Using Scipion for stream image processing at Cryo-EM facilities

Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

CFD simulation of fluid dynamic and biokinetic processes within activated sludge reactors under intermittent aeration regime

Due to the aeration system, biological reactors are the most energy-consuming facilities of convectional WWTPs. Many biological reactors work under intermittent aeration regime; the optimization of the aeration process (air diffuser layout, air flow rate per diffuser, aeration length …) is necessary to ensure an efficient performance; satisfying the effluent requirements with the minimum energy consumption. This work develops a CFD modelling of an activated sludge reactor (ASR) which works under intermittent aeration regime. The model considers the fluid dynamic and biological processes within the ASR. The biological simulation, which is transient, takes into account the intermittent aeration regime. The CFD modelling is employed for the selection of the aeration system of an ASR. Two different aeration configurations are simulated. The model evaluates the aeration power consumption necessary to satisfy the effluent requirements. An improvement of 2.8% in terms of energy consumption is achieved by modifying the air diffuser layout. An analysis of the influence of the air flow rate per diffuser on the ASR performance is carried out. The results show a reduction of 14.5% in the energy consumption of the aeration system when the air flow rate per diffuser is reduced. The model provides an insight into the aeration inefficiencies produced within ASRs.

High reliability of morphokinetic annotations among embryologists

STUDY QUESTION

Are morphokinetic measurements of time lapse-videos of human embryos comparable among operators?

SUMMARY ANSWER

There is little variation among morphokinetic measurements taken by different operators when analyzing the same time lapse-videos of human embryos.

WHAT IS KNOWN ALREADY

Morphokinetic analysis of preimplantation embryo development is a complementary method of embryo assessment increasingly used in IVF laboratories. Time-lapse videos of embryo development are normally viewed by trained embryologists and annotated with the times when specific developmental events occur. Such annotations form the basis of embryo selection algorithms, used to rank the embryos for transfer. It is unknown whether the reliability of morphokinetic annotations is related to the morphological characteristics of the analyzed embryo or to the ability of the embryologists performing the annotation. One study so far reported the reliability of morphokinetic annotations among three embryologists using the time-lapse system (TLS), but larger studies with different setups are needed to address this issue further.

STUDY DESIGN SIZE DURATION

A prospective study was carried out between October 2015 and June 2016. Six embryologists with various degrees of experience in static, morphology-based evaluation, individually annotated the same 93 videos of preimplantation development, corresponding to 18 IVF/ICSI cycles, recorded with a TLS.

PARTICIPANTS/MATERIALS SETTING METHODS

Times of second polar body extrusion, appearance and disappearance of pronuclei, and embryo cleavages (times from 2-cell to 5-cell stage: t2, t3, t4, t5) were annotated. Each embryologist was blinded to the annotations of the others. Intra- and inter-observer agreement was evaluated by computing intra-class correlation coefficients (ICCs).

MAIN RESULTS AND THE ROLE OF CHANCE

In the inter-observer analysis, most ICCs obtained were higher than 0.80, indicating a high level of agreement: t2: 0.93; t3: 0.80; t4: 0.89; t5: 0.89; disappearance of two pronuclei: 0.98. However, the ICCs obtained for second polar body extrusion and the appearance of two pronuclei annotations was lower: 0.51 and 0.63, respectively, indicating an average level of agreement. The ICCs obtained from the intra-observer analysis were also higher than 0.80 (t2: 0.96; t3: 0.89; t4: 0.88; t5: 0.86; disappearance of two pronuclei: 0.96). The ICCs obtained from second polar body extrusion and the appearance of two pronuclei annotations were 0.77 and 0.66, respectively. These results indicate that developmental timings, annotated in time-lapse videos, are highly reliable both within and among observers.

LIMITATIONS REASONS FOR CAUTION

The events at the developmental stages from 6-cells to blastocyst were not evaluated; since some morphokinetic algorithms use times past the 6-cell stage in their calculations, further studies should be carried out to understand the variations among observers in these cases.

WIDER IMPLICATIONS OF THE FINDINGS

Time-lapse measurement should be as objective as possible, especially for the first embryo cleavages, because they are often measured to define algorithms to assess the embryonic implantation potential. Our results show that measurements using this particular TLS are consistent and reliable both within and among operators.

STUDY FUNDING/COMPETING INTERESTS

None.

TRIAL REGISTRATION NUMBER

Not applicable.

The role of IGF-1 and the distribution of body fat in decreasing the number of prostate rebiopsies

OBJECTIVE

To assess the usefulness of IGF-1 and internal organ fat measured by bioelectrical impedance audiometry to avoid rebiopsies in patients with persistently high prostate-specific antigen (PSA) levels.

MATERIAL AND METHOD

A prospective study was conducted with 92 patients who underwent prostate rebiopsy due to high PSA levels with negative results in the rectal examination and a lack of preneoplastic lesions. The patients previously had their IGF-1 levels measured and had undergone an impedance audiometry test using the abdominal Fat Analyser AB-140 TANITA system. We calculated the receiver operating characteristic (ROC) curves for the PSA levels, %PSA, internal organ fat and IGF-1 and PSA density.

