Lessons learned from automated screening of COVID-19 preprints

Preprints occupied the spotlight early in the pandemic, as scientists, the media and the public sought information on the evolving pandemic. While some in the scientific community embraced this shift, others were concerned about the quality of these papers, which had not yet undergone peer review. Furthermore, the flood of COVID-19 preprints quickly overwhelmed the scientific community's ability to monitor and assess new preprints. Automated screening tools that detect beneficial practices, or common problems, in preprints are one potential solution to this problem. These tools could potentially provide individualized feedback, allowing authors to improve their manuscripts prior to publication in a peer-reviewed journal. We have combined many tools into a single pipeline, called ScreenIT. ScreenIT assess factors such as open data and open code, blinding, randomization, power calculations, limitations sections, and data visualization problems. Since June 2020, we have used ScreenIT to screen and post daily reports on more than 23,000 new COVID-19 preprints deposited on bioRxiv and medRxiv. Results show that practices such as sharing data and code are relatively uncommon. Sample size calculations, blinding and randomization are rarely reported and most papers do not report the sex of participants, animals or samples. This work demonstrates the feasibility of using automated tools to rapidly screen many preprints in real time, and provide authors and readers with rapid feedback. However, this approach has important limitations. Automated screening tools can make mistakes. Tools can't always determine whether an item is relevant to a particular manuscript. Further studies are needed to determine whether feedback from automated tools is effective in encouraging authors to improve reporting.

DNAJC13 p.Asn855Ser mutation screening in Parkinson's disease and pathologically confirmed Lewy body disease patients

BACKGROUND

Recently, a novel mutation in exon 24 of DNAJC13 gene (p.Asn855Ser, rs387907571) has been reported to cause autosomal dominant Parkinson's disease (PD) in a multi-incident Mennonite family.

METHODS

In the present study the mutation containing exon of the DNAJC13 gene has been sequenced in a Caucasian series consisting of 1938 patients with clinical PD and 838 with pathologically diagnosed Lewy body disease (LBD).

RESULTS

Our sequence analysis did not identify any coding variants in exon 24 of DNAJC13. Two previously described variants in intron 23 (rs200204728 and rs2369796) were observed.

CONCLUSION

Our results indicate that the region surrounding the DNAJC13 p.Asn855Ser substitution is highly conserved and mutations in this exon are not a common cause of PD or LBD among Caucasian populations.

Ready or not? Lung cancer diagnosis in 2015

Lung cancer remains a significant health issue in Canada, with more than 26,000 new cases reported in 2014 [...]

Changes in motility, ATP content, morphology and fertilisation capacity during the movement phase of tetraploid Pacific oyster (Crassostrea gigas) sperm

Changes in sperm features during the movement phase are especially interesting to study in external fertilization species whose sperm duration movement is long because this implies a significant adaptation of moving cells to the external medium. This study describes the changes in tetraploid Pacific oyster sperm characteristics in relation to time post activation. Sperm individually collected on three tetraploid males were activated in seawater. Their features were analysed over a 24h period and compared to a sperm pool collected on three diploid males as a reference. The percentage of motile spermatozoa, the intracellular ATP content, and the fine structure of spermatozoa were studied in relation to time post activation. Furthermore, the fertilisation capacity of sperm individually collected on five diploid males was assessed after 1 and 24h post activation. A forward progressive movement was maintained for at least a 20h duration. Compared to diploid males, the percentage of motile spermatozoa was lower in tetraploid males. The intracellular ATP concentration was higher in spermatozoa from tetraploid males than in spermatozoa from diploid males. A decrease in ATP content was observed in the first 6h post activation and severe alterations were observed in sperm morphology after 24h. Then, a lower fertilisation capacity of sperm from diploid males was observed at the end of the movement phase. The cessation of Pacific oyster sperm motility was unlikely caused by ATP consumption as ATP concentration was still high at the end of sperm movement but rather caused by drastic changes in sperm morphology. Compared to sperm collected on diploid males, the lower quality of sperm from tetraploid males was emphasized by a shorter movement duration and deeper morphological alterations at the end of the movement phase.

[Influence of lipids on ice formation during the freezing of cryoprotective medium]

The influence of lipids on ice formation during the freezing of cryoprotective medium for the semen of rainbow trout has been studied by the cryomicroscopy technique. It was shown that the lipids extracted from marine vertebrates and liposomes from the lipids of trout sperm effectively inhibit the ice formation in cryoprotective solutions during freezing, fundamentally changing the form and size of ice crystals. At high concentrations of lipids, either the crystallization does not occur in the cryoprotective medium or, even if ice crystals are formed, they have a broken shape and blurred borders. The addition of egg yolk sligthly increases the size and essentially changes the shape of ice crystals during the freezing of solution.

