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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology
- Pablo Conesa, Yunior C. Fonseca, Jorge Jiménez de la Morena, Grigory Sharov, Jose Miguel de la Rosa-Trevín, Ana Cuervo, Alberto García Mena, Borja Rodríguez de Francisco, Daniel del Hoyo, David Herreros, Daniel Marchan, David Strelak, Estrella Fernández-Giménez, Erney Ramírez-Aportela, Federico Pedro de Isidro-Gómez, Irene Sánchez, James Krieger, José Luis Vilas, Laura del Cano, Marcos Gragera, Mikel Iceta, Marta Martínez, Patricia Losana, Roberto Melero, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano
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- Journal:
- Biological Imaging / Volume 3 / 2023
- Published online by Cambridge University Press:
- 29 June 2023, e13
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- Article
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Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.
Oviductal and endometrial mRNA expression of implantation candidate biomarkers during early pregnancy in rabbit
- Ayman Moustafa Saeed, María de los Desamparados Saenz de Juano, Francisco Marco Jiménez, José Salvador Vicente
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Prenatal losses are a complex problem. Pregnancy requires orchestrated communication between the embryo and the uterus that includes secretions from the embryo to signal pregnancy recognition and secretion and remodelling from the uterine epithelium. Most of these losses are characterized by asynchronization between embryo and uterus. To better understand possible causes, an analysis was conducted of gene expression of a set of transcripts related to maternal recognition and establishment of rabbit pregnancy (uteroglobin, SCGB1A1; integrin α1, ITGA1; interferon-γ, IFNG; vascular endothelial growth factor, VEGF) in oviduct and uterine tissue at 16, 72 or 144 h post-ovulation and insemination. In the oviduct tissue, a significant decrease in the level of SCGB1A1 mRNA expression was observed from 144 h post-ovulation. In the case of ITGA1, the transcript abundance was initially lower, but mRNA expression increased significantly at 72 and 144 h post-ovulation. For IFNG, a huge decrease was observed from 16 to 72 h post-ovulation. Finally, no significant differences were observed in the VEGF transcript. For the endometrium, the results showed a significant decline in the level of SCGB1A1 mRNA expression from 16 to 144 h post-ovulation induction. The highest levels of ITGA1 transcript were detected at 144 h, followed by the 16 h group and lower at 72 h post-ovulation. For IFNG there were no significant differences among post-ovulation induction times. Finally, it was possible to observe that VEGF mRNA abundance was present at low levels at 16 h post-ovulation and remained low at 72 h, but increased at 144 h. The functional significance of these observations may provide new insights into the maternal role in prenatal losses.
Centromedian nucleus stimulation for epilepsy Clinical, electroencephalographic, and behavioral observations
- Francisco Velasco, Marcos Velasco, Fiacro Jimenez, Ana Luisa Velasco, Beatriz Rojas, Martha Luisa Perez
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- Journal:
- Thalamus & Related Systems / Volume 1 / Issue 4 / June 2002
- Published online by Cambridge University Press:
- 12 April 2006, pp. 387-398
- Print publication:
- June 2002
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A series of 49 cases with difficult to control seizures and non-candidates for ablation of the epileptic focus has been treated with electrical stimulation of the centromedian thalamic nuclei (ESCM).
Selected cases were: (1) epilepsia partialis continua (EPC) (n = 5); (2) partial complex seizures (n = 16); (3) bilateral frontal parasagittal seizures (n = 6); (4) Lennox-Gastaut syndrome (n = 22). All patients had four contact electrodes placed bilaterally through frontal parasagittal burr holes and guided by ventriculograms. Plotting of electrodes on sagittal and frontal sections of the Schaltenbrand and Bailey’s atlas permitted to determine their location. Electrodes were left externalized for periods of weeks to months to carry out the following tests. (1) Recordings of spontaneous seizures occurring during wakefulness and sleep. (2) Electrophysiological confirmation of their position by means of recruiting responses and desynchronization induced by low and high frequency stimulation. (3) Effects of high frequency stimulation on interictal and ictal activities. Electrodes were internalized and connected to a subcutaneous pulse generator programmed for alternating right and left ESCM 1 min ON and 4 min OFF at 60–130 Hz, 0.21–0.45 ms, 3–5 V forward and backward for 24 h per day. Repeated EEG recordings and a calendar of seizures were used for follow-up from 1 to 9 years.
CM paroxysmal discharges followed the initiation of seizures in cortical areas, occurred simultaneously with spike wave (SKW) complexes in cortical areas in Lennox-Gastaut syndrome and preceded the initiation of cortical SKW and clinical seizures in typical absences. Low frequency stimulation (6–8 cps) induced recruiting responses that were associated with those electrodes that produced best seizure control. Good to excellent results were obtained in cases of EPC and Lennox-Gastaut syndrome and on generalized tonic clonic convulsions (GTCs) and atypical absences (AA) with tonic or clonic components.
Consequently, we came to the conclusions that the CM participates in the propagation of most seizure types and also in the genesis of some of them and that ESCM is a safe and useful alternative for the treatment of some of the most difficult cases of uncontrollable seizures.