Shear-induced transitions in colloidal and polymeric liquids.

This review reflects different aspects of wide current studies of the phenomena related to the shear-induced structure transformation in various complex liquids. Experimental data, being the basis of this discussion, were obtained for polymeric liquids (melts, blends, solutions) and different dispersions (colloidal solutions, suspensions, emulsions). The general initial input of shearing is the creation of inhomogeneities which can continue to remain as separate domains, become the nuclei of new phases, or become diffuse, leading to phase separation. The following effects are discussed: diffusion-induced phase separation, phase transitions occurring mainly due to the deformation-driven orientation of polymer chains and worm-like micelles that results in the formation of a liquid-crystal state, as well as self-assembly effects. It can be stressed that the appearance of regular structures takes place in systems that can coexist in different concentrations or phase states at the same stress or shear rate. This is linked with the existence of two-value points on flow curves (part of a flow curve with negative slope) or transient regimes of deformation that lead to instability of the flow. The described experimental facts are briefly discussed on the basis of the application of different constitutive molecular or phenomenological rheological models.

Wall slip for complex liquids - Phenomenon and its causes.

In this review, we tried to qualify different types and mechanisms of wall slip phenomenon, paying particular attention to the most recent publications and issues. The review covers all type of fluids - homogeneous low molecular weight liquids, polymer solution, multi-component dispersed media, and polymer melts. We focused on two basic concepts - fluid-solid wall interaction and shear-induced fluid-to-solid transitions - which are the dominant mechanisms of wall slip. In the first part of the review, the theoretical and numerical studies of correlation of wetting properties and wall slip of low molecular weight liquids and polymeric fluids are reviewed along with some basic experimental results. The influence of nanobubbles and microcavities on the effectiveness of wall slip is illuminated with regard to the bubble dynamics, as well as their stability at smooth and rough interfaces, including superhydrophobic surfaces. Flow of multi-component matter (microgel pastes, concentrated suspensions of solid particles, compressed emulsions, and colloidal systems) is accompanied by wall slip in two cases. The first one is typical of viscoplastic media which can exist in two different physical states, as solid-like below the yield point and liquid-like at the applied stresses exceeding this threshold. Slip takes place at low stresses. The second case is related to the transition from fluid to solid states at high deformation rates or large deformations caused by the strain-induced glass transition of concentrated dispersions. In the latter case, the wall effects consist of apparent slip due to the formation of a low viscous thin layer of fluid at the wall. The liquid-to-solid transition is also a dominant mechanism in wall slip of polymer melts because liquid polymers are elastic fluids which can be in two relaxation states depending on the strain rate. The realization of these mechanisms is determined by polymer melt interaction with the solid wall.

Generation of Subterahertz Superradiance Pulses Based on Excitation of a Surface Wave by Relativistic Electron Bunches Moving in Oversized Corrugated Waveguides.

The first experiments on the observation of short pulsed superradiant (SR) emission with the excitation of a surface wave by a relativistic electron bunch moving in an oversized corrugated waveguide were performed. Subterahertz SR pulses with a central frequency of 0.14 THz, an ultrashort duration of 150 ps, and an extremely high peak power of 50-70 MW were generated. The experiments were based on a theoretical consideration including the quasioptical approach and direct particle-in-cell simulations.

Using Two-Dimensional Distributed Feedback for Synchronization of Radiation from Two Parallel-Sheet Electron Beams in a Free-Electron Maser.

A spatially extended planar 75 GHz free-electron maser with a hybrid two-mirror resonator consisting of two-dimensional upstream and traditional one-dimensional downstream Bragg reflectors and driven by two parallel-sheet electron beams 0.8 MeV/1 kA has been elaborated. For the highly oversized interaction space (cross section 45×2.5 vacuum wavelengths), the two-dimensional distributed feedback allowed realization of stable narrow-band generation that includes synchronization of emission from both electron beams. As a result, spatially coherent radiation with the output power of 30-50 MW and a pulse duration of ∼100 ns was obtained in each channel.

