2,278 research outputs found
Native PAGE experiments on SL1-wt RNA kissing dimer (KD) in the presence of sub-stoichiometric amounts of NCp7, run in the TBE buffer
No full text<p><b>Copyright information:</b></p><p>Taken from "Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding"</p><p></p><p>Nucleic Acids Research 2007;35(6):2026-2034.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874624.</p><p>© 2007 The Author(s)</p> KD of SL1-wt was incubated with NCp7 at ambient temperature for 18 h in the RNA strand-to-protein ratio of 2:0, 2:2, 2:1.6, 2:0.8, 2:0.4 and 2:0.2, as indicated. The upper band in each lane (‘LD’) corresponds to mature linear dimer, while the lower monomer band (‘M’) emanates from the residual KD that dissociates during PAGE in the TBE buffer. Increasing intensity of the monomer band and simultaneous decrease in the dimer band across the lanes correlates with the amount of NCp7 present in each complex
Unlocking the potential of saliva-based test to detect HPV-driven oropharyngeal cancer
No full textBackground: The incidence of human papillomavirus (HPV)-driven oropharyngeal cancer (OPC) is increasing in the developed countries including Australia. Accumulating evidence supports the notion that an accurate HPV testing is crucial for clinical decision making and treatment planning in these patients.
Methods: HPV positivity in patients who have been diagnosed with OPC tumours (n = 105) was examined using p16INK4A immunohistochemistry (IHC) analysis. HPV-16 genotyping and physical status in salivary oral rinse and tumour samples were analyzed using qPCR method.
Results: The inter-rater agreement between OPC tumour p16INK4A expression and oral HPV-16 infection was considered as fair (k = 0.387). Salivary HPV-16 DNA (E2 and/or E6/7) was detected in 73 out of 95 p16INK4A-positive OPC patients. Importantly, HPV-16 genotyping and the ratio of HPV16 E2 DNA to HPV16 E6/7 DNA were concordant between the salivary oral rinse and tumour samples. Consistent with previous studies, for the majority of OPC patients, a mixed HPV-16 form (episomal and integrated) was detected in both sample methods, suggesting that salivary HPV-16 could be used as a potential biomarker for OPC.
Conclusions: HPV-16 detection in saliva is an attractive non-invasive method that can easily be implemented either as a dentist-chair side test or as a laboratory developed test to detect HPV-driven OPC.
Legal entity responsible for the study: Saliva Translational Research Group.
Funding: Atlantic Philanthropies, the Queensland Government.
Disclosure: All authors have declared no conflicts of interest.No Full Tex
Therapeutic studies in hepatic encephalopathy
No full textThis article has arisen from presentations made at the 4th International Hannover Conference on Hepatic Encephalopathy held in Dresden, 2006. Each author as listed describes their presentation given as part of a section entitled "Therapeutic Studies in Hepatic Encephalopathy." The first section deals with the justification for placebo-controlled trials in hepatic encephalopathy. The other two sections discuss, in detail, outcome parameters for therapeutic studies in the clinical and research setting, respectivel
Schematic diagram of the essence of knowledge distillation (KD).
No full textSchematic diagram of the essence of knowledge distillation (KD).</p
Concurrent linearizable nearest neighbour search in lockfree-kd-Tree
No full textThe Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modi-fications are allowed, a linearizable implementation of NNS is highly desirable. This paper introduces the LockFree-kD-Tree (LFkD-Tree): A lock-free concurrent kD-Tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-Tree use single-word read and compare-And-swap (CAS) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-Tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves signi cant speed-up compared to the implementations of an existing sequential kD-Tree and a recently proposed multidimensional indexing structure, PH-Tree.\ua0\ua9 2018 Copyright held by the owner/author(s)
The meridional scale of baroclinic waves with latent heat relase
No full textAn analytical theory of two-level, moist, quasi-geostrophic baroclinic waves with meridional variation, but without the fl-effect, is developed. The formulation is similar to that of Tang and Fichtl (1983) except that the meridional variation of the waves isallowed. The basic parameters are a rotational Froude number F = (where f is the Coriolis parameter, Sd the static stability in descending portion of the wave, p2 the pressure at the middle level, kd the zonal wave number in the descending portion of the wave, ℓ(=π/D) the meridional wave number and D the meridional extent of the wave) and a heating parameter e which is proportional to the midlevel vertical gradient of the mean flow saturation mixing ratio. For ε ≠ 0 the disturbances are characterized by an unequal zonal length of