Hydrostatic pressure effects on eel mitochondrial functioning and membrane fluidity

Aerobic metabolism which is required for long swimming activities during the eel's spawning migration at depth, is a potential target for pressure effects due to its components located in the inner mitochondrial membrane (respiratory chain and oxidative phosphorylation). Previous studies have evidenced that eels are able to acclimatize to pressure through membrane fluidity adjustment. However these studies were performed on the premigratory stage (yellow stage), which never encounters high pressure. Metamorphosis (silvering) seems to preadapt eels (at the silver stage) to most of the environmental changes they will encounter during migration. Is it also true for pressure resistance? This study shows that yellow eels exhibit a higher pressure sensitivity than silver eels (compression effects). The acclimatization period (21 days at 10.1 MPa) cancels the differences in pressure sensitivity and in aerobic metabolism observed at 0.1 MPa between the two stages. The mechanisms, which take place in yellow eels during acclimatization to high pressure, appear to be already present in silver eels before pressure exposure. Indeed at 0.1 MPa, silver eels exhibit higher membrane fluidity and proportions of membrane polyunsaturated fatty acids. Metamorphosis, by improving membrane fluidity, seems to allow silver eels to cope with hydrostatic pressure without spending energy in acclimatization processes.

Effect of sperm cryopreservation on sperm DNA stability and progeny development in rainbow trout

This study was carried out to test how sperm cryopreservation affected nuclear DNA stability and whether progeny development was modified when eggs were fertilized with cryopreserved spermatozoa. The "comet assay" (alkaline single-cell gel electrophoresis assay) was adapted to trout spermatozoa to estimate DNA stability as measured by alkali-induced DNA strand break formation. Because trout eggs develop in water after fertilization (oviparous species) and that eggshell is easy to clear up after fixative treatment, progeny development was assessed from the blastodisc flattening stage of the embryos to the first feeding stage of the hatched fries by direct observation. All parameters under study were analyzed on each sperm and comparisons between parameters were made using paired data. Freeze-thawing of sperm slightly but significantly increased the percentage of nuclei showing altered DNA after comet assay. This increase was correlated to the decrease in fertilization rates of sperm, but the absolute percentage of altered nuclei was not predictive of the absolute fertilization ability of sperm. Assessment of progeny development showed that survival rate and abnormality rate obtained after fertilization with cryopreserved sperm were not different from those obtained with fresh sperm. It is concluded that trout sperm cryopreservation only slightly affected sperm DNA stability and that the use of cryopreserved spermatozoa did not impair offspring survival and quality.

Thermal acclimation and dietary lipids alter the composition, but not fluidity, of trout sperm plasma membrane

The effect of a long-term adaptation of rainbow trout to 8 and 18 degrees C combined with a corn oil- or a fish oil-supplemented diet on the characteristics of the spermatozoan plasma membrane was investigated. The experiment lasted up to 22 mon during which spermatozoa were collected from the mature males. Spermatozoan plasma membranes were isolated by nitrogen cavitation, and the cholesterol content, phospholipid composition and fatty acid pattern were investigated. Membrane viscosity was assessed on whole cells by electron spin resonance using spin-labeled phospholipids. Neither diet nor rearing temperature influenced the cholesterol content of the plasma membrane nor the phospholipid class distribution. The rearing temperature of the broodstock only slightly affected the phospholipid fatty acids. A minor decrease in 18:0 and increase in monounsaturated fatty acids was observed for the cold-adapted fish. These modifications were not sufficient to affect membrane fluidity, and we conclude that trout spermatozoa do not display any homeoviscous adaptations in these conditions. On the contrary, the dietary fatty acid intake greatly modified the fatty acid profile of plasma membrane phospholipids. The fish oil-fed trout displayed a much higher n-3/n-6 fatty acid ratio than did the corn oil-fed ones, but the 22:6n-3 levels remained unchanged. Modifications in plasma membrane composition by the diet were obtained although neither of the two diets was deficient in essential fatty acids. The enrichment in n-3 fatty acids, however, did not affect plasma membrane fluidity which was unchanged by the diets.

Monoiodo-[Trp11]neurotensin, a highly radioactive ligand of neurotensin receptors. Preparation, biological activity, and binding properties to rat brain synaptic membranes

Iodination of [Trp11]neurotensin, a neurotensin analogue in which tyrosine 11 has been substituted by a tryptophan, led to the incorporation of one or two iodine atoms on the single tyrosine residue in position 3. Both mono- and diiodinated derivatives were purified by ion exchange chromatography and their biological activity in an in vitro bioassay involving rat ileum was found to be similar to that of native neurotensin. The 125I-labeled monoiodo derivative of [Trp11]neurotensin bound specifically and reversibly to rat brain synaptic membranes. The binding isotherm was biphasic and could be described by postulating the existence of two different classes of independent binding sites with dissociation constants of 0.1 and 4.7 nM. The specificity of a series of neurotensin analogues for both high and low affinity binding sites was the same as that previously observed in other neurotensin radioreceptor assays. The low affinity binding sites appeared to be similar to the single class of sites described in other binding studies. The high affinity binding sites which were not previously detected might represent either a new class of neurotensin receptors or a high affinity state for a fraction of a single population of neurotensin receptors.