Raman spectroscopy for cytopathology of exfoliated cervical cells.

Cervical cancer is the fourth most common cancer affecting women worldwide but mortality can be decreased by early detection of pre-malignant lesions. The Pap smear test is the most commonly used method in cervical cancer screening programmes. Although specificity is high for this test, it is widely acknowledged that sensitivity can be poor mainly due to the subjective nature of the test. There is a need for new objective tests for the early detection of pre-malignant cervical lesions. Over the past two decades, Raman spectroscopy has emerged as a promising new technology for cancer screening and diagnosis. The aim of this study was to evaluate the potential of Raman spectroscopy for cervical cancer screening using both Cervical Intraepithelial Neoplasia (CIN) and Squamous Intraepithelial Lesion (SIL) classification terminology. ThinPrep® Pap samples were recruited from a cervical screening population. Raman spectra were recorded from single cell nuclei and subjected to multivariate statistical analysis. Normal and abnormal ThinPrep® samples were discriminated based on the biochemical fingerprint of the cells using Principal Component Analysis (PCA). Principal Component Analysis - Linear Discriminant Analysis (PCA-LDA) was employed to build classification models based on either CIN or SIL terminology. This study has shown that Raman spectroscopy can be successfully applied to the study of routine cervical cytology samples from a cervical screening programme and that the use of CIN terminology resulted in improved sensitivity for high grade cases.

3D quasioptical theory of terahertz superradiance of an extended electron bunch moving over a corrugated surface.

We consider the superradiance of an extended relativistic electron bunch moving over a periodically corrugated surface for the generation of multimegawatt terahertz pulses. To study the above process we have developed a three-dimensional, self-consistent, quasioptical theory of Cherenkov stimulated emission which includes a description of the formation of an evanescent wave over a corrugated surface and its excitation by rf current induced in the electron bunch.

Self-organization in the flow of complex fluids (colloid and polymer systems). Part 2: Theoretical models.

Flow induced transitions in complex fluids are usually accompanied by changes in the internal media structure and the flow symmetry. In this review paper, we discuss the theoretical models and approaches that have been used for the analysis of different types of flow instabilities and flow patterns. The main attention is focused on the basic fluid models which reveal vortex and banding flow structures at high shear rates. The Oldroyd-B fluid is one of such models. The Reynolds and the Weissenberg (or Deborah) numbers are the parameters governing its flow behavior. For this model, the secondary flow patterns arising in viscometric flows of different geometries at the bifurcation point are described. Complex fluids which are able to exist in multiple states can form coexisting bands of different structures with different rheological properties and flowing with different shear rates at the same shear stress. Shear banding is typical for fluids demonstrating non-monotonous flow curves described by such models as the diffusive Johnson-Segalman fluid model, for example. Recent progress in exploring this phenomenon is discussed.

Self-organization in the flow of complex fluids (colloid and polymer systems): part 1: experimental evidence.

Different types of regular and irregular self-organized structures observed in deformation of colloid and polymer substances ("complex fluids") are discussed and classified. This review is focused on experimental evidence of structure formation and self-organization in shear flows, which have many similar features in systems of different types. For single-phase (uniform) polymer systems regular periodic surface structures are observed. Two main types of these structures are possible: small-scale regular screw-like periodic structures along the whole stream (usually called "shark-skin") and long-period smooth and distorted parts of a stream attributed as a "stick-slip" effect. The origin of surface irregularities of both types is elasticity of a liquid. In the limiting case of high enough Weissenberg numbers, medium loses fluidity and should be treated as a rubbery matter. The liquid-to-rubbery transition at high Weissenberg numbers is considered as the dominating mechanism of instability, leading in particular to the wall slip and rupture of a stream. Secondary flows ("vorticity") in deformation polymeric substances and complex fluids are also obliged to their elasticity and the observed Couette-Taylor-like cells, though being similar to well-known inertial secondary flows, are completely determined by elasticity of colloid and polymeric systems. In deformation of colloidal systems, suspensions and other dense concentrated heterophase materials, structure formation takes place at rest and the destroying of the structure happens as the yield stress. In opposite to this case, strong deformations can lead to the shear-induced structure formation and jamming. These effects are of general meaning for any complex fluids as well as for dense suspensions and granular media. Strong deformations also lead to separation of a stream into different parts (several "bands") with various properties of liquids in these parts. So, two principal effects common for any polymers and complex fluids can be pointed at as the physical origin of self-organization in shearing. This is elasticity of a liquid and a possibility of its existence in different phases or relaxation states, while in many cases elasticity of a fluid is considered as the most important provoking factor for transitions between different types of rheological behavior, e.g. the fluid-to-rubbery-like behavior at high deformation rates and the transition from the real laminar flow to wall slip.

