Silicon Photomultipliers (SiPM) as novel photodetectors for PET

Next generation PET scanners should fulfill very high requirements in terms of spatial, energy and timing resolution. Modern scanner performances are inherently limited by the use of standard photomultiplier tubes. The use of Silicon Photomultipliers (SiPMs) is proposed for the construction of a 4D-PET module of 4.8×4.8 cm2 aimed to replace the standard PMT based PET block detector. The module will be based on a LYSO continuous crystal read on two faces by Silicon Photomultipliers. A high granularity detection surface made by SiPM matrices of 1.5 mm pitch will be used for the x–y photon hit position determination with submillimetric accuracy, while a low granularity surface constituted by 16 mm2 SiPM pixels will provide the fast timing information (t) that will be used to implement the Time of Flight technique (TOF). The spatial information collected by the two detector layers will be combined in order to measure the Depth of Interaction (DOI) of each event (z). The use of large area multi-pixel Silicon Photomultiplier (SiPM) detectors requires the development of a multichannel Data Acquisition system (DAQ) as well as of a dedicated front-end in order not to degrade the intrinsic detector capabilities and to manage many channels. The paper describes the progress made on the development of the proof of principle module under construction at the University of Pisa.

Floating-point exponentiation units for reconfigurable computing

The high performance and capacity of current FPGAs makes them suitable as acceleration co-processors. This article studies the implementation, for such accelerators, of the floating-point power function xy as defined by the C99 and IEEE 754-2008 standards, generalized here to arbitrary exponent and mantissa sizes. Last-bit accuracy at the smallest possible cost is obtained thanks to a careful study of the various subcomponents: a floating-point logarithm, a modified floating-point exponential, and a truncated floating-point multiplier. A parameterized architecture generator in the open-source FloPoCo project is presented in details and evaluated.

Uncertainty Estimation for Performance Evaluation of a Confocal Microscope as Metrology Equipment

Both in industry and research, the quality control of micrometric manufactured parts is based on the measurement of parameters whose traceability is sometimes difficult to guarantee. In some of these parts, the confocal microscopy shows great aptitudes to characterize a measurand qualitatively and quantitatively. The confocal microscopy allows the acquisition of 2D and 3D images that are easily manipulated. Nowadays, this equipment is manufactured by many different brands, each of them claiming a resolution probably not in accord to their real performance. The Laser Center (Technical University of Madrid) has a confocal microscope to verify the dimensions of the micro mechanizing in their own research projects. The present study pretends to confirm that the magnitudes obtained are true and reliable. To achieve this, a methodology for confocal microscope calibration is proposed, as well as an experimental phase for dimensionally valuing the equipment by 4 different standard positions, with its seven magnifications and the six objective lenses that the equipment currently has, in the x–y and z axis. From the results the uncertainty will be estimated along with an effect analysis of the different magnifications in each of the objective lenses.

AVALIAÇÃO DA COMPRESSÃO DA IMAGEM DIGITAL DA TELERRADIOGRAFIA LATERAL NA REPRODUTIBILIDADE DA MARCAÇÃO DE PONTOS CEFALOMÉTRICOS

A imagem digital adquirida pelo sistema da placa de fósforo foto ativada é visualizada no monitor do computador em um formato denominado DICOM. Este formato ocupa muito espaço para armazenamento, o que dificulta o arquivamento e transmissão da imagem pela Internet. O objetivo deste estudo foi avaliar a influência da compressão JPEG, nos Fatores de Qualidade 100, 80 e 60 na reprodutibilidade da marcação de pontos cefalométricos em imagens de telerradiografias em norma lateral comparadas com o formato DICOM. A amostra consistiu de 120 imagens de telerradiografias em norma lateral obtidas a partir de 30 indivíduos, dos quais se obteve uma radiografia digital no formato DICOM. Essas imagens foram convertidas para o formato JPEG. Após o cegamento e randomização da amostra, três Ortodontistas calibrados marcaram a localização de 12 pontos cefalométricos em cada imagem utilizando o sistema de coordenadas X e Y. Esse procedimento foi repetido após 1 mês. A reprodutibilidade intra e inter observador foi calculada usando o teste de correlação intraclasse. Para comparação entre os grupos de compressão e DICOM na reprodutibilidade de marcação dos pontos utilizou se a Análise de Variância (ANOVA) a um critério para medidas repetidas. Os resultados mostraram que as marcações dos pontos cefalométricos foram bastante reprodutíveis, exceto para o ponto Órbita na coordenada X. Os diferentes formatos de arquivo mostraram estatisticamente iguais para cada ponto e eixo aferido. As compressões JPEG estudadas das imagens de telerradiografias em norma lateral não tiveram efeito na reprodutibilidade da marcação dos pontos cefalométricos testados.

AVALIAÇÃO DA COMPRESSÃO DA IMAGEM DIGITAL DA TELERRADIOGRAFIA LATERAL NA REPRODUTIBILIDADE DA MARCAÇÃO DE PONTOS CEFALOMÉTRICOS

A imagem digital adquirida pelo sistema da placa de fósforo foto ativada é visualizada no monitor do computador em um formato denominado DICOM. Este formato ocupa muito espaço para armazenamento, o que dificulta o arquivamento e transmissão da imagem pela Internet. O objetivo deste estudo foi avaliar a influência da compressão JPEG, nos Fatores de Qualidade 100, 80 e 60 na reprodutibilidade da marcação de pontos cefalométricos em imagens de telerradiografias em norma lateral comparadas com o formato DICOM. A amostra consistiu de 120 imagens de telerradiografias em norma lateral obtidas a partir de 30 indivíduos, dos quais se obteve uma radiografia digital no formato DICOM. Essas imagens foram convertidas para o formato JPEG. Após o cegamento e randomização da amostra, três Ortodontistas calibrados marcaram a localização de 12 pontos cefalométricos em cada imagem utilizando o sistema de coordenadas X e Y. Esse procedimento foi repetido após 1 mês. A reprodutibilidade intra e inter observador foi calculada usando o teste de correlação intraclasse. Para comparação entre os grupos de compressão e DICOM na reprodutibilidade de marcação dos pontos utilizou se a Análise de Variância (ANOVA) a um critério para medidas repetidas. Os resultados mostraram que as marcações dos pontos cefalométricos foram bastante reprodutíveis, exceto para o ponto Órbita na coordenada X. Os diferentes formatos de arquivo mostraram estatisticamente iguais para cada ponto e eixo aferido. As compressões JPEG estudadas das imagens de telerradiografias em norma lateral não tiveram efeito na reprodutibilidade da marcação dos pontos cefalométricos testados.

Conversion of cucumber linoleate 13-lipoxygenase to a 9-lipoxygenating species by site-directed mutagenesis

Multiple lipoxygenase sequence alignments and structural modeling of the enzyme/substrate interaction of the cucumber lipid body lipoxygenase suggested histidine 608 as the primary determinant of positional specificity. Replacement of this amino acid by a less-space-filling valine altered the positional specificity of this linoleate 13-lipoxygenase in favor of 9-lipoxygenation. These alterations may be explained by the fact that H608V mutation may demask the positively charged guanidino group of R758, which, in turn, may force an inverse head-to-tail orientation of the fatty acid substrate. The R758L+H608V double mutant exhibited a strongly reduced reaction rate and a random positional specificity. Trilinolein, which lacks free carboxylic groups, was oxygenated to the corresponding (13S)-hydro(pero)xy derivatives by both the wild-type enzyme and the linoleate 9-lipoxygenating H608V mutant. These data indicate the complete conversion of a linoleate 13-lipoxygenase to a 9-lipoxygenating species by a single point mutation. It is hypothesized that H608V exchange may alter the orientation of the substrate at the active site and/or its steric configuration in such a way that a stereospecific dioxygen insertion at C-9 may exclusively take place.

Compositional differences within and between eukaryotic genomes

Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are based on the profile of dinucleotide relative abundance values (The profile is ρ*XY = f*XY/f*Xf*Y for all XY, where f*X denotes the frequency of the nucleotide X and f*XY denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complement). Previous studies with respect to prokaryotes and this study document that profiles of different DNA sequence samples (sample size ≥50 kb) from the same organism are generally much more similar to each other than they are to profiles from other organisms, and that closely related organisms generally have more similar profiles than do distantly related organisms. On this basis we refer to the collection {ρ*XY} as the genome signature. This paper identifies ρ*XY extremes and compares genome signature differences for a diverse range of eukaryotic species. Interpretations on the mechanisms maintaining these profile differences center on genome-wide replication, repair, DNA structures, and context-dependent mutational biases. It is also observed that mitochondrial genome signature differences between species parallel the corresponding nuclear genome signature differences despite large differences between corresponding mitochondrial and nuclear signatures. The genome signature differences also have implications for contrasts between rodents and other mammals, and between monocot and dicot plants, as well as providing evidence for similarities among fungi and the diversity of protists.

Derivation of pluripotent stem cells from cultured human primordial germ cells

Human pluripotent stem cells would be invaluable for in vitro studies of aspects of human embryogenesis. With the goal of establishing pluripotent stem cell lines, gonadal ridges and mesenteries containing primordial germ cells (PGCs, 5–9 weeks postfertilization) were cultured on mouse STO fibroblast feeder layers in the presence of human recombinant leukemia inhibitory factor, human recombinant basic fibroblast growth factor, and forskolin. Initially, single PGCs in culture were visualized by alkaline phosphatase activity staining. Over a period of 7–21 days, PGCs gave rise to large multicellular colonies resembling those of mouse pluripotent stem cells termed embryonic stem and embryonic germ (EG) cells. Throughout the culture period most cells within the colonies continued to be alkaline phosphatase-positive and tested positive against a panel of five immunological markers (SSEA-1, SSEA-3, SSEA-4, TRA-1–60, and TRA-1–81) that have been used routinely to characterize embryonic stem and EG cells. The cultured cells have been continuously passaged and found to be karyotypically normal and stable. Both XX and XY cell cultures have been obtained. Immunohistochemical analysis of embryoid bodies collected from these cultures revealed a wide variety of differentiated cell types, including derivatives of all three embryonic germ layers. Based on their origin and demonstrated properties, these human PGC-derived cultures meet the criteria for pluripotent stem cells and most closely resemble EG cells.

The human sex-reversing ATRX gene has a homologue on the marsupial Y chromosome, ATRY: Implications for the evolution of mammalian sex determination

Mutations in the ATRX gene on the human X chromosome cause X-linked α-thalassemia and mental retardation. XY patients with deletions or mutations in this gene display varying degrees of sex reversal, implicating ATRX in the development of the human testis. To explore further the role of ATRX in mammalian sex differentiation, the homologous gene was cloned and characterized in a marsupial. Surprisingly, active homologues of ATRX were detected on the marsupial Y as well as the X chromosome. The Y-borne copy (ATRY) displays testis-specific expression. This, as well as the sex reversal of ATRX patients, suggests that ATRY is involved in testis development in marsupials and may represent an ancestral testis-determining mechanism that predated the evolution of SRY as the primary mammalian male sex-determining gene. There is no evidence for a Y-borne ATRX homologue in mouse or human, implying that this gene has been lost in eutherians and its role supplanted by the evolution of SRY from SOX3 as the dominant determiner of male differentiation.

Loss of sequences 3' to the testis-determining gene, SRY, including the Y pseudoautosomal boundary associated with partial testicular determination.

The condition termed 46,XY complete gonadal dysgenesis is characterized by a completely female phenotype and streak gonads. In contrast, subjects with 46,XY partial gonadal dysgenesis and those with embryonic testicular regression sequence usually present ambiguous genitalia and a mix of Müllerian and Wolffian structures. In 46,XY partial gonadal dysgenesis gonadal histology shows evidence of incomplete testis determination. In 46,XY embryonic testicular regression sequence there is lack of gonadal tissue on both sides. Various lines of evidence suggest that embryonic testicular regression sequence is a variant form of 46,XY gonadal dysgenesis. The sex-determining region Y chromosome gene (SRY) encodes sequences for the testis-determining factor. To date germ-line mutations in SRY have been reported in approximately 20% of subjects with 46,XY complete gonadal dysgenesis. However, no germ-line mutations of SRY have been reported in subjects with the partial forms. We studied 20 subjects who presented either 46,XY partial gonadal dysgenesis or 46,XY embryonic testicular regression sequence. We examined the SRY gene and the minimum region of Y-specific DNA known to confer a male phenotype. The SRY-open reading frame (ORF) was normal in all subjects. However a de novo interstitial deletion 3' to the SRY-ORF was found in one subject. Although it is possible that the deletion was unrelated to the subject's phenotype, we propose that the deletion was responsible for the abnormal gonadal development by diminishing expression of SRY. We suggest that the deletion resulted either in the loss of sequences necessary for normal SRY expression or in a position effect that altered SRY expression. This case provides further evidence that deletions of the Y chromosome outside the SRY-ORF can result in either complete or incomplete sex reversal.

Characterization of the promoter region of the mouse Xist gene.

The mouse Xist gene is expressed exclusively from the inactive X chromosome and may be implicated in initiating X inactivation. To better understand the mechanisms underlying the control of Xist expression, we investigated the upstream regulatory region of the mouse Xist promoter. A 1.2-kb upstream region of the Xist gene was sequenced and promoter activity was studied by chloramphenicol acetyltransferase (CAT) assays after transfection in murine XX and XY cell lines. The region analyzed (-1157 to +917 showed no in vitro sex-specific promoter activity. However, a minimal constitutional promoter was assigned to a region from -81 to +1, and a cis element from -41 to -15 regulates promoter activity. We showed that a nuclear factor binds to an element located at -30 to -25 (TTAAAG). A second sequence at -41 to -15 does not act as an enhancer and is unable to confer transcriptional activity to the Xist gene on its own. A third region from -82 to -41 is needed for correct expression. Deletion of the segment -441 to -231 is associated with an increase in CAT activity and may represent a silencer element.