ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.

Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.

TomoEED: fast edge-enhancing denoising of tomographic volumes.

Summary: TomoEED is an optimized software tool for fast feature-preserving noise filtering of large 3D tomographic volumes on CPUs and GPUs. The tool is based on the anisotropic nonlinear diffusion method. It has been developed with special emphasis in the reduction of the computational demands by using different strategies, from the algorithmic to the high performance computing perspectives. TomoEED manages to filter large volumes in a matter of minutes in standard computers. Availability and implementation: TomoEED has been developed in C. It is available for Linux platforms at http://www.cnb.csic.es/%7ejjfernandez/tomoeed. Supplementary information: Supplementary data are available at Bioinformatics online.

Introducing improvements in the mass rearing of the housefly: biological, morphometric and genetic characterization of laboratory strains.

Understanding the biology of the housefly (Musca domestica L.) is crucial for the development of mass-rearing protocols in order to use this insect as a degradation agent for livestock waste. In this study, the biological and genetic differences between different laboratory strains of M. domestica were analysed. Additionally, hybrids were obtained by mixing the strains and their biological parameters were also measured. The three strains of M. domestica presented differences in their biological and morphological parameters, the main differences were: size, egg production and developmental time. The strain A (specimens from Central Europe) had the best qualities to be used in mass-rearing conditions: it produced the largest quantities of eggs (5.77±0.38 eggs per female per day), the individuals were larger (12.62±0.22 mg) and its developmental time was shorter (15.22±0.21 days). However, the strain C (specimens from SW Europe) produced the fewest eggs (3.15±0.42 eggs per female per day) and needed 18.16±0.49 days to develop from larva to adult, whilst the females from strain B (from South America) produced 4.25±0.47 eggs per day and needed 17.11±0.36 days to complete its development. Genetic analysis of the original laboratory strains showed four different mtDNA cytochrome c oxidase subunit I haplotypes. Statistical parsimony network analysis showed that the SW Europe and South-American strains shared haplotypes, whereas the Central Europe strain did not. Upon hybridizing the strains, variations in egg production and in developmental time were observed in between hybrids and pure strains, and when mixing Central European and South-American strains only males were obtained.

Phenotypic variation of the housefly, Musca domestica: amounts and patterns of wing shape asymmetry in wild populations and laboratory colonies.

Musca domestica L. (Diptera: Muscidae) is a vector of a range variety of pathogens infecting humans and animals. During a year, housefly experiences serial population bottlenecks resulted in reduction of genetic diversity. Population structure has also been subjected to different selection regimes created by insect control programs and pest management. Both environmental and genetic disturbances can affect developmental stability, which is often reflected in morphological traits as asymmetry. Since developmental stability is of great adaptive importance, the aim of this study was to examine fluctuating asymmetry (FA), as a measure of developmental instability, in both wild populations and laboratory colonies of M. domestica. The amount and pattern of wing shape FA was compared among samples within each of two groups (laboratory and wild) and between groups. Firstly, the amount of FA does not differ significantly among samples within the group and neither does it differ between groups. Regarding the mean shape of FA, contrary to non-significant difference within the wild population group and among some colonies, the significant difference between groups was found. These results suggest that the laboratory colonies and wild samples differ in buffering mechanisms to perturbations during development. Hence, inbreeding and stochastic processes, mechanisms dominating in the laboratory-bred samples contributed to significant changes in FA of wing shape. Secondly, general patterns of left-right displacements of landmarks across both studied sample groups are consistent. Observed consistent direction of FA implies high degrees of wing integration. Thus, our findings shed light on developmental buffering processes important for population persistence in the environmental change and genetic stress influence on M. domestica.

14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation.

We previously established the scaffold protein 14-3-3ζ as a critical regulator of adipogenesis and adiposity, but the temporal specificity of its action during adipocyte differentiation remains unclear. To decipher if 14-3-3ζ exerts its regulatory functions on mature adipocytes or on adipose precursor cells (APCs), we generated Adipoq14-3-3ζKO and Pdgfra14-3-3ζKO mouse models. Our findings revealed a pivotal role for 14-3-3ζ in APC differentiation in a sex-dependent manner, whereby male and female Pdgfra14-3-3ζKO mice display impaired or potentiated weight gain, respectively, as well as fat mass. To better understand how 14-3-3ζ regulates the adipogenic transcriptional program in APCs, CRISPR-Cas9 was used to generate TAP-tagged 14-3-3ζ-expressing 3T3-L1 preadipocytes. Using these cells, we examined if the 14-3-3ζ nuclear interactome is enriched with adipogenic regulators during differentiation. Regulators of chromatin remodeling, such as DNMT1 and HDAC1, were enriched in the nuclear interactome of 14-3-3ζ, and their activities were impacted upon 14-3-3ζ depletion. The interactions between 14-3-3ζ and chromatin-modifying enzymes suggested that 14-3-3ζ may control chromatin remodeling during adipogenesis, and this was confirmed by ATAC-seq, which revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Moreover, 14-3-3ζ-dependent chromatin accessibility was found to directly correlate with the expression of key adipogenic genes. Altogether, our study establishes 14-3-3ζ as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3ζ interactome to identify novel pro-adipogenic factors and pathways.