Chlamydia trachomatis detection in cervical PreservCyt specimens from an Irish urban female population.

OBJECTIVE: The aim of this study was to determine the prevalence of cervical Chlamydia trachomatis infection by polymerase chain reaction (PCR) in urban women undergoing routine cervical cytological screening and to investigate the relationship with age, cytology, smoking status and concurrent human papillomavirus (HPV) infection. METHODS: A total of 996 women (age range 16-69 years) attending general practitioners for routine liquid-based cervical smear screening in the Dublin area were recruited in the study of prevalence of C. trachomatis. Informed consent was obtained and liquid-based cytology (LBC) specimens were sent for cytological screening. DNA was extracted from residual LBC and tested for C. trachomatis by PCR using the highly sensitive C. trachomatis plasmid (CTP) primers and for HPV infection using the MY09/11 primers directed to the HPV L1 gene in a multiplex format. RESULTS: The overall prevalence of C. trachomatis was 5.4%. Prevalence was highest in the <25 years age group (10%). Coinfection with HPV and C. trachomatis occurred in 1% of the screening population. A higher rate of smoking was observed in women positive for C. trachomatis, HPV infections or those with abnormal cervical cytology. Chlamydia trachomatis infection was not associated with abnormal cytology. CONCLUSIONS: Women (5.4%) presenting for routine cervical screening are infected with C. trachomatis. Opportunistic screening for C. trachomatis from PreservCyt sample taken at the time of cervical cytological screening may be a possible strategy to screen for C. trachomatis in the Irish female population.

Human papillomavirus prevalence and genotypes in an opportunistically screened Irish female population.

This study aims to evaluate human papillomavirus (HPV) prevalence and predominating genotypes in liquid-based cervical cytology samples from an Irish urban female population. In addition to use of routine cervical cytology testing, women are screened for HPV using the MY09/11 primers for the HPV L1 gene and primers for beta-globin amplification in a multiplex format. Overall, 996 women between the ages of 16 and 72 years (average age: 35) are included in the study and HPV prevalence was 19.8%. Cytology results showed that 88.9% were normal, 9% borderline or mild dyskaryosis, 1.1% moderate dyskaryosis and 0.9% severe dyskaryosis. Human papillomavirus prevalence in women under 25 was 31%, reducing to 23% in women in the 25-35 age group and to 11% in women over 35. Human papillomavirus prevalence increased with grade of cytology from 11.4% (normal) through 85.4% (borderline), 84% (mild), 100% (moderate) to 100% (severe dyskaryosis). HPV 16 (20%) and 18 (12%) were the most common high-risk types detected in the study. Other common high-risk types were (in descending order) HPV 66, 33, 53, 31 and 58. HPV 66 was associated with the detection of borderline abnormalities by cytology. This is the first population-based study of HPV prevalence in the normal healthy cervical screening population in the Republic of Ireland.

Comparison of DNA extraction from cervical cells collected in PreservCyt solution for the amplification of Chlamydia trachomatis.

