Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Why do patients with myositis die? A retrospective analysis of a single-centre cohort

OBJECTIVES: Causes of death in inflammatory myopathies have rarely been studied. We have assessed a cohort of myositis patients followed in a single centre over a 37-year period, reviewing the mortality rate, causes of death and predictors of poor prognosis. METHODS: We performed a single-centre, retrospective study on patients aged ≥16 years fulfilling 3 or 4 of the Bohan and Peter criteria, noting their demographic data, clinical features, serology, treatment and outcome. RESULTS: Of 97 patients identified, 74.2% were female. The mean age at diagnosis was 40.5 years (SD 13.2). 38.1% had adult-onset dermatomyositis, 36.1% adult-onset polymyositis and 25.8% overlap myositis. 96.9% had upper and lower limb involvement (UL+/LL+) and 62.9% had a highest CK≥10 times the upper limit of normal. 33% had significant infection(s). The disease course was chronic persistent in 29.9%, relapsing and remitting in 34% and monophasic in 36.1%. All received steroids and 92.8% other immunosuppressant(s). The median follow-up was 9 years (IQR 11.5). The estimated cumulative proportion survival at 5, 10, 15 and 20 years were 94.6%, 82.2%, 72,1% and 66.1%, respectively. 24.7% of patients died, mostly due to infection (29.2%). In univariate analysis, lung involvement (HR 1.78, p=0.013), infection (HR 4.18, p=0.003) and UL+/LL+ (HR 0.13, p=0.010) were statistically significantly associated with the risk of death. In the multivariate analysis infection (HR 3.68, p=0.009) and UL+/LL+ (HR 0.16, p=0.027) were statistically significantly associated with survival. CONCLUSIONS: A good long-term survival is reported. Nevertheless, careful follow-up of myositis patients is important

Creep behaviour and tensile response of adhesively bonded polyethylene joints: Single-Lap and Double-Strap

The static and time-dependent behaviours of adhesively bonded polyethylene Double-Strap (DS) joints were investigated to assess the viability of this joint configuration relative to the Single-Lap (SL) joints. Both experiments and finite element simulations are conducted. First, we individually characterise the tensile and creep behaviour of the adhesive and adherent materials; an epoxy-based adhesive and polyethylene, respectively. This information is used to develop suitable constitutive models that are then implemented in the commercial finite element package ABAQUS by means of user material subroutines, UMATs. The numerical models are used to design the creep tests on the adhesive joints. Afterwards, an extensive experimental campaign is conducted where we characterise the static and creep behaviour of two joint configurations, SL and DS joints, and three selected values of the overlap length. In regard to the static case, results reveal an increase in the failure load with increasing overlap length, of up to 10% for an overlap length of 39 mm. Also, slightly better performance is observed for the SL joint configuration. For the creep experiments, we show that the DS adhesive joint configuration leads to much shorter elongations, relative to the SL joints. These differences diminish with increasing overlap length but remain substantial in all cases. In both joint configurations, the elongation increases with decreasing overlap length. For instance, increasing the overlap length to 39 mm led to a 50% and a 30% reduction in elongation for SL and DS joints, respectively. Moreover, the numerical predictions show a good agreement with the experiments. The stress redistribution is investigated and it is found that the shear stress is highly sensitive to the testing time, with differences being more noticeable for the DS joint system

Magnetoelastic coupling in the cobalt adipate metal-organic framework from quasi-harmonic lattice dynamics

Magnetic interactions in hybrid materials are poorly understood compared to those in purely inorganic materials. The high flexibility of many metal-organic systems introduces a strong temperature dependence of the magnetic exchange interactions owing to changes in the crystal structure. Here, we study the cobalt adipate system, for which anisotropic thermal expansion was recently shown to be a result of magnetoelastic coupling. The combination of density functional theory with quasi-harmonic lattice dynamics is shown to be a powerful tool for describing temperature dependent thermodynamic potentials that determine magnetic interactions. It is demonstrated that the effect of phonons can be sufficient to switch the preference for ferromagnetic versus antiferromagnetic ordering

Thermoreversible gels for the encapsulation of macrophages: evaluation of polymer type on rheology and cytocompatibility

