previously unreported condition. Since the obstruction point is located immediately after Meckel’s diverticulum in our patients, we attempt to introduce “localized peristalsis insufficiency” as a new etiology for small intestine obstruction while reviewing the findings of previous studies.Conclusion. Intestinal obstruction in the setting of Meckel’s diverticulum and with orange and meat bezoar is a rare, previously unreported condition. Considering the previous reports, we may present the theory oflocalized peristalsis insufficiencyin patients with Meckel’s diverticulum.
Global Existence of Strong Solutions to a Class of Fully Nonlinear Wave Equations with Strongly Damped Terms
Authors: Pan Zhigang , Luo Hong , Ma Tian
Published: July 2012

We consider the global existence of strong solution u, corresponding to a class of fully nonlinear wave equations with strongly damped terms utt − kΔut = f(x, Δu) + g(x, u, Du, D2u) in a bounded and smooth domain Ω in Rn, where f(x, Δu) is a given monotone in Δu nonlinearity satisfying some dissipativity and growth restrictions and g(x, u, Du, D2u) is in a sense subordinated to f(x, Δu). By using spatial sequence techniques, the Galerkin approximation method, and some monotonicity arguments, we obtained the global existence of a solution .
Fertility Intentions and Interest in Integrated Family Planning Services among Women Living with HIV in Nyanza Province, Kenya: A Qualitative Study
Authors: Harrington Elizabeth K. , Newmann Sara J. , Onono Maricianah , Schwartz Katie D. , Bukusi Elizabeth A. , Cohen Craig R. , Grossman Daniel
Published: July 2012

Despite increasing efforts to address the reproductive health needs of people living with HIV, a high unmet need for contraception exists among HIV+ women in sub-Saharan Africa. This study explores the fertility intentions and family planning (FP) preferences of Kenyan women accessing HIV treatment. We conducted 30 semistructured interviews and qualitatively analyzed the data with a grounded theory approach. Fears of premature death, financial hardship, and perinatal HIV transmission emerged as reasons for participants’ desire to delay/cease childbearing. Participants strongly identified FP needs, yet two-thirds were using male condoms alone or no modern method of contraception. Women preferred the HIV clinic as the site of FP access for reasons of convenience, provider expertise, and a sense of belonging, though some had privacy concerns. Our findings support the acceptability of integrated FP and HIV services. Efforts to empower women living with HIV to prevent unintended pregnancies must expand access to contraceptive methods, provide confidential services, and take into account women's varied reproductive intentions.
Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues
Authors: Schneider Luke V. , Likhte Varsha , Wright William H. , Chu Frances , Cambron Emma , Baldwin-Burnett Anne , Krakow Jessica , Smejkal Gary B.
Published: July 2012

Integral membrane proteins play key biological roles in cell signaling, transport, and pathogen invasion. However, quantitative clinical assays for this critical class of proteins remain elusive and are generally limited to serum-soluble extracellular fragments. Furthermore, classic proteomic approaches to membrane protein analysis typically involve proteolytic digestion of the soluble pieces, resulting in separation of intra- and extracellular segments and significant informational loss. In this paper, we describe the development of a new method for the quantitative extraction of intact integral membrane proteins (including GPCRs) from solid metastatic ovarian tumors using pressure cycling technology in combination with a new (ProteoSolve-TD) buffer system. This new extraction buffer is compatible with immunoaffinity methods (e.g., ELISA and immunoaffinity chromatography), as well as conventional proteomic techniques (e.g., 2D gels, western blots). We demonstrate near quantitative recovery of membrane proteins EDG2, EDG4, FASLG, KDR, and LAMP-3 by western blots. We have also adapted commercial ELISAs for serum-soluble membrane protein fragments (e.g., sVEGFR2) to measure the tissue titers of their transmembrane progenitors. Finally, we demonstrate the compatibility of the new buffers with immunoaffinity enrichment/mass spectrometric characterization of tissue proteins.
Thymoquinone β‐Cyclodextrin Nanoparticles System: A Preliminary Study
Authors: Cardoso T. , Galhano C. I. C. , Ferreira Marques M. F. , Moreira da Silva A.
Published: July 2012

Thymoquinone is a natural product, the main constituent of Nigella sativa seeds, which exhibits anti‐inflammatory and anticancer activities. Among several existing molecules capable of forming an inclusion compound structure, cyclodextrins are applied in the pharmaceutical industry either to increase solubility of hydrophobic molecules or to protect molecules from inactivation or degradation. β‐Cyclodextrin is currently the most common cyclodextrin in pharmaceutical formulations and probably the best studied in humans. In order to study the properties of inclusion compounds based on cyclodextrins and thymoquinone Fourier Transform Infrared (FTIR), Ultraviolet‐Visible, Positron Annihilation Lifetime (PAL) Spectroscopies and calorimetric studies by Differential Scanning Calorimetry (DSC) were used. The obtained results indicate the formation of a 1 : 1 inclusion compound between cyclodextrin and thymoquinone. PALS and DSC measurements also provided evidence of the inclusion compound′s activity.
Determination of Thiocyanate by Kinetic Spectrophotometric Flow Injection Analysis
Authors: Keyvanfard Mohsen , Alizad Khadijeh , Elahian Parinaz
Published: July 2012