Larval morphology, development and forensic importance of Synthesiomyia nudiseta (Diptera: Muscidae) in Europe: a rare species or just overlooked?

The muscid Synthesiomyia nudiseta (van der Wulp, 1883) is a species with forensic importance in tropical and subtropical regions of the world. This fly has recently been introduced into southern Europe and, until now, had not been recorded in forensic cases in this region. Here, morphology of all larval instars of S. nudiseta is documented in detail by using a combination of light and scanning electron microscopy. Literature data concerning larval morphology are revised and characters allowing identification from other forensically important Muscidae are listed. The life cycle of this species was studied at four constant temperatures: 15, 20, 25 and 30 °C. Total development varied between 46.50 ± 0.97 days at 15 °C and 15.39 ± 0.32 days at 30 °C. Moreover, we report this species breeding in human corpses, for the first time in Europe, in forensic cases from autopsies at the Anatomical Forensic Institute of Madrid and the Institute of Legal Medicine of Alicante, Spain.

Diptera of forensic importance in the Iberian Peninsula: larval identification key.

A revision of the species and families of sarcosaprophagous flies (Diptera: Calliphoridae, Sarcophagidae, Muscidae, Fanniidae, Drosophilidae, Phoridae, Piophilidae and Stratiomyidae) suitable for forensic purposes in the Iberian Peninsula is presented. Morphological characteristics that allow the accurate identification of third instars of the species present in the Iberian Peninsula are described and presented in the form of a diagnostic key. For larval Calliphoridae, characteristics such as the spines of the body segments were useful for the genus Calliphora whereas features of the anal segment and the cephalopharyngeal skeleton were useful for larvae of Lucilia. Identification of three Chrysominae species present in the Iberian Peninsula is included. For larval Sarcophagidae, characters such as the arrangement and shape of spiracular openings, structures of the anal segment and the cephalopharyngeal skeleton were used for the first time. A new record of Sarcophaga cultellata Pandellé, from a human corpse, is also included as well as recent incursions into the European cadaveric entomofauna such as Synthesiomyia nudiseta (van der Wulp) and Hermetia illucens (Linnaeus). This work provides useful new information that could be applied to forensic investigations in the Iberian Peninsula and in southern Europe.

Wolff-Parkinson-White syndrome associated to scimitar syndrome. Percutaneous radiofrequency catheter ablation previous to surgical repair.

Scimitar syndrome and Wolff-Parkinson-White association has not been reported during the era of catheter ablation. We present our personal experience with percutaneous radiofrequency ablation, a technical challenge related with Scimitar's anatomical variants and follow-up after surgical repair of the latter.

First record of Fannia leucosticta (Meigen) (Diptera: Fanniidae) breeding in human corpses.

A case where Fannia leucosticta (Meigen, 1838) was breeding in human corpses is reported for the first time. One larva and one unemerged puparium were recovered from two corpses in an advanced stage of decomposition, found in autumn in Alicante province, Spain.

A mathematical model applied for assisting the estimation of PMI in a case of forensic importance. First record of Conicera similis (Diptera: Phoridae) in a corpse.

We present a forensic case associated with skeletonized human remains found inside a cistern in a coastal town located in the eastern Iberian Peninsula (Valencian Regional Government, Spain). In order to analyse the particular environmental conditions that occurred during oviposition and development of the collected insects, estimated temperatures at the crime scene were calculated by a predictive mathematical model. This model analyses the correlation between the variability of the internal temperature depending on the variability of the external ones. The amplitude of the temperature oscillations inside the tank and the containment of the enclosure is reduced by the presence of water. Such variation occurred within about 2h due to the time required for heat exchange. The differential equations employed to model differences between outdoor and indoor temperatures were an essential tool which let us estimate the post-mortem interval (PMI) that was carried out by the study of the insect succession and the development time of the collected Diptera specimens under the adjusted temperatures. The presence of live larvae and pupae of Sarcophagidae and empty pupae of Calliphoridae, Sarcophagidae, Fanniidae, Muscidae, Phoridae and Piophilidae and the decomposition stage suggested the possibility that the remains were in the tank at least a year. We highlight the absence of Calliphora and Lucilia spp., and the first occurrence of the phorid Conicera similis in a human cadaver among the entomological evidence.

Annual and spatial activity of dung flies and carrion in a Mediterranean holm-oak pasture ecosystem.

The annual activity and spatial distribution of Muscidae and Calliphoridae were investigated in a holm-oak ('dehesa') ecosystem in western Spain over two years in pasture and woodland habitats, using wind-orientated traps baited with a mixture of fresh cattle faeces, liver and sodium sulphide solution. Lucilia sericata (Meigen) was always the dominant species and, with Chrysomya albiceps (Weidemann), Hydrotaea ignava (Harris), Muscina levida (Harris) and Muscina prolapsa (Harris), was more abundant during the second than the first year. By contrast, Calliphora vicina Robineau-Desvoidy, Calliphora vomitoria (L.), Hydrotaea armipes (Fallén), Hydrotaea penicillata (Rondani) and Hydrotaea dentipes (Fabricius) were more numerous during the first than the second year of the study. In summer, the Diptera sampled were significantly more abundant in a wooded than a pasture area. However, in autumn, while H. penicillata remained significantly more abundant in woodland, L. sericata became more abundant in the pasture, whereas C. vicina was captured in open and wooded areas in similar proportions. During winter and spring the populations sampled were relatively small. The changing patterns of abundance are discussed in relation to differences in climate within and between years.

Diagnosis of Berry syndrome in an infant by two-dimensional and color Doppler echocardiography.

A 6-month-old male infant with coexistent type B interrupted aortic arch, distal aortopulmonary window, and anomalous origin of the right pulmonary artery arising from the ascending aorta was diagnosed by two-dimensional echocardiography, color Doppler, and cardiac catheterization. Review of the available literature reveals this patient to be the fourteenth reported case of this unusual association of cardiovascular defects.

[Kawasaki disease: the echocardiographic diagnosis of coronary aneurysms. A report of 2 cases]. / Enfermedad de Kawasaki: diagnóstico ecocardiográfico de los aneurismas coronarios. Informe de dos casos.

We report two infants with Kawasaki disease and coronary aneurysms diagnosed by echocardiography. First case, a one year old male with abnormalities of left coronary artery, developed a myocardial infarction and died three weeks later. Second case a two months old male with aneurysm in the right coronary artery who doing well three months after the diagnosis was made. Echocardiography is the primary tool for evaluation and follow up of coronary abnormalities.

[Systemic candidiasis in the newborn. Report of 3 cases]. / Candidiasis sistémica en el lactante. Presentación de tres casos.

The clinical picture of 3 infants with systemic candidiasis who recovered spontaneously is described and a correlation is made between the clinical findings and laboratory data. The clinical picture is similar to that of 16 patients who died, some with septicemia of bacterial origin. The authors consider predisposing factors favoring the development of systemic mycotic infection such as: use of multiple antibiotics, continuous use of catheters, deficiency of IGA (in one patient). The diagnosis was suspected due to the prolonged course, the ill-defined toxic and infectious manifestations, the poor or lack of response to antibiotics and the negativity of bacterial blood cultures. The presence of Candida in various sites and cultures with positive serologic tests for Candida confirmed the diagnosis. Some considerations about antimycotic therapy are made and some circumstances that make the spontaneous cures of mycosis possible are considered.

[Coarctation of the aorta associated with interventricular communication]. / Coartación de aorta asociada a comunicación interventricular.

The association of coarctation of the aorta (CoAo) and ventricular septal defect (VSD) reaches a high mortality rate of approximately 75% in the first year of life without surgical treatment. We present our experience in the study of twenty cases with this combination of congenital heart defects with ages varying from 5 days to 13 years; half of them were under 6 months of age: there was a slight female predominance. Congestive heart failure was the first clinical manifestation in 75% of the patients; all of them showed clinical evidence of VSD with pulmonary hypertension. Twelve patients were surgically treated; in five, a subclavia flap technic was used; in another five, a rhomboid patch was placed at the site of CoAo and in the remaining two, the repair was done by end to end anastomosis. Banding of the pulmonary artery was performed in two cases and both survived; in three cases, in which the CoAo and VSD repair was done simultaneously, only one survived. We have an overall surgical mortality of 25%. Due to the short follow-up we have been unable to determine which cases may require reoperation later in life.

[Stents in aortic coarctation. Immediate results]. / Stents en coartación aórtica. Resultados inmediatos.

From September 1996 to March 1997 we implanted stents Palmaz (P-308 Johnson & Johnson) in six patients with aortic coarctation. Age ranged from 13 to 30 years (mean = 20), 3 female and 3 male. We implanted the stent without predilation. Balloon diameter was 12 mm in two cases and 15 mm in four cases for complete expansion we used 14 to 20 mm balloon diameter in five instances and in one case we used a dual balloon 15 + 15 mm. The gradient pre-stent ranged from 30 to 65 mmHg (mean = 44) and decreased to 0 mmHg in five cases and in one patient the residual gradient was 4 mmHg. Systolic aortic pressure pre-stent was 135 mmHg and decreased to 117 mmHg. There were no significant complications. In conclusion, we have demonstrated the feasibility of balloon-expandable stent implantation as a method of alleviation the obstruction in coarctation of the aorta in this group of patients. It is an excellent alternative to surgical treatment and it is better than balloon angioplasty that results in marked improvement in the angiographic appearance of the thoracic aorta. It eliminates the gradient, has minimum morbidity and no mortality, no aneurysm formation. Late restenosis and possible aneurysm formation remains an unlikely complication in view of the ample luminal diameter and the high velocity of flow.

Rotura traqueal postintubación tratada con prótesis en Y de Dumon / Post-tracheal intubation rupture treated with a Dumon-Y Stent

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