Thermoresponsive polymers have become a highly sought-after “smart material” due to their ability to modify their physical characteristics due to temperature changes. This research aimed to determine the biocompatibility of specific thermoreversible gels for immunocompetent cell models containing ImmuPHAGETM, human alveolar macrophage-like cells. Four polymers were selected based on their transition temperatures, including three commercially available pharmaceutical excipients, namely poloxamer 407, soluplus, and methylcellulose. The fourth system, poly(N-isopropyl acrylamide)-b-poly(ethylene oxide)-b-poly(N-isopropyl acrylamide), was synthesised in-house. Initially, the phase behaviour of these four polymers was evaluated visually by warming the polymer solutions and determining the state of the solution by vial inversion. Subsequently, a combination of rheological measurements was employed to compare the properties of these thermoreversible gels in culture media. The physical characterisation was followed by conducting cytocompatibility tests using human alveolar macrophages to assess their suitability as a scaffold for cell culture in vitro and to determine the cell response to different culturing environments. The study concluded that methylcellulose is the most promising and cost-effective material worth further exploration as a responsive matrix for immune cell encapsulation. Keywords: Thermoresponsive, Thermogelling, Alveolar macrophages, Foamy macrophages, immunocompetent in vitro models

The Large Quasar Reference Frame (LQRF) - an optical representation of the ICRS

The large number and all-sky distribution of quasars from different surveys, along with their presence in large, deep astrometric catalogs,enables the building of an optical materialization of the ICRS following its defining principles. Namely: that it is kinematically non-rotating with respect to the ensemble of distant extragalactic objects; aligned with the mean equator and dynamical equinox of J2000; and realized by a list of adopted coordinates of extragalatic sources. Starting from the updated and presumably complete LQAC list of QSOs, the initial optical positions of those quasars are found in the USNO B1.0 and GSC2.3 catalogs, and from the SDSS DR5. The initial positions are next placed onto UCAC2-based reference frames, following by an alignment with the ICRF, to which were added the most precise sources from the VLBA calibrator list and the VLA calibrator list - when reliable optical counterparts exist. Finally, the LQRF axes are inspected through spherical harmonics, contemplating to define right ascension, declination and magnitude terms. The LQRF contains J2000 referred equatorial coordinates for 100,165 quasars, well represented across the sky, from -83.5 to +88.5 degrees in declination, and with 10 arcmin being the average distance between adjacent elements. The global alignment with the ICRF is 1.5 mas, and the individual position accuracies are represented by a Poisson distribution that peaks at 139 mas in right ascension and 130 mas in declination. It is complemented by redshift and photometry information from the LQAC. The LQRF is designed to be an astrometric frame, but it is also the basis for the GAIA mission initial quasars' list, and can be used as a test bench for quasars' space distribution and luminosity function studies.Comment: 23 pages, 23 figures, 6 tables Accepted for publication by Astronomy & Astrophysics, on 25 May 200

Ontogenia larval comparativa de duas esp?cies (Characiformes e Siluriformes) end?micas do rio S?o Francisco