OBJECTIVE: The aim of this study was to compare and evaluate three methods of DNA extraction for the amplification of Chlamydia trachomatis in uterine cervical samples collected in PreservCyt solution. ThinPrep is the trade name for the slide preparation. METHODS: Thirty-eight samples collected in LCx buffer medium, which were identified as C. trachomatis infected by ligase chain reaction (LCR), were selected for this study. DNA from the PreservCyt samples was extracted by three methods: (i) QIAamp kit, (ii) boiling in Tris-EDTA buffer with Chelex purification, and (iii) Proteinase K digestion with Chelex purification. Sample DNA was tested for the presence of C. trachomatis by PCR using cryptic plasmid research (CTP) primers and major outer membrane protein research momp gene (MOMP) primers. Real-time (LightCycler) PCR for relative C. trachomatis quantification following DNA extraction was performed using primers (Hsp 60) for the 60 kDa heat-shock protein hsp60 gene. RESULTS: Amplification using CTP primers was the most successful with each of the extraction protocols. Boiling in buffer was the least successful extraction method. QIAamp was the best extraction method, yielding the most positives with both the CTP and MOMP primers. Proteinase K-Chelex extraction gave similar sensitivity to QIAamp extraction with CTP primers but lower for MOMP primers. CONCLUSIONS: The DNA extraction method must be carefully selected to ensure that larger PCR amplicons can be successfully produced by PCR and to ensure high sensitivity of detection of C. trachomatis. In this study it was found that the QIAamp extraction method followed by PCR with the CTP primers was the most successful for amplification of C. trachomatis DNA.

Macromolecular crystal growth investigations using atomic force microscopy.

Direct visualization of macromolecular crystal growth using atomic force microscopy (AFM) has provided a powerful tool in the delineation of mechanisms and the kinetics of the growth process. It has further allowed us to evaluate the wide variety of impurities that are incorporated into crystals of proteins, nucleic acids, and viruses. It is possible, using AFM, to image the defects and imperfections that afflict these crystals, the impurity layers that poison their surfaces, and the consequences of various factors on morphological development. All of these can be recorded under normal growth conditions, in native mother liquors, over time intervals ranging from minutes to days, and at the molecular level.

Structure of intracellular mature vaccinia virus visualized by in situ atomic force microscopy.

Vaccinia virus, the basis of the smallpox vaccine, is one of the largest viruses to replicate in humans. We have used in situ atomic force microscopy (AFM) to directly visualize fully hydrated, intact intracellular mature vaccinia virus (IMV) virions and chemical and enzymatic treatment products thereof. The latter included virion cores, core-enveloping coats, and core substructures. The isolated coats appeared to be composed of a highly cross-linked protein array. AFM imaging of core substructures indicated association of the linear viral DNA genome with a segmented protein sheath forming an extended approximately 16-nm-diameter filament with helical surface topography; enclosure of this filament within a 30- to 40-nm-diameter tubule which also shows helical topography; and enclosure of the folded, condensed 30- to 40-nm-diameter tubule within the core by a wall covered with peg-like projections. Proteins observed attached to the 30- to 40-nm-diameter tubules may mediate folding and/or compaction of the tubules and/or represent vestiges of the core wall and/or pegs. An accessory "satellite domain" was observed protruding from the intact core. This corresponded in size to isolated 70- to 100-nm-diameter particles that were imaged independently and might represent detached accessory domains. AFM imaging of intact virions indicated that IMV underwent a reversible shrinkage upon dehydration (as much as 2.2- to 2.5-fold in the height dimension), accompanied by topological and topographical changes, including protrusion of the satellite domain. As shown here, the chemical and enzymatic dissection of large, asymmetrical virus particles in combination with in situ AFM provides an informative complement to other structure determination techniques.

Repair of impurity-poisoned protein crystal surfaces.

