Treatment effect of semaglutide 2.4 mg on health-related quality of life from STEP 1 SF-6D derived from SF-36 with Australian weights.

AIM: This study aimed to determine the comparative treatment effects of semaglutide 2.4 mg and placebo on health utility index scores [6-dimension short-form survey (SF-6D)] with Australian weights in full analysis set (FAS) and in post-hoc subgroups of the STEP 1 trial, defined according to different body mass index (BMI) cut-off points and presence of comorbidities at baseline. The study also explored the correlation between baseline BMI and SF-6D in the STEP 1 trial population. METHODS: The 36-item SF survey (SF-36) scores from STEP 1 were mapped to SF-6D health states and converted to utility index scores using an Australian valuation algorithm. The change from baseline in SF-6D utility score (95% confidence intervals) was compared between semaglutide 2.4 mg and placebo at week 68 using the mixed model for repeated measurements approach. The relationship between utility scores and BMI at baseline was assessed by multiple linear regression analyses, controlling for demographic and clinical parameters. RESULTS: The estimated mean treatment difference in SF-6D utility score favoured semaglutide 2.4 mg, and, at week 68, it was 0.057 (0.038-0.076) for the FAS. A greater treatment effect was noted in subgroups with presence of symptomatic comorbidities, i.e. 0.077 (0.027-0.128) to 0.105 (0.030-0.179) at week 68. A 1-unit increase in BMI was associated with a utility loss of 0.0075 (-0.0089 to -0.0062) for the FAS population, while controlling for demographic and clinical parameters. CONCLUSION: To our knowledge, this is the first study showing statistically significant and clinically meaningful improvements in SF-6D utility scores with weight-loss pharmacotherapy in Australia.

Predicting base editing outcomes using position-specific sequence determinants.

CRISPR/Cas base editors promise nucleotide-level control over DNA sequences, but the determinants of their activity remain incompletely understood. We measured base editing frequencies in two human cell lines for two cytosine and two adenine base editors at ∼14 000 target sequences and find that base editing activity is sequence-biased, with largest effects from nucleotides flanking the target base. Whether a base is edited depends strongly on the combination of its position in the target and the preceding base, acting to widen or narrow the effective editing window. The impact of features on editing rate depends on the position, with sequence bias efficacy mainly influencing bases away from the center of the window. We use these observations to train a machine learning model to predict editing activity per position, with accuracy ranging from 0.49 to 0.72 between editors, and with better generalization across datasets than existing tools. We demonstrate the usefulness of our model by predicting the efficacy of disease mutation correcting guides, and find that most of them suffer from more unwanted editing than pure outcomes. This work unravels the position-specificity of base editing biases and allows more efficient planning of editing campaigns in experimental and therapeutic contexts.

"More support, less distress?": Examining the role of social norms in alleviating practitioners' psychological distress in the context of assisted dying services.

This study explores how providing assisted dying services affects the psychological distress of practitioners. It investigates the influence of professional norms that endorse such services within their field. Study 1 included veterinarians (N = 137, 75.2% female, Mage = 43.1 years, SDage = 12.7 years), and Study 2 health practitioner students (N = 386, 71.0% female, Mage = 21.0 years, SDage = 14.4 years). In both studies, participants indicated their degree of psychological distress following exposure to scenarios depicting assisted dying services that were relevant to their respective situations. In Study 1, we found that higher willingness to perform animal euthanasia was associated with lower distress, as were supportive norms. In Study 2, a negative association between a greater willingness to perform euthanasia and lower psychological distress occurred only when the provision of such services was supported by professional norms. In conclusion, psychological distress is buffered by supportive professional norms.

Using Latent Profile Analysis to Understand Health Practitioners' Attitudes Toward Voluntary Assisted Dying.