Objetivou-se com este trabalho comparar histologicamente o desenvolvimento ontogen?tico de duas esp?cies de peixes end?micos da bacia do rio S?o Francisco, Prochilodus argenteus (curimat?-pacu) e Lophiosilurus alexandri (pacam?). As coletas para as an?lises histol?gicas foram realizadas a cada 24 horas a partir do momento da eclos?o at? o 14? dia p?s-eclos?o (DPE) para a observa??o do desenvolvimento larval e at? o 39? DPE para a observa??o do desenvolvimento gonadal. As larvas foram fixadas inteiras em solu??o de Bouin e as l?minas histol?gicas foram coradas pelo m?todo de Hematoxilina-Eosina. Larvas de pacam? exibiram um tamanho corporal maior em rela??o ?s larvas de curimat?-pacu desde a eclos?o. Larvas de pacam? apresentaram a abertura da boca e in?cio da pigmenta??o dos olhos no momento da eclos?o, enquanto que nas larvas de curimat?-pacu, esses eventos foram observados no 1? DPE. No curimat?-pacu a visualiza??o e a insufla??o da bexiga natat?ria ocorreram no 1? e 3? DPE, respectivamente, sendo esses eventos mais tardios no pacam?, com visualiza??o no 2? e insufla??o no 8? DPE. Os gr?nulos de vitelo foram absorvidos no 4? DPE pelo curimat?-pacu e no 10? DPE pelo pacam?. No 7? DPE, o tubo digest?rio do pacam? apresentou-se mais diferenciado em rela??o ao curimat?-pacu. O sistema digest?rio de ambas as esp?cies ao 14? DPE demonstraram caracter?sticas relacionadas aos seus respectivos h?bitos alimentares, com est?mago amplo e intestino curto no pacam?, t?picos de h?bito carn?voro; est?mago com fun??o mec?nica e intestino longo no curimat?-pacu, t?picos de h?bito detrit?voro. O tecido epitelial de revestimento, formado por uma ?nica camada de c?lulas nas larvas rec?m-eclodidas (0 DPE), apresentou diferencia??o ao longo dos dias, exibindo presen?a de escamas no curimat?-pacu e numerosas c?lulas ?club? na regi?o epitelial intermedi?ria do pacam?, em avalia??es realizadas ao 39? DPE. Analisando os indiv?duos com 39 DPE, verificou-se a presen?a de g?nadas indiferenciadas com c?lulas som?ticas e c?lulas germinativas primordiais que foram observadas realizando migra??o no sentido caudo-cranial desde o 1? DPE em ambas as esp?cies. P?de-se concluir que as altera??es anat?micas observadas durante a ontogenia de larvas P. argenteus e L. alexandri est?o diretamente relacionadas ao h?bito alimentar e ao comportamento inerente ? cada esp?cie, sendo uma detrit?vora que nada ativamente na coluna d??gua, e outra carn?vora que habita regi?es de fundo, respectivamente. Aos 39 dias p?s-eclos?o, em ambas as esp?cies n?o foram observados ind?cios histol?gicos de diferencia??o sexual.Banco do Nordeste do Brasil (BNB)Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq)Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES)Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Zootecnia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2016.The objective of this work was to compare histologically the ontogenetic development of two endemic species of fish from the S?o Francisco river basin, Prochilodus argenteus (curimat?-pacu) and Lophiosilurus alexandri (pacam?). The samples for the histological analyzes were performed every 24 hours since the moment of hatching until the 14th day post-hatching (DPH) for observation of the larval development and until the 39th DPH for the observation of gonadal development. The whole larvae were fixed in Bouin's solution and the histological slides were stained by the Hematoxylin-Eosin method. Pacam? larvae exhibited a larger body size relative than the curimat?-pacu larvae since hatching. Pacam? larvae presented the mouth opening and pigmentation of eyes beginning at the time of hatching, whereas in curimat?-pacu larvae, these events were observed in the 1st DPH. The visualization and the inflation of the swim bladder in the curimat?-pacu, occurred in the 1st and 3rd DPH, respectively, being these events in the pacam? later, with visualization in the 2nd and insufflation in the 8th DPH. The yolk granules were absorbed in the 4th DPH by the curimat?-pacu and in the 10th DPE by the pacam?. In the 7th DPH, the pacam??s digestive tube was more differentiated than curimat?-pacu. The digestive system of both species at the 14th DPH has features of it eating habits the pacam?, with a broad stomach and a short intestine in the pacam?, typical of a carnivorous habit; stomach with a mechanical function and a long intestine in curimat?-pacu, typical of detritivorous habit. The epithelial lining tissue, formed by a single layer of cells in the newly hatched larvae (0 DPH), showed a differentiation throughout the days, exhibiting scales in curimat?-pacu and numerous club cells in the middle epithelial region of the pacam?, at evaluations carried at the 39th DPH. Analyzing the individuals with 39 DPH, the presence of undifferentiated gonads with somatic cells and primordial germinative cells were observed, which has a caudate-cranial migration since 1st DPH in both species. It was concluded that the anatomical alterations of the ontogeny of P. argenteus and L. alexandri larvae are directly associated to the feeding habit and the inherent behavior of each species, being these detritivorous that nothing actively in the column of water and carnivorous that inhabits bottom regions, respcectively. At the 39 day post-hatching, both species hasn't evidenced of sexual differentiation

Canard Cycles and Poincar\'e Index of Non-Smooth Vector Fields on the Plane

This paper is concerned with closed orbits of non-smooth vector fields on the plane. For a subclass of non-smooth vector fields we provide necessary and sufficient conditions for the existence of canard kind solutions. By means of a regularization we prove that the canard cycles are singular orbits of singular perturbation problems which are limit periodic sets of a sequence of limit cycles. Moreover, we generalize the Poincar\'e Index for non-smooth vector fields.Comment: 20 pages, 25 figure

Light-quark dipole operators at the LHC

We study the effect of operators generating dipole couplings of the light quarks to electroweak gauge bosons on several observables at the LHC. We start by demonstrating that the determination of the gauge- boson self-couplings from electroweak diboson production at LHC is robust under the inclusion of those quark dipole operators even when let them totally unconstrained in the analysis. Conversely, we determine the bounds that the diboson data imposes on the light-quark dipole couplings and show that they represent a significant improvement over the limits arising from Z and W electroweak precision measurements. We also explore the sensitivity of the Drell-Yan cross section determination at LHC Run 1, and the results on resonance searches in high invariant-mass lepton pair production at Run 2 to further constrain the electroweak dipole couplings of the light quarks