The surface morphology of Bence-Jones protein (BJP) crystals was investigated during growth and dissolution by using in situ atomic force microscopy (AFM). It was shown that over a wide supersaturation range, impurities adsorb on the crystalline surface and ultimately form an impurity adsorption layer that prevents further growth of the crystal. At low undersaturations, this impurity adsorption layer prevents dissolution. At greater undersaturation, dissolution takes place around large particles incorporated into the crystal, leading to etch pits with impurity-free bottoms. On restoration of supersaturation conditions, two-dimensional nucleation takes place on the impurity-free bottoms of these etch pits. After new growth layers fill in the etch pits, they cover the impurity-poisoned top layer of the crystal face. This leads to the resumption of its growth. Formation of an impurity-adsorption layer can explain the termination of growth of macromolecular crystals that has been widely noted. Growth-dissolution-growth cycles could be used to produce larger crystals that otherwise would have stopped growing because of impurity poisoning.

Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology.

Atomic force microscopy (AFM) investigation revealed the sources of disorder and mechanisms of their formation in crystals of an icosahedral plant virus, Cucumber Mosaic Virus (CMV) and structure of the Herpes Simplex Virus (HSV-1). The combination of defects and local disorder in CMV crystals presented here are likely the physical bases for mosaicity in virus crystals, and may be largely responsible for their limited diffraction resolution. High-resolution images of intact, enveloped HSV-1 and the underlying capsid structure demonstrate capabilities of AFM to probe structures of large macromolecular assemblies.

Evaluation of liquid-based cytology in cervical screening of high-risk populations: a split study of colposcopy and genito-urinary medicine populations.

A split study evaluated the ThinPrep(R) PapTesttrade mark (TP; Cytyc Corp., Boxborough, MA) compared with current methodologies of cervical cytology in two high-risk cohorts. One thousand, three hundred cases from a colposcopy clinic and a genito-urinary medicine outpatient clinic were examined. The TP reported increased detection of all grades of dyskaryosis (mild, moderate and severe; + 4.5%) and a decrease in borderline and unsuitable cases (- 4.9%). Four cases of high-grade dyskaryosis (moderate or severe) were detected only using the TP, while an additional four cases classified as high-grade dyskaryosis with the TP were reported as borderline by our conventional methods. The split-study finding of increased sensitivity with the TP provides for improved clinical management of patients in our high-risk cohorts.

Self-repair of biological fibers catalyzed by the surface of a virus crystal.

Helical fibers, presumably proteinaceous and of microbial origin, have been visualized by atomic force microscopy on the surfaces of crystals of satellite tobacco mosaic virus. If the crystals are growing, then the fibers are incorporated intact into the crystal lattice. If broken on the crystal surface, then within a few minutes, the fibers self-reassemble to reestablish continuity. This, we believe, is the first observation of such a crystal surface-catalyzed repair of a biological structure. The surfaces of virus crystals provide ideal workbenches for the visualization and manipulation of nanoscale objects, particularly extended structures such as these fibers.

Atomic force microscopy applications in macromolecular crystallography.

Atomic force microscopy (AFM) can be applied both in situ and ex situ to study the growth of crystals from solution. The method is particularly useful for investigating the crystallization of proteins, nucleic acids and viruses because it can be carried out in the mother liquor and in a non-perturbing fashion. Interactions and transformations between various growth mechanisms can be directly visualized as a function of supersaturation, as can the incorporation of diverse impurities and the formation and propagation of defects. Because the crystals can be observed over long periods, it is also possible to obtain precise quantitative measures of the kinetic parameters for nucleation and growth. Finally, AFM has allowed us to identify a number of previously unsuspected phenomena that influence nucleation, rate of growth and the ultimate perfection of macromolecular crystals. These are all features which are important in determining the ultimate resolution and quality of a crystal's diffraction pattern.

X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin.

The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 A resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 A, alpha = beta = gamma = 111.1 degrees. The resulting R and R(free) were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C222(1), unit-cell parameters a = 136.5, b = 150.3, c = 133.4 A) was also refined with threefold non-crystallographic symmetry restraints. R and R(free) were 0.181 and 0.226, respectively, for 2.6 A resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478-489; Ko et al. (1993), Plant Physiol. 101, 729-744]. A phosphate ion was identified in the lumen of the C-terminal beta-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both 'top-up' and 'bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C222(1) crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations.