Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a \u2018tube model\u2019 approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the \u2018CamTube\u2019 force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 \u3bcs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost

The clinical usefulness of optical coherence tomography during cancer interventions

Surgical oncolog

Diurnal rhythmicity in breast-milk glucocorticoids, and infant behavior and sleep at age 3 months

Purpose: In previous studies, associations between breast-milk cortisol levels obtained on one occasion and infant neurodevelopment were demonstrated. However, more recent evidence indicates that breast-milk cortisol and cortisone concentrations follow the diurnal rhythm of maternal hypothalamus-pituitary-adrenal axis, peaking in the early morning and with a nadir at midnight. We studied associations between breast-milk glucocorticoid (GC) rhythmicity, and infant behavior and sleep. Methods: We included 59 mothers, and their infants, of whom 17 had consulted an expert center during pregnancy for an increased risk of psychological distress. At 1 month postpartum, breast milk was sampled (on averag

Menus for Feeding Black Holes

Black holes are the ultimate prisons of the Universe, regions of spacetime where the enormous gravity prohibits matter or even light to escape to infinity. Yet, matter falling toward the black holes may shine spectacularly, generating the strongest source of radiation. These sources provide us with astrophysical laboratories of extreme physical conditions that cannot be realized on Earth. This chapter offers a review of the basic menus for feeding matter onto black holes and discusses their observational implications.Comment: 27 pages. Accepted for publication in Space Science Reviews. Also to appear in hard cover in the Space Sciences Series of ISSI "The Physics of Accretion onto Black Holes" (Springer Publisher

Integrated analysis of viral blips, residual viremia, and associated factors in people with HIV: Results from a retrospective cohort study

The etiology of viral blips is not yet fully elucidated. One of the hypotheses is that blips reflect variations in residual viremia (RV) near the detectability threshold. In this study, we evaluated whether RV is associated with viral blips and which factors are associated with RV. All treatment regimens in 2010–2020 consisting of two nucleos(-t)ide reverse transcriptase inhibitors and one anchor (integrase strand transfer inhibitor [INSTI], non-nucleoside reverse transcriptase inhibitor [NNRTI], or protease inhibitor [PI]) in people with HIV (PWH) were evaluated for RV (detectable viremia <50 cp/mL) and blips (isolated viral loads [VLs] 50–499 cp/mL between measurements <50 cp/mL). All medical records were reviewed and regimens in which a VL ≥ 50 cp/mL was deemed to result from non-adherence (based on the documented conclusion by the treating physician) were excluded. Factors associated with blips and RV were identified using generalized linear mixed models. In total, 24 518 VLs from 1658 PWH were analyzed. VLs were measured during INSTI- (n = 5119; 20.9%), PI- (n = 8935; 36.4%), and NNRTI-use (n = 10 464; 42.7%). VLs were categorized as blips in 1.4% (n = 332). The 24,186 non-blip VLs were RNAneg (no RV) (n = 15 326; 63.4%), 1–19 cp/mL (n = 6318; 26.1%), 20–49 cp/mL (n = 1620; 6.7%), or <50 cp/mL with an unknown RV level (n = 922; 3.8%). In 193/1658 PWH (11.6%), the RV level was RNAneg in all VLs assessed. RV 1–19 cp/mL and 20–49 cp/mL (vs. RNAneg) were significantly associated with subsequent viral blips (respective odds ratio 2.66 and 4.90 [95% confidence intervals: 1.98–3.58 and 3.41–7.04]). Zenith VL and use of PIs (vs. INSTIs/NNRTIs) were associated with higher RV and blip odds. This large cohort study showed that blips were associated with higher preceding RV. Both the anchor type and factors previously linked to the latent viral reservoir were associated with RV, suggesting blips having a multifactorial origin

Vedolizumab for Inflammatory Bowel Disease: Two-Year Results of the Initiative on Crohn and Colitis (ICC) Registry, A Nationwide Prospective Observational Cohort Study: ICC Registry – Vedolizumab

Prospective data of vedolizumab treatment for patients with inflammatory bowel disease (IBD) beyond 1 year of treatment is scarce but needed for clinical decision making. We prospectively enrolled 310 patients with IBD (191 with Crohn's disease (CD) and 119 patients with ulcerative colitis (UC)) with a follow-up period of 104 weeks (interquartile range: 103–104) in a nationwide registry. The corticosteroid-free clinical remission rate (Harvey Bradshaw Index ≤ 4, Short Clinical Colitis Activity index ≤ 2) at weeks 52 and 104 were 28% and 19% for CD and 27% and 28% for UC, respectively. Fifty-nine percent maintained corticosteroid-free clinical remission between weeks 52 and 104. Vedolizumab with concomitant immunosuppression showed comparable effectiveness outcomes compared with vedolizumab monotherapy (week 104: 21% vs. 23%; P = 0.77), whereas 8 of 13 severe infections occurred in patients treated with concomitant immunosuppression. To conclude, the clinical effect was 19% for CD and 28% for UC after 2 years of follow-up regardless of concomitant immunosuppression

Effect of water table management and elevated CO 2 on radish productivity and on CH 4 and CO 2 fluxes from peatlands converted to agriculture

Anthropogenic activity is affecting the global climate through the release of greenhouse gases (GHGs) e.g. CO2 and CH4. About a third of anthropogenic GHGs are produced from agriculture, including livestock farming and horticulture. A large proportion of the UK's horticultural farming takes place on drained lowland peatlands, which are a source of significant amounts of CO2 into the atmosphere. This study set out to establish whether raising the water table from the currently used − 50 cm to − 30 cm could reduce GHGs emissions from agricultural peatlands, while simultaneously maintaining the current levels of horticultural productivity. A factorial design experiment used agricultural peat soil collected from the Norfolk Fens (among the largest of the UK's lowland peatlands under intensive cultivation) to assess the effects of water table levels, elevated CO2, and agricultural production on GHG fluxes and crop productivity of radish, one of the most economically important fenland crops. The results of this study show that a water table of − 30 cm can increase the productivity of the radish crop while also reducing soil CO2 emissions but without a resultant loss of CH4 to the atmosphere, under both ambient and elevated CO2 concentrations. Elevated CO2 increased dry shoot biomass, but not bulb biomass nor root biomass, suggesting no immediate advantage of future CO2 levels to horticultural farming on peat soils. Overall, increasing the water table could make an important contribution to global warming mitigation while not having a detrimental impact on crop yield