A simple and rapid flow injection spectrophotometric method has been developed for the determination of amount of thiocyanate in wastewaters and well water samples. It is based on the reaction of thiocyanate in hydrochloric acid with janus green and bromate. Reaction was monitored spectrophotometrically by measuring janus green absorbance at λmax = 554 nm. The calibration graph was linear over the range 0.02–1.0 μg mL−1 and the detection limit was 0.016 μg mL−1 (s/n = 3). The throughput was 25 samples per hour.
Multi‐Component Adsorption of Benzene, Toluene, Ethylbenzene, and Xylene from Aqueous Solutions by Montmorillonite Modified with Tetradecyl Trimethyl Ammonium Bromide
Authors: Nourmoradi H. , Khiadani Mehdi , Nikaeen M.
Published: July 2012

Multicomponent adsorption of benzene, toluene, ethylbenzene, and xylene (BTEX) was assessed in aqueous solutions by montmorillonite modified with tetradecyl trimethyl ammonium bromide (TTAB‐Mt). Batch experiments were conducted to determine the influences of parameters including loading rates of surfactant, contact time, pH, adsorbate concentration, and temperature on the adsorption efficiency. Scanning electron microscope (SEM) and X‐ray diffractometer (XRD) were used to determine the adsorbent properties. Results showed that the modification of the adsorbent via the surfactant causes structural changes of the adsorbent. It was found that the optimum adsorption condition achieves with the surfactant loading rate of 200% of the cation exchange capacity (CEC) of the adsorbent for a period of 24 h. The sorption of BTEX by TTAB‐Mt was in the order of B < T < E < X. The experimental data were fitted by many kinetic and isotherm models. The results also showed that the pseudo‐second‐order kinetic model and Freundlich isotherm model could, respectively, be fitted to the experimental data better than other available kinetic and isotherm models. The thermodynamic study indicated that the sorption of BTEX with TTAB‐Mt was achieved spontaneously and the adsorption process was endothermic as well as physical in nature. The regeneration results of the adsorbent also showed that the adsorption capacity of adsorbent after one use was 51% to 70% of original TTAB‐Mt.
The Use of Quantitative Real-Time Reverse Transcriptase PCR for 5′ and 3′ Portions of ALK Transcripts to Detect ALK Rearrangements in Lung Cancers
Authors: Wang Rui , Pan Yunjian , Li Chenguang , Hu Haichuan , Zhang Yang , Li Hang , Luo Xiaoyang , Zhang Jie , Fang Zhaoyuan , Li Yuan , Shen Lei , Ji Hongbin , Garfield David , Sun Yihua , Chen Haiquan
Published: July 2012

Purpose: Approximately 3% to 7% of non–small cell lung cancers (NSCLC) harbor an ALK fusion gene, thus defining a tumor group that may be responsive to targeted therapy. The breakpoint in ALK consistently occurs at exon 20 and EML4 or other fusion partners, thus driving a strong expression of ALK kinase domain and resulting in an unbalanced expression in 5′ and 3′ portions of ALK transcripts. We have developed a rapid and accurate method by simultaneously detecting the expression in 5′ and 3′ portions of ALK mRNA.

Experimental Design: Quantitative real-time reverse transcriptase PCR (qRT-PCR) was used to examine expression levels of the 5′ and 3′ portions of ALK transcripts in177 NSCLCs, in which EGFR, KRAS, HER2, and BRAF mutations were absent. If unbalanced ALK mRNA expression was seen, ALK rearrangement was assumed to exist. ALK FISH was used to confirm the accuracy of qRT-PCR. RT-PCR and 5′ RACE coupling sequencing identified the fusion variants.

Results: Real-time RT-PCR showed excellent sensitivity and specificity (100% and 100%, respectively) for detection of ALK rearrangements in resected specimens. In addition, six novel ALK fusion variants were identified, including one KIF5B-ALK (E17;A20) and five EML4-ALK variants (E6a;A19, E6a/b ins 18;A20, E17b ins 39;A20, E10a/b, E13;A20, and E17 ins 65;A20).

Conclusions: Real-time RT-PCR is a rapid and accurate method for diagnosing ALK-rearranged lung cancers. Coupling of 5′ RACE to this method should further facilitate rapid identification of novel ALK fusion genes. Clin Cancer Res; 18(17); 4725–32. ©2012 AACR.