Prior work has documented considerable diversity among health practitioners regarding their support for voluntary assisted dying (VAD). We examined whether their attitudes are characterised by different combinations of personal support, normative support by other health practitioners, and whether they are predisposed to vicariously experience others' emotions (i.e., empathy). We also examined whether these profiles experienced different mental health outcomes (i.e., burnout and posttraumatic stress) in relation to VAD. To test this, 104 Australian health practitioners were surveyed after VAD was legalised in Victoria, Australia in 2019. Results indicated that practitioners' attitudes were characterised by three profiles: 1) strong personal and normative support (strong VAD supporters), 2) moderate personal and normative support (moderate VAD supporters), and 3) lower personal and normative support (apprehensive practitioners). However, each profile reported similar mental health outcomes. Findings suggest that the normative environments in which health practitioners operate may explain their diverse attitudes on VAD.

JACKS: joint analysis of CRISPR/Cas9 knockout screens.

Genome-wide CRISPR/Cas9 knockout screens are revolutionizing mammalian functional genomics. However, their range of applications remains limited by signal variability from different guide RNAs that target the same gene, which confounds gene effect estimation and dictates large experiment sizes. To address this problem, we report JACKS, a Bayesian method that jointly analyzes screens performed with the same guide RNA library. Modeling the variable guide efficacies greatly improves hit identification over processing a single screen at a time and outperforms existing methods. This more efficient analysis gives additional hits and allows designing libraries with a 2.5-fold reduction in required cell numbers without sacrificing performance compared to current analysis standards.

Within-group male relatedness reduces harm to females in Drosophila.

To resolve the mechanisms that switch competition to cooperation is key to understanding biological organization. This is particularly relevant for intrasexual competition, which often leads to males harming females. Recent theory proposes that kin selection may modulate female harm by relaxing competition among male relatives. Here we experimentally manipulate the relatedness of groups of male Drosophila melanogaster competing over females to demonstrate that, as expected, within-group relatedness inhibits male competition and female harm. Females exposed to groups of three brothers unrelated to the female had higher lifetime reproductive success and slower reproductive ageing compared to females exposed to groups of three males unrelated to each other. Triplets of brothers also fought less with each other, courted females less intensively and lived longer than triplets of unrelated males. However, associations among brothers may be vulnerable to invasion by minorities of unrelated males: when two brothers were matched with an unrelated male, the unrelated male sired on average twice as many offspring as either brother. These results demonstrate that relatedness can profoundly affect fitness through its modulation of intrasexual competition, as flies plastically adjust sexual behaviour in a manner consistent with kin-selection theory.

The risk of rhegmatogenous retinal detachment following anterior vitrectomy during cataract surgery: with versus without pars plana vitrectomy.

PURPOSE: To compare the rates of rhegmatogenous retinal detachment (RRD) following an anterior vitrectomy (AV) alone during cataract surgery, compared to cases requiring a subsequent pars plana vitrectomy (PPV) for dropped nuclear lens fragments (DNLFs). METHODS: Retrospective electronic note review of consecutive patients with a posterior capsular rupture (PCR) requiring either AV or subsequent PPV for DNLF over a 5-year period. RESULTS: A total of 20,235 cataract operations were performed during the defined period with 199 cases (eyes) of PCR (0.98%). One hundred forty-four of these (72.4%) were managed with AV, and the remaining 55 cases were further complicated by DNLF and thus underwent secondary PPVs. A total of 80.0% of cases in the AV group had a final BCVA of 0.30 logMAR or better, and 77.35% in the DNLF group had a BCVA of 0.30 logMAR or better (p = 0.069). Final BCVA was 0.30 (range-0.18 to 3.0) in the AV group and 0.32 (range-0.18 to 1.8) in the DNLF group (p = 0.82). Final BCVA in those patients who suffered a RRD was poorer than the rest of the cohort in the AV group (p = 0.03). Seven of 144 cases in the AV group went on to develop a RRD with a median time of 11 months (range 1-18 months). None of the cases in the DNLF group went on to develop a RRD (P = 0.048). CONCLUSION: Following an anterior vitrectomy during complicated cataract surgery, the risk of RRD may be lower in patients who require a subsequent PPV for management of DNLF compared to patients who are managed with anterior vitrectomy alone.

Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification.