the ascending or wet portion of the wave (a) and zonal length of the descending or dry portion of the wave (b). The first mode has a small region of strong ascending motion and a large region of weak descending motion (a/b < 1) with the reverse for the second mode (a/b > 1). These features are similar to those obtained by Tang and Fichtl (1983). In the present paper a meridional-scale equation is derived, expressing three possibilities: (i) FORMULA = 0 (no meridional variation of baroclinic waves, discussed in Tang and Fichtl, 1983); (ii) ε = 0 (dry model, discussed in Phillips, 1954, with β-effect ignored, ℓ being arbitrary); and (iii) a biquadratic equation in ℓ/kd. This latter equation essentially contains the information of the influence of latent heat release on the meridional scale of baroclinic waves. The model of meridionally uniform baroclinic waves (ε = 0) and the dry model (e = 0) are singular in that the characteristics of these two models cannot be deduced by setting ℓ/kd → 0 or ε → 0 in this biquadratic equation. For ε < 0.464, the ratio of the meridional extent D of the zonal domain, a + b, is less than 0.7. For a given e and a given F, this ratio is larger for the first mode than for the second mode. The growth rate in the ascending region is equal to that in the descending region. The growth rate depends on both F and ℓ/kd. For a given F, the larger the heating parameter e, the larger the growth rate. .SE DESARROLLA UNA TEORIA DE ONDAS BAROCLINICAS EN DOS NIVELES, CON HUMEDAD, CUASI-GEOSTROPICAS Y CON VARIACION MERIDIONAL, PERO SIN EFECTO B. LA FORMULACION ES SIMILAR A LA DE TANG Y FICHTL (1983) EXCEPTO QUE SE PERMITEN VARIACIONES MERIDIONALES. LOS PARAMETROS BASICOS SON EL NUMERO ROTACIONAL DE FROUDE F = 2F2 [SDP22(K2D)]-1 (DONDE F ES EL PARAMETRO DE CORIOLIS, SD LA ESTABILIDAD ESTATICA EN LA PORCION DESCENDENTE DE LA ONDA, P2 LA PRESION EN EL NIVEL MEDIO, KD EL NUMERO DE ONDA ZONAL EN LA PARTE DESCENDENTE DE LA ONDA, L( ) EL NUMERO DE ONDA MERIDIONAL Y D ES LA EXTENSION MERIDIONAL DE LA ONDA) Y UN PARAMETRO DE CALENTAMIENTO L QUE ES PROPORCIONAL AL GRADIENTE VERTICAL EN EL NIVEL CENTRAL DE FLUJO MEDIO DE LA RAZON DE MEZCLA DE SATURACION. PARA LAS PERTURBACIONES SE CARACTERIZAN POR UNA LONGITUD ZONAL DESIGUAL DE LA PORCION ASCENDENTE O HUMEDA DE LA ONDA (A) CON RESPECTO A LA LONGITUD ZONAL DE LA PORCION DESCENDENTE O SECA DE LA ONDA (B). EL PRIMER MODO TIENE UNA PEQUEÑA REGION DE FUERTE MOVIMIENTO ASCENDENTE Y UNA GRAN REGION DE DEBIL MOVIMIENTO DESCENDETE ( ), SUCEDIENDO LO CONTRARIO PARA EL SEGUNDO MODO ( ). ESTAS CARACTERISTICAS SON SIMILARES A LAS OBTENIDAD POR TANG Y FICHTL (1983). EN EL PRESENTE TRABAJO SE DEDUCE UNA ECUACION A ESCALA MERIDIONAL, MOSTRANDO TRES POSIBILIDADES: (I) L/KD = 0 (ONDAS BAROCLINICAS SIN VARIACIONES MERIDIONALES, DISCUTIDO EN TANG Y FICHTL, 1983), (II) (II) E=0 (MODELO SECO, DISCUTIDO EN PHILLIPS, 1954 SIN EL EFECTO B, Y CON L ARBITRARIA); Y (III) UNA ECUACION BICUADRATICA EN L/KD. LA ULTIMA ECUACION CONTIENE ESENCIALMENTE LA INFORMACION DE LA INFLUENCIA DE LA LIBERACION DE CALOR LATENTE EN LA ESCALA MERIDIONAL DE LAS ONDAS BAROCLINICAS. EL MODELO DE ONDAS BAROCLINICAS MERIDIONALMENTE UNIFORMES (L/KD =0) Y EL MODELO SECO (E = 0) SON SINGULARES EN TANTO QUE SUS CARACTERISTICAS NO SE PUEDEN DEDUCIR HACIENDO --- EN ESTA ECUACION BICUADRATICA. PARA -, LA RAZON DE LA EXTENSION MERIDIONAL D DEL DOMINIO ZONAL, A, ES MENOR QUE 0.7. PARA - Y F DADAS, ESTA RAZON ES MAYOR PARA EL PRIMER MODO QUE PARA EL SEGUNDO. LA RAZON DE CRECIMIENTO EN LA REGION ASCENDENTE ES LA MISMA QUE EN LA REGION DESCENDENTE. LA RAZON DE CRECIMIENTO DEPENDE DE F Y ----. PARA UNA F DADA, LA RAZON DE CRECIMIENTO SERA MAYOR CUANTO MAYOR SEA EL PARAMETRO DE CALENTAMIENTO
Dispersive to nondispersive transition in the plane wake and channel flows
No full textBy varying the wavenumber over a large and finely discretized interval of values, we analyse the phase and group velocity of linear three-dimensional travelling waves both in the plane wake and channel flows to get the transition between dispersive and non-dispersive behaviour. The dispersion relation is computed from the Orr-Sommerfeld and Squire eigenvalue problem by observing the least stable mode, see figure 2, panels (a,b) and the comparison with [1, 2, 4–11, 15, 16]. The group velocity vg is also shown. The Reynolds number varies in the 20-100, 1000-8000 ranges for the wake and the channel flow, respectively, while we consider wavenumbers in the range 0.1-10. The wake basic flow consists of the first two orders of the Navier-Stokes matched asymptotic expansion described in [3, 13, 14]. At low wavenumbers we observe a dispersive behaviour where the phase speed and the group velocity substantially differ. The relevant perturbed solution is amenable to the typical solution belonging to the left branch of the eigenvalue spectrum, see the two examples shown in figure 1 (channel flow: Re = 6000; k = 1; wake