RESULTS

Twenty-five patients were diagnosed with prostate cancer. These patients had significantly higher PSA, PSAd and IGF-1 values and a tendency towards higher internal organ fat levels and lower %PSA readings (p=.001, p=.003, p=.001, p=.24 and P=0.28, respectively). The ROC curve showed an area under the curve for IGF-1 and PSA of .82 and .81, respectively. Using the cutoff points for 95% sensitivity and using the 3 criteria as an indication of rebiopsy, 74% of the biopsies would have been spared, leaving undiagnosed only 1 patient with clinically significant cancer -Gleason score>7 (4+3)-. The positive and negative predictive values for the set of variables were higher than for each one separately (PPV: 66/NPV: 63). The cost of both determinations was 82 euros.

CONCLUSIONS

Our results suggest that measuring IGF-1 could significantly decrease the number of unnecessary rebiopsies in an inexpensive and safe manner.

Organosilane-functionalization of nanostructured indium tin oxide films

Fabrication and organosilane-functionalization and characterization of nanostructured ITO electrodes are reported. Nanostructured ITO electrodes were obtained by electron beam evaporation, and a subsequent annealing treatment was selectively performed to modify their crystalline state. An increase in geometrical surface area in comparison with thin-film electrodes area was observed by atomic force microscopy, implying higher electroactive surface area for nanostructured ITO electrodes and thus higher detection levels. To investigate the increase in detectability, chemical organosilane-functionalization of nanostructured ITO electrodes was performed. The formation of 3-glycidoxypropyltrimethoxysilane (GOPTS) layers was detected by X-ray photoelectron spectroscopy. As an indirect method to confirm the presence of organosilane molecules on the ITO substrates, cyclic voltammetry and electrochemical impedance spectroscopy (EIS) were also carried out. Cyclic voltammograms of functionalized ITO electrodes presented lower reduction-oxidation peak currents compared with non-functionalized ITO electrodes. These results demonstrate the presence of the epoxysilane coating on the ITO surface. EIS showed that organosilane-functionalized electrodes present higher polarization resistance, acting as an electronic barrier for the electron transfer between the conductive solution and the ITO electrode. The results of these electrochemical measurements, together with the significant difference in the X-ray spectra between bare ITO and organosilane-functionalized ITO substrates, may point to a new exploitable oxide-based nanostructured material for biosensing applications. As a first step towards sensing, rapid functionalization of such substrates and their application to electrochemical analysis is tested in this work. Interestingly, oxide-based materials are highly integrable with the silicon chip technology, which would permit the easy adaptation of such sensors into lab-on-a-chip configurations, providing benefits such as reduced size and weight to facilitate on-chip integration, and leading to low-cost mass production of microanalysis systems.

The response of a fast scintillator screen (YAP:Ce) to low energy ions (0-40 keV) and its use to detect fast-ion-loss in stellarator TJ-II

A systematic study of scintillation materials was undertaken to improve the time resolution of the fast ion diagnostic currently installed at TJ-II stellarator. It was found that YAP:Ce (formula YAlO₃:Ce, Yttrium Aluminum Perovskite doped with Cerium) ionoluminescence offers better sensitivity and time response compared to the standard detector material, SrGa₂S₄:Eu (TG-Green), currently used in TJ-II. A comparison between both materials was carried out by irradiating them with H⁺ ions of up to 40 keV using a dedicated laboratory setup. It is found that for the low energy ions of interest at TJ-II, YAP:Ce offers 20 times higher sensitivity than TG-Green and much faster decay time, 27 ns versus 540 ns. It is expected that the use of YAP:Ce in combination with a faster data acquisition and an ion counting software as part of the TJ-II ion luminescent probe will provide 20 times faster data on ion loss.

A LIBS method for simultaneous monitoring of the impurities and the hydrogenic composition present in the wall of the TJ-II stellarator

The study of plasma-wall interactions and impurity transport in the plasma fusion devices is critical for the development of future fusion reactors. An experiment to perform laser induced breakdown spectroscopy, using minor modifications of our existing laser blow-off impurity injection system, has been set up thus making both experiments compatible. The radiation produced by the laser pulse focused at the TJ-II wall evaporates a surface layer of deposited impurities and the subsequent radiation produced by the laser-produced plasma is collected by two separate lens and fiber combinations into two spectrometers. The first spectrometer, with low spectral resolution, records a spectrum from 200 to 900 nm to give a survey of impurities present in the wall. The second one, with high resolution, is tuned to the wavelengths of the Hα and Dα lines in order to resolve them and quantify the hydrogen isotopic ratio present on the surface of the wall. The alignment, calibration, and spectral analysis method will be described in detail. First experimental results obtained with this setup will be shown and its relevance for the TJ-II experimental program discussed.