We describe a tool, competitive fragmentation modeling for electron ionization (CFM-EI) that, given a chemical structure (e.g., in SMILES or InChI format), computationally predicts an electron ionization mass spectrum (EI-MS) (i.e., the type of mass spectrum commonly generated by gas chromatography mass spectrometry). The predicted spectra produced by this tool can be used for putative compound identification, complementing measured spectra in reference databases by expanding the range of compounds able to be considered when availability of measured spectra is limited. The tool extends CFM-ESI, a recently developed method for computational prediction of electrospray tandem mass spectra (ESI-MS/MS), but unlike CFM-ESI, CFM-EI can handle odd-electron ions and isotopes and incorporates an artificial neural network. Tests on EI-MS data from the NIST database demonstrate that CFM-EI is able to model fragmentation likelihoods in low-resolution EI-MS data, producing predicted spectra whose dot product scores are significantly better than full enumeration "bar-code" spectra. CFM-EI also outperformed previously reported results for MetFrag, MOLGEN-MS, and Mass Frontier on one compound identification task. It also outperformed MetFrag in a range of other compound identification tasks involving a much larger data set, containing both derivatized and nonderivatized compounds. While replicate EI-MS measurements of chemical standards are still a more accurate point of comparison, CFM-EI's predictions provide a much-needed alternative when no reference standard is available for measurement. CFM-EI is available at https://sourceforge.net/projects/cfm-id/ for download and http://cfmid.wishartlab.com as a web service.

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra.

CFM-ID is a web server supporting three tasks associated with the interpretation of tandem mass spectra (MS/MS) for the purpose of automated metabolite identification: annotation of the peaks in a spectrum for a known chemical structure; prediction of spectra for a given chemical structure and putative metabolite identification--a predicted ranking of possible candidate structures for a target spectrum. The algorithms used for these tasks are based on Competitive Fragmentation Modeling (CFM), a recently introduced probabilistic generative model for the MS/MS fragmentation process that uses machine learning techniques to learn its parameters from data. These algorithms have been extensively tested on multiple datasets and have been shown to out-perform existing methods such as MetFrag and FingerId. This web server provides a simple interface for using these algorithms and a graphical display of the resulting annotations, spectra and structures. CFM-ID is made freely available at http://cfmid.wishartlab.com.

Convergence yet Continued Complexity: A Systematic Review and Critique of Health Economic Models of Relapsing-Remitting Multiple Sclerosis in the United Kingdom.

OBJECTIVES: Several disease-modifying therapies have marketing authorizations for the treatment of relapsing-remitting multiple sclerosis (RRMS). Given their appraisal by the National Institute for Health and Care Excellence, the objective was to systematically identify and critically evaluate the structures and assumptions used in health economic models of disease-modifying therapies for RRMS in the United Kingdom. METHODS: Embase, MEDLINE, The Cochrane Library, and the National Institute for Health and Care Excellence Web site were searched systematically on March 3, 2014, to identify articles relating to health economic models in RRMS with a UK perspective. Data sources, techniques, and assumptions of the included models were extracted, compared, and critically evaluated. RESULTS: Of 386 results, 26 full texts were evaluated, leading to the inclusion of 18 articles (relating to 12 models). Early models varied considerably in method and structure, but convergence over time toward a Markov model with states based on disability score, a 1-year cycle length, and a lifetime time horizon was apparent. Recent models also allowed for disability improvement within the natural history of the condition. Considerable variety remains, with increasing numbers of comparators, the need for treatment sequencing, and different assumptions around efficacy waning and treatment withdrawal. CONCLUSIONS: Despite convergence over time to a similar Markov structure, there are still significant discrepancies between health economic models of RRMS in the United Kingdom. Differing methods, assumptions, and data sources render the comparison of model implementation and results problematic. The commonly used Markov structure leads to problems such as incapability to deal with heterogeneous populations and multiplying complexity with the addition of treatment sequences; these would best be solved by using alternative models such as discrete event simulations.

HMDB 3.0--The Human Metabolome Database in 2013.

