Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments

Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.</p

Endometrial compaction to predict pregnancy outcomes in patients undergoing assisted reproductive technologies: a systematic review and meta-analysis.

Study questionDoes endometrial compaction (EC) help predict pregnancy outcomes in those undergoing ART?Summary answerEC is associated with a significantly higher clinical pregnancy rate (CPR) and ongoing pregnancy rate (OPR), but this does not translate to live birth rate (LBR).What is known alreadyEC describes the progesterone-induced decrease in endometrial thickness, which may be observed following the end of the proliferative phase, prior to embryo transfer. EC is proposed as a non-invasive tool to help predict pregnancy outcome in those undergoing ART, however, published data is conflicting.Study design size durationA literature search was carried out by two independent authors using PubMed, Cochrane Library, MEDLINE, Embase, Science Direct, Scopus, and Web of Science from inception of databases to May 2023. All peer-reviewed studies reporting EC and pregnancy outcomes in patients undergoing IVF/ICSI treatment were included.Participants/materials setting methodsThe primary outcome is LBR. Secondary outcomes included other pregnancy metrics (positive pregnancy test (PPT), CPR, OPR, miscarriage rate (MR)) and rate of EC. Comparative meta-analyses comparing EC and no EC were conducted for each outcome using a random-effects model if I 2 > 50%. The Mantel-Haenszel method was applied for pooling dichotomous data. Results are presented as odds ratios (OR) with 95% CI.Main results and the role of chanceOut of 4030 screened articles, 21 cohort studies were included in the final analysis (n = 27 857). No significant difference was found between LBR in the EC versus the no EC group (OR 0.95; 95% CI 0.87-1.04). OPR was significantly higher within the EC group (OR 1.61; 95% CI 1.09-2.38), particularly when EC ≥ 15% compared to no EC (OR 3.52; 95% CI 2.36-5.23). CPR was inconsistently defined across the studies, affecting the findings. When defined as a viable intrauterine pregnancy Limitations reasons for cautionHeterogeneity due to differences between reported pregnancy outcomes, definition of EC, method of ultrasound, and cycle protocol may account for the lack of translation between CPR/OPR and LBR findings; thus, all pooled data should be viewed with an element of caution.Wider implications of the findingsIn this dataset, the significantly higher CPR/OPR with EC does not translate to LBR. Although stratification of women according to EC cannot currently be recommended in clinical practice, a large and well-designed clinical trial to rigorously assess EC as a non-invasive predictor of a successful pregnancy is warranted. We urge for consistent outcome reporting to be mandated for ART trials so that data can be pooled, compared, and concluded on.Study funding/competing interestsH.A. was supported by the Hewitt Fertility Centre. S.G.P. and J.W. were supported by the Liverpool University Hospital NHS Foundation Trust. D.K.H. was supported by a Wellbeing of Women project grant (RG2137) and MRC clinical research training fellowship (MR/V007238/1). N.T. was supported by the National Institute for Health and Care Research. D.K.H. had received honoraria for consultancy for Theramex and has received payment for presentations from Theramex and Gideon Richter. The remaining authors have no conflicts of interest to report.Registration numberPROSPERO CRD42022378464

Regulator of calcineurin-2 is a centriolar protein with a role in cilia length control

Almost every cell in the human body extends a primary cilium. Defective cilia function leads to a set of disorders known as ciliopathies characterised by debilitating developmental defects affecting many tissues. Here we report a new role for regulator of calcineurin 2, RCAN2, in primary cilia function. It localises to centrioles and the basal body and is required to maintain normal cilia length. RCAN2 was identified as the most strongly upregulated gene from a comparative RNAseq analysis of cells in which expression of the Golgi matrix protein giantin had been abolished by gene editing. In contrast to previous work where we showed that depletion of giantin by RNAi results in defects in ciliogenesis and in cilia length control, giantin knockout cells generate normal cilia on serum withdrawal. Furthermore, giantin knockout zebrafish show increased expression of RCAN2. Importantly, suppression of RCAN2 expression in giantin knockout cells results in the same defects in cilia length control seen on RNAi of giantin itself. Together these data define RCAN2 as a regulator of cilia function that can compensate for loss of giantin function.</jats:p

Switching of the electron-phonon interaction in 1T-VSe2 assisted by hot carriers

Funding: We gratefully acknowledge funding from VILLUM FONDEN through the Young Investigator Program (Grant. No.15375) and the Centre of Excellence for Dirac Materials (Grant. No. 11744), the Danish Council for Independent Research, Natural Sciences under the Sapere Aude program (Grant Nos. DFF-9064-00057B and DFF-6108-00409) and the Aarhus University Research Foundation. This work is also supported by National Research Foundation (NRF) grants funded by the Korean government (nos. NRF-2020R1A2C200373211 and 2019K1A3A7A09033389) and by the International MaxPlanck Research School for Chemistry and Physics of Quantum Materials (IMPRS-CPQM). The authors also acknowledge The Royal Society and The Leverhulme Trust. R.S acknowledges financial support provided by the Ministry of Science and Technology in Taiwan under project number MOST-108-2112-M-001-049-MY2 & MOST 109-2124-M-002-001 and Sinica funded i-MATE financial Support AS-iMATE-109-13. Access to the Artemis Facility was funded by STFC. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.We apply an intense infrared laser pulse in order to perturb the electronic and vibrational states in the three-dimensional charge density wave material 1T-VSe2. Ultrafast snapshots of the light-induced hot carrier dynamics and non-equilibrium quasiparticle spectral function are collected using time- and angle-resolved photoemission spectroscopy. The hot carrier temperature and time-dependent electronic self-energy are extracted from the time-dependent spectral function, revealing that incoherent electron-phonon interactions heat the lattice above the charge density wave critical temperature on a timescale of (200 ± 40)~fs. Density functional perturbation theory calculations establish that the presence of hot carriers alters the overall phonon dispersion and quenches efficient low-energy acoustic phonon scattering channels, which results in a new quasi-equilibrium state that is experimentally observed.Publisher PDFPeer reviewe

Defining predictors of responsiveness to advanced therapies in Crohn’s disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine

Introduction: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient’s quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients. Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures. IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments. Methods and analysis: This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures. Ethics and dissemination: Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk. Trial registration number: ISRCTN96296121

Ultrafast triggering of insulator-metal transition in two-dimensional VSe2

Funding: VILLUM FONDEN through the Young Investigator Program (Grant. No. 15375) and the Centre of Excellence for Dirac Materials (Grant. No. 11744), the Danish Council for Independent Research, Natural Sciences under the Sapere Aude program (Grant Nos. DFF-9064-00057B and DFF-6108-00409) and the Aarhus University Research Foundation. This work is also supported by National Research Foundation (NRF) grants funded by the Korean government (nos. NRF-2020R1A2C200373211 and 2019K1A3A7A09033389) and by the International Max PlanckResearch School for Chemistry and Physics of Quantum Materials (IMPRS-CPQM). The authors also acknowledge The Royal Society and The Leverhulme Trust.The transition-metal dichalcogenide VSe2 exhibits an increased charge density wave transition temperature and an emerging insulating phase when thinned to a single layer. Here, we investigate the interplay of electronic and lattice degrees of freedom that underpin these phases in single-layer VSe2 using ultrafast pump–probe photoemission spectroscopy. In the insulating state, we observe a light-induced closure of the energy gap, which we disentangle from the ensuing hot carrier dynamics by fitting a model spectral function to the time-dependent photoemission intensity. This procedure leads to an estimated time scale of 480 fs for the closure of the gap, which suggests that the phase transition in single-layer VSe2 is driven by electron–lattice interactions rather than by Mott-like electronic effects. The ultrafast optical switching of these interactions in SL VSe2 demonstrates the potential for controlling phase transitions in 2D materials with light.PostprintPostprintPeer reviewe

Early cranial ultrasound findings among infants with neonatal encephalopathy in Uganda: an observational study.

BACKGROUND: In sub-Saharan Africa, the timing and nature of brain injury and their relation to mortality in neonatal encephalopathy (NE) are unknown. We evaluated cranial ultrasound (cUS) scans from term Ugandan infants with and without NE for evidence of brain injury. METHODS: Infants were recruited from a national referral hospital in Kampala. Cases (184) had NE and controls (100) were systematically selected unaffected term infants. All had cUS scans <36 h reported blind to NE status. RESULTS: Scans were performed at median age 11.5 (interquartile range (IQR): 5.2-20.2) and 8.4 (IQR: 3.6-13.5) hours, in cases and controls respectively. None had established antepartum injury. Major evolving injury was reported in 21.2% of the cases vs. 1.0% controls (P < 0.001). White matter injury was not significantly associated with bacteremia in encephalopathic infants (odds ratios (OR): 3.06 (95% confidence interval (CI): 0.98-9.60). Major cUS abnormality significantly increased the risk of neonatal death (case fatality 53.9% with brain injury vs. 25.9% without; OR: 3.34 (95% CI: 1.61-6.95)). CONCLUSION: In this low-resource setting, there was no evidence of established antepartum insult, but a high proportion of encephalopathic infants had evidence of major recent and evolving brain injury on early cUS imaging, suggesting prolonged or severe acute exposure to hypoxia-ischemia (HI). Early abnormalities were a significant predictor of death

Low-energy unphysical saddle in polynomial molecular potentials

Vibrational spectra of polyatomic molecules are often obtained from a polynomial expansion of the adiabatic potential around a minimum. For several molecules, we show that such an approximation displays an unphysical saddle point of comparatively small energy, leading to a region where the potential is negative and unbounded. This poses an upper limit for a reliable evaluation of vibrational levels. We argue that the presence of such saddle points is general.Comment: The preprint version of the published Mol. Phys. paper, 19 pages, 3 figure

Emollients for preventing atopic eczema: Cost‐effectiveness analysis of the BEEP trial

BackgroundRecent discoveries have led to the suggestion that enhancing skin barrier from birth might prevent eczema and food allergy. ObjectiveTo determine the cost‐effectiveness of daily all‐over‐body application of emollient during the first year of life for preventing atopic eczema in high‐risk children at 2 years from a health service perspective. We also considered a 5‐year time horizon as a sensitivity analysis. MethodsA within‐trial economic evaluation using data on health resource use and quality of life captured as part of the BEEP trial alongside the trial data. Parents/carers of 1394 infants born to families at high risk of atopic disease were randomised 1:1 to the emollient group, which were advised to apply emollient (Doublebase Gel or Diprobase Cream) to their child at least once daily to the whole body during the first year of life or usual care. Both groups received advice on general skin care. The main economic outcomes were incremental cost‐effectiveness ratio (ICER), defined as incremental cost per percentage decrease in risk of eczema in the primary cost‐effectiveness analysis. Secondary analysis, undertaken as a cost‐utility analysis, reports incremental cost per Quality‐Adjusted Life Year (QALY) where child utility was elicited using the proxy CHU‐9D at 2 years. ResultsAt 2 years, the adjusted incremental cost was £87.45 (95% CI −54.31, 229.27) per participant, whilst the adjusted proportion without eczema was 0.0164 (95% CI −0.0329, 0.0656). The ICER was £5337 per percentage decrease in risk of eczema. Adjusted incremental QALYs were very slightly improved in the emollient group, 0.0010 (95% CI −0.0069, 0.0089). At 5 years, adjusted incremental costs were lower for the emollient group, −£106.89 (95% CI −354.66, 140.88) and the proportion without eczema was −0.0329 (95% CI −0.0659, 0.0002). The 5‐year ICER was £3201 per percentage decrease in risk of eczema. However, when inpatient costs due to wheezing were excluded, incremental costs were lower and incremental effects greater in the usual care group. ConclusionsIn line with effectiveness endpoints, advice given in the BEEP trial to apply daily emollient during infancy for eczema prevention in high‐risk children does not appear cost‐effective