Spitz tumour with ALK rearrangement: A case report and literature review.

Spitz tumour with ALK rearrangement is a recently described entity and a rare tumour. The incidence of Spitz tumour was estimated at 3.63 per 100,000 persons in American paediatric population; while there is no data in Asian population. Here we reported a case of an eleven-year-old Asian boy who presented with a left shin nodule of two months' duration. The skin biopsy revealed a Spitz tumour with predominantly spindle cell morphology arranged in fascicles, vertically orientated nests and radial growth pattern. Junctional component, melanin pigment or Kamino bodies were not identified. Immunohistochemical study displayed homogenous cytoplasmic staining for ALK. Fluorescence in-situ hybridisation (FISH) analysis confirmed ALK rearrangement. Review of the literatures demonstrated that positive ALK immunohistochemistry may not correlate with ALK rearrangement. ALK-rearranged Spitz tumour confirmed with FISH analysis favour clinically benign behaviour despite atypical histomorphology or positive sentinel lymph node. Therefore, correlation of histomorphology, immunohistochemical stain and molecular study are important for the definitive diagnosis of this entity.

Idiopathic ileal volvulus with multiple concomitant infections in a starving man.

BACKGROUND: Small bowel volvulus is defined as the torsion of the small intestine, potentially leading to bowel obstruction, gangrene and perforation. It is a rare condition, especially in adults. CASE PRESENTATION: A 30-year-old man was retrieved from the jungle with severe weight loss and abdominal symptoms. He succumbed to death despite 22 days of intensive medical treatment. An autopsy revealed a ruptured gangrenous ileal volvulus with peritonitis and subdiaphragmatic abscess. Further laboratory analysis detected systemic Candida tropicalis and intestinal gramnegative bacterial sepsis, systemic Zika virus viremia, leptospirosis complicating rhabdomyolysis and disseminated intravascular coagulopathy, Type I Herpes Simplex virus infection of the tongue and upper gastrointestinal tract. The cause of death was the ruptured ileal volvulus, complicated with upper gastrointestinal bleeding due to Herpes simplex virus esophagitis in a malnourished patient with resolving leptospirosis and underlying Zika virus co-infection. CONCLUSION: Rare clinical scenarios of adult-onset intestinal volvulus with concomitant multiple infections precludes clinical diagnosis and early treatment, leading to devastating consequences of clinical outcome. The positive clinical and postmortem correlation is a good learning lesson in many disciplines of medicine and science.

Intraoperative frozen section sentinel lymph node assessment in breast cancer: A tertiary institution experience.

INTRODUCTION: Intraoperative frozen section lymph node assessment helps to predict axillary lymph node metastasis in breast cancer. However, the accuracy of this frozen section analysis may vary among institutions. This study describes our institution's experience in intraoperative analysis of sentinel lymph node and aims to determine the accuracy, sensitivity and specificity of our assessment. MATERIALS AND METHODS: We retrospectively analysed the histopathological material and data from 82 breast cancer patients diagnosed over a period of four years who underwent intraoperative frozen section evaluation of sentinel lymph nodes. RESULTS: Frozen section analysis detected metastasis in 13 out of 82 cases and definitive pathological examination on the paraffin section confirmed these positive findings. There was no false positive case (specificity of 100%). The true positive cases comprised seven macrometastases, five micrometastases and one isolated tumour cells. Sampling error was noted in two cases in which the malignant cells were only present in the deeper final paraffin sections (false negative rate of 13.3%). The test sensitivity was 86.7% and the accuracy rate was 97.5%. These findings are comparable to other published data. CONCLUSION: Intraoperative frozen section analysis is a safe and reliable method for assessment of sentinel lymph node. Knowledge on limitation of frozen section analysis with diligent evaluation of frozen section specimen will be beneficial in reducing interpretation error.

Broadband signal response of thermo-acoustic devices and its applications.

Thermo-acoustic (TA) transducers are generation of sound speakers without any mechanical vibration system which exhibit an extremely wide frequency response range. In this paper, acoustic field responses to broadband input signals applied to both free-standing and nano-thinfilm-substrate thermo-acoustic devices are developed theoretically by using the Fourier transformation. A series of signals, including single-frequency signal, square root signal, periodic triangle wave signal, and periodic rectangular pulse signal, are applied to these TA devices in simulations and the acoustic pressure responses are investigated. The reproducibility of input signals is predicted. The single frequency results show good agreement with previously published experimental results. Alternative methods for reproducing the original signals with small distortion and low power consumption are introduced. The excellent performance of the TA devices on broadband signal responses will provide a design approach for sound parametric array and underwater communication equipment.