The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40,000 (a 600% increase). This enormous expansion is a result of the inclusion of both 'detected' metabolites (those with measured concentrations or experimental confirmation of their existence) and 'expected' metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.).

Cas9-induced large deletions and small indels are controlled in a convergent fashion.

Repair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation.

Efficacy and safety data for the Ab interno XEN45 gel stent implant at 3 Years: A retrospective analysis.

PURPOSE: To report efficacy and safety measures of the XEN45 gel stent at 36 months in the UK National Health Service setting. METHODS: Retrospective non-comparative audit of the records of patients who underwent XEN45 implantation between June 2015 and May 2017 was performed. Main outcome measures were intraocular pressure and number of antihypertensive medications used. Failure was defined as need for further surgery or stent removal. Success was defined as a 20% decrease in intraocular pressure without the need for additional glaucoma medications or a reduction in antihypertensive medications without an increase in baseline intraocular pressure. Needling rates and preoperative factors effect were assessed. RESULTS: The cohort included 205 patients (205 eyes) with primary open angle glaucoma (84.4%), angle closure glaucoma (7.8%), or refractory glaucoma (7.8%), 62.9% had a stand-alone procedure and 37.1%, a combined phaco-XEN45 procedure. Mean intraocular pressure was 22.6 ± 7.0 mmHg at baseline compared to 14.7 ± 3.8 mmHg at 24 months and 14.0 ± 2.9 mmHg at 36 months (p < 0.001 for both). Mean number of medications used was 2.6 ± 1.1 at baseline compared to 0.5 ± 0.9 and 0.6 ± 1.0, at 24- and 36-months, respectively (p < 0.001 for both). The failure rate at 36 months was 25%. Needling was required in 36.6%. Evaluation of background factors yielded an increased failure rate in non-Caucasians compared to Caucasians (74% vs 21%, p < 0.001). CONCLUSION: XEN45 implantation is effective and safe at 36 months' follow-up. Patients should be advised regarding the risk of failure and possible need for bleb revisions. Careful patient selection may be required.

Minimal genome-wide human CRISPR-Cas9 library.

CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.

Efficacy and safety data for the XEN45 implant at 2 years: a retrospective analysis.

AIM: To report efficacy and safety measures for XEN45 in a National Health Service setting after 24-month follow-up. METHODS: This is a retrospective, non-comparative audit of records of patients who underwent XEN45 procedure between June 2015 and May 2017. The main outcome measures were intraocular pressure (IOP) reduction and number of antihypertensive medications at each timepoint. Failure was defined as requiring further surgery or removal of XEN. Success was defined as 20% reduction of IOP without additional glaucoma medications or reduction in antihypertensive medications without increase in baseline IOP. Needling rates were assessed and subgroup analysis was performed. RESULTS: A total of 151 eyes were included in the study. The main diagnoses were primary open angle glaucoma (84.1%), angle closure glaucoma (8.6%) and refractory glaucoma (7.3%). Stand-alone procedure was performed in 62.3% and combined phaco-XEN was done in 37.7%. The mean IOP at baseline was 22.1±6.5 mm Hg, and the mean IOP at 12 and 24 months was 15.4±5.9 mm Hg and 14.5±3.3 mm Hg, respectively (p<0.001). The mean number of medications was 2.77±1.1 at baseline, and 0.3±0.7 and 0.5±1.0 medications at 12 and 24 months, respectively (p<0.001). 25% of patients failed at the 24-month timepoint. Needling was required in 37.7% of patients at 24 months. Non-Caucasian ethnicity was found to be related to higher failure rate. No significant adverse events were noted. CONCLUSION: XEN45 is a viable, effective and safe procedure after 2 years of follow-up. Patients should be advised regarding failure rate as well as possible need for bleb revisions and medication use.

Electronic gaming machine gambling: measuring motivation.

Electronic gambling machines (EGMs) are known to be a particularly risky form of gambling (Petry. Addiction 98(5):645-655, 2003). It is vital that researchers and clinicians are aware of factors which could lead to people having