Re = 100; k = 0:7). By rising the wave number value, we observe a sharp transition from the dispersive to the nondispersive regime. This transition is located at a critical wave number kd which is a function of the Reynolds number Re, the wave angle _, and the wake downstream observation point x0. Precisely, kd increases with Re and decreases with _ for the wake flow, while these trends are reversed for the channel flow, see tables 1,2. Beyond the wavenumber threshold, the observed least-stable mode belongs to the right branch of the spectrum. The asymptotic solutions in the dispersive region are wall modes for the channel flow , and in-wake modes for the wake flow. This means that, for both the flows, the dispersive behaviour is related to perturbations with high momentum variations (high vorticity) in correspondence to the base flow high-shear region. On the contrary, if k > kd the solutions are central modes for the channel case, and out-of-wake modes for the wake flow. In these cases, the disturbance has high variations outside the base flow high-shear region. To understand the physical mechanism of the dispersive-nondispersive transition we focused on time variation of the wave kinetic energy associated to the convective transport. Figure 2 (c,d) shows the convective term as a function of the wavenumber for the two least stable modes. We observe that the dispersive-nondisperive transition allows waves k > kd to keep the lowest possible temporal variation of kinetic energy, i.e. the lowest decay. This remains true also when all the other more stable modes are considered. In practice nondispersive waves maintain their convective energy with k
Periplakin, a novel component of cornified envelopes and desmosomes that belongs to the plakin family and forms complexes with envoplakin
No full textThe cornified envelope is a layer of transglutaminase cross-linked protein that is assembled under the plasma membrane of keratinocytes in the outermost layers of the epidermis. We have determined the cDNA sequence of one of the proteins that becomes incorporated into the cornified envelope of cultured epidermal keratinocytes, a protein with an apparent molecular mass of 195 kD that is encoded by a mRNA with an estimated size of 6.3 kb. The protein is expressed in keratinizing and nonkeratinizing stratified squamous epithelia and in a number of other epithelia. Expression of the protein is upregulated during the terminal differentiation of epidermal keratinocytes in vivo and in culture. Immunogold electron microscopy was used to demonstrate an association of the 195-kD protein with the desmosomal plaque and with keratin filaments in the differentiated layers of the epidermis. Sequence analysis showed that the 195-kD protein is a member of the plakin family of proteins, to which envoplakin, desmoplakin, bullous pemphigoid antigen 1, and plectin belong. Envoplakin and the 195-kD protein coimmunoprecipitate. Analysis of their rod domain sequences suggests that the formation of both homodimers and heterodimers would be energetically favorable. Confocal immunofluorescent microscopy of cultured epidermal keratinocytes revealed that envoplakin and the 195-kD protein form a network radiating from desmosomes, and we speculate that the two proteins may provide a scaffolding onto which the cornified envelope is assembled. We propose to name the 195-kD protein periplakin
Characteristics of involved KD patients in all included studies.
No full textCharacteristics of involved KD patients in all included studies.</p
A Hybrid Improved SAC-IA with a KD-ICP Algorithm for Local Point Cloud Alignment Optimization
No full textTo overcome incomplete point cloud data obtained from laser scanners scanning complex surfaces, multi-viewpoint cloud data needs to be aligned for use. A hybrid improved SAC-IA with a KD-ICP algorithm is proposed for local point cloud alignment optimization. The scanned point cloud data is preprocessed with statistical filtering, as well as uniform down-sampling. The sampling consistency initial alignment (SAC-IA) algorithm is improved by introducing a dissimilarity vector for point cloud initial alignment. In addition, the iterative closest point (ICP) algorithm is improved by incorporating bidirectional KD-tree to form the KD-ICP algorithm for fine point cloud alignment. Finally, the algorithms are compared in terms of runtime and alignment accuracy. The implementation of the algorithms is based on the Visual Studio 2013 software configurating point cloud library environment for testing experiments and practical experiments. The overall alignment method can be 40%~50% faster in terms of running speed. The improved SAC-IA algorithm provides better transformed poses, combined with the KD-ICP algorithm to select the corresponding nearest neighbor pairs, which improves the accuracy, as well as the applicability of the alignment
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