Nonlinear wave propagation in porous materials based on the Biot theory.

Nonlinearity must be considered with some porous granular media because of the large deformation under seismic waves. In this study, the propagation of nonlinear waves in porous media is studied based on the Biot theory and the governing equations are obtained by the Lagrangian formulation. Three new nonlinear parameters are introduced to consider the coupled nonlinearity between the solid and fluid components in porous media. It is shown that an additional nonlinear wave with a double frequency is generated by the coupling effect of linear fast and slow waves. When only a shear wave is applied at the source, no double-frequency nonlinear wave is predicted and three nonlinear longitudinal waves are generated. On the basis of the practical case studies, the effect of strong nonlinearity is computed under the influence of a one-dimensional single longitudinal wave source and a single shear wave source.

Use of density functional theory method to calculate structures of neutral carbon clusters Cn (3 ≤ n ≤ 24) and study their variability of structural forms.

In this work, we present modifications to the well-known basin hopping (BH) optimization algorithm [D. J. Wales and J. P. Doye, J. Phys. Chem. A 101, 5111 (1997)] by incorporating in it the unique and specific nature of interactions among valence electrons and ions in carbon atoms through calculating the cluster's total energy by the density functional tight-binding (DFTB) theory, using it to find the lowest energy structures of carbon clusters and, from these optimized atomic and electronic structures, studying their varied forms of topological transitions, which include a linear chain, a monocyclic to a polycyclic ring, and a fullerene/cage-like geometry. In this modified BH (MBH) algorithm, we define a spatial volume within which the cluster's lowest energy structure is to be searched, and introduce in addition a cut-and-splice genetic operator to increase the searching performance of the energy minimum than the original BH technique. The present MBH/DFTB algorithm is, therefore, characteristically distinguishable from the original BH technique commonly applied to nonmetallic and metallic clusters, technically more thorough and natural in describing the intricate couplings between valence electrons and ions in a carbon cluster, and thus theoretically sound in putting these two charged components on an equal footing. The proposed modified minimization algorithm should be more appropriate, accurate, and precise in the description of a carbon cluster. We evaluate the present algorithm, its energy-minimum searching in particular, by its optimization robustness. Specifically, we first check the MBH/DFTB technique for two representative carbon clusters of larger size, i.e., C60 and C72 against the popular cut-and-splice approach [D. M. Deaven and K. M. Ho, Phys. Rev. Lett. 75, 288 (1995)] that normally is combined with the genetic algorithm method for finding the cluster's energy minimum, before employing it to investigate carbon clusters in the size range C3-C24 studying their topological transitions. An effort was also made to compare our MBH/DFTB and its re-optimized results carried out by full density functional theory (DFT) calculations with some early DFT-based studies.

Precursory signatures of protein folding/unfolding: from time series correlation analysis to atomistic mechanisms.

Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and ß hairpin, but also the important role played by weaker correlations in such protein folding dynamics.

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in ß-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended ß-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form ß turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.

Characterization of the novel HLA-DPA1*02:02:04 allele.

HLA-DPA1*02:02:04 is identical to DPA1*02:02:03 except for a synonymous change at nucleotide position 138 (C to G) in exon 2.

Identification of a novel HLA-B allele, B*07:162, in a Taiwanese individual.

The new allele, HLA-B*07:162, is identical to HLA-B*07:12 in exon 2 but has a non-synonymous substitution at position 419 (A to C) in exon 3.

Epitaxial growth of graphene on 6H-silicon carbide substrate by simulated annealing method.

We grew graphene epitaxially on 6H-SiC(0001) substrate by the simulated annealing method. The mechanisms that govern the growth process were investigated by testing two empirical potentials, namely, the widely used Tersoff potential [J. Tersoff, Phys. Rev. B 39, 5566 (1989)] and its more refined version published years later by Erhart and Albe [Phys. Rev. B 71, 035211 (2005)]. Upon contrasting the results obtained by these two potentials, we found that the potential proposed by Erhart and Albe is generally more physical and realistic, since the annealing temperature at which the graphene structure just coming into view at approximately 1200 K is unambiguously predicted and close to the experimentally observed pit formation at 1298 K within which the graphene nucleates. We evaluated the reasonableness of our layers of graphene by calculating carbon-carbon (i) average bond-length, (ii) binding energy, and (iii) pair correlation function. Also, we compared with related experiments the various distance of separation parameters between the overlaid layers of graphene and substrate surface.

Melting behavior of Ag14 cluster: an order parameter by instantaneous normal modes.

This paper studies the melting behavior of Ag(14) cluster employing the instantaneous normal mode (INM) analysis that was previously developed for bimetallic cluster Ag(17)Cu(2). The isothermal Brownian-type molecular dynamics simulation is used to generate atom configurations of Ag(14) at different temperatures up to 1500 K. At each temperature, these atomic configurations are then analyzed by the INM technique. To delve into the melting behavior of Ag(14) cluster which differs from Ag(17)Cu(2) by the occurrence of an anomalous prepeak in the specific heat curve in addition to the typical principal peak, we appeal to examining the order parameter τ(T) defined in the context of the INM method. Two general approaches are proposed to calculate τ(T). In one, τ(T) is defined in terms of the INM vibrational density of states; in another, τ(T) is defined considering the cluster as a rigid body with its rotational motions described by three orthogonal eigenvectors. Our results for Ag(14) by these two methods indicate the mutual agreement of τ(T) calculated and also the consistent interpretation of the melting behavior with the specific heat data. The order parameter τ(T) provides in addition an insightful interpretation between the melting of clusters and the concept of broken symmetry which has been found successful in studies of the melting transition of bulk systems.

Metadynamics molecular dynamics and isothermal Brownian-type molecular dynamics simulations for the chiral cluster Au18.

In an effort to gain insight into enantiomeric transitions, their transition mechanism, time span of transitions and distribution of time spans etc, we performed molecular dynamics (MD) simulations on chiral clusters Au10, Au15and Au18, and found that viable reaction coordinates can be deduced from simulation data for enlightening the enantiomeric dynamics for Au10and Au15, but not so for Au18. The failure in translating the Au18-L ⇌ Au18-R transitions by MD simulations has been chalked up to the thermal energykBTat 300 K being much lower than energy barriers separating the enantiomers of Au18. Two simulation strategies were taken to resolve this simulation impediment. The first one uses the well-tempered metadynamics MD (MMD) simulation, and the second one adeptly applies first a somewhat crude MMD simulation to locate a highly symmetrical isomer Au18Sand subsequently employed it as initial configuration in the MD simulation. In both strategies, we work in collective variable space of lower dimensionality. The well-tempered MMD simulation tactic was carried out aiming to offer a direct verification of Au18enantiomers, while the tactic to conduct MMD/MD simulations in two consecutive simulation steps was intended to provide an indirect evidence of the existence of enantiomers of Au18given that energy barriers separating them are much higher than ca.kBTat 300 K. This second tactic, in addition to confirming indirectly Au18-L and Au18-R starting from the symmetrical cluster Au18S, the simulation results shed light also on the mechanism akin to associative/nonassociative reaction transitions.

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation.

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat.

Identification of the novel allele HLA-B*13:01:03 by sequence-based typing method in a Taiwanese individual.

A new human leukocyte antigen (HLA)-B allele, B*13:01:03 (B*130103), has been found in a Taiwanese individual. It differs from B*13:01:01 (B*130101) by a synonymous substitution at codon 113 (CAT->CAC).

Identification of the novel allele HLA-B*51:84 by sequence-based typing method in a Taiwanese individual.

A new human leukocyte antigen-B allele, B*51:84 (B*5184), has been found in Taiwan. It differs from B*51:01:01(B*510101) by one nucleotide substitution at codon 145 (CGC →GGC), resulting to one amino acid change (Arginine to Glycine).

Phase diagram of colloid-rod system.

The semigrand ensemble theory [H. N. W. Lekkerkerker, W. C. K. Poon, P. N. Pusey, A. Stroobants, and P. B. Warren, Europhys. Lett. 20, 559 (1992)] in conjunction with the fundamental measure density functional theory [V. B. Warshavsky and X. Song, Phys. Rev. E 69, 061113 (2004)] are used to construct the Helmholtz free energy densities of a mixture of uncharged colloidal hard spheres and colloidal rods in its solid and liquid phases. Given these free energy density functions, we apply the free energy density minimization method [G. F. Wang and S. K. Lai, Phys. Rev. E 70, 051402 (2004)] to crosshatch the system's regions of phases in coexistence. The calculated results show that the triangular area bounded by gas-liquid, gas-solid, and liquid-solid coexisting two phases which has been called the coexistence region of gas-liquid-solid corresponds in fact to sets of two phases in coexistence. The phase boundaries which define our calculated coexistence domains compare very well with previous theoretical calculations. The relevance of the phase-diagram domains to three phases in coexistence will be discussed.

Free energy landscapes and volumes of coexisting phases for a colloidal dispersion.

Treating the repulsive part of a pairwise potential by the hard-sphere form and its attractive part by the effective depletion potential form, we calculate using this model potential the colloidal domains of phase separation. Differing from the usual recipe of applying the thermodynamic conditions of equal pressure and equal chemical potential where the branches of coexisting phases are the ultimate target, we employ the free energy density minimization approach [G. F. Wang and S. K. Lai, Phys. Rev. E 70, 051402 (2004)] to crosshatch the domains of equilibrium phases, which consist of the gas, liquid, and solid homogeneous phases as well as the coexistence of these phases. This numerical procedure is attractive since it yields naturally the colloidal volume of space occupied by each of the coexisting phases. In this work, we first examine the change in structures of the fluid and solid free energy density landscapes with the effective polymer concentration. We show by explicit illustration the link between the free energy density landscapes and the development of both the metastable and stable coexisting phases. Then, attention is paid to the spatial volumes predicted at the triple point. It is found here that the volumes of spaces of the three coexisting phases at the triple point vary one dimensionally, whereas for the two coexisting phases, they are uniquely determined.

The Association between health-related quality of life and prosthetic status and prosthetic needs in Taiwanese adults.

The objective of this study was to describe aspects of prosthetic statuses and needs and to evaluate their relationship with health-related quality of life in Taiwan. The study participants, aged 18 years and above, were recruited from a community survey, and each of the total 2469 participants received a dental examination and completed a questionnaire. Multivariable analysis was used to assess the adjusted means of health-related quality of life (SF-36) in both prosthetic status and need. The results showed that 12.6% of those aged 65 years and above were edentulous. The proportion of prosthetic need increased as age increased (39.7% to 61.3%). Multivariate analysis revealed that participants with 'removable prosthesis' had higher physical health scores than those with 'non-removable prosthesis'. The scores of mental health measurement decreased in people with need for full prostheses in relation to people without need for any prosthesis. Therefore, fulfilling prosthetic needs is not only about recovering oral masticatory function, but also concerns improvement of both physical and mental health-related quality of life.

Antinociceptive and anti-inflammatory effects of Stachytarpheta jamaicensis (L.) Vahl (Verbenaceae) in experimental animal models.

OBJECTIVE: The present study was carried out to explore the antinociceptive as well as the anti-inflammatory effects of an ethanol extract of Stachytarpheta jamaicensis (L.) Vahl (EESJ) using 3 models of nociception and 2 models of inflammation in experimental animals. MATERIALS AND METHODS: EESJ was prepared by overnight soaking of the oven-dried (50 degrees C; 72 h) ground leaves (500 g) in 80% ethanol (1:5; w/v). The filtrate was evaporated to dryness (50 degrees C), resuspended in distilled water at concentrations to provide the desired doses of 50, 100 and 150 mg/kg. For antinociceptive effects, 3 models were used: acetic acid-induced abdominal writhing, hot-plate- and formalin-induced paw-licking tests; for anti-inflammatory effects, 2 models were used--carrageenan-induced paw edema and cotton-pellet-induced granuloma tests. Appropriate doses were administered intraperitoneally (i.p.) to mice/rats prior to each test. The mechanisms of antinociceptive action of the extract were also investigated by pretreatment with naloxone (5 mg/kg, i.p.). RESULTS: The extract exhibited significant (p < 0.05) antinociceptive activity in all nociceptive models tested with dose-dependent activity observed using the abdominal writhing and formalin tests. Pretreatment with naloxone partially, but significantly (p < 0.05) reversed the antinociceptive activity of the extract when assessed using the abdominal-writhing- and formalin-induced paw-licking tests, and completely inhibited its activity when the hot-plate test was used. The extract also showed significant (p < 0.05) anti-inflammatory activity in both the acute (carrageenan-induced paw edema test) and the chronic (cotton-pellet granuloma test) tests. CONCLUSION: This study showed the potential of EESJ to exert antinociceptive and anti-inflammatory activities, the former being modulated via peripheral and central mechanisms and involving, in part, activation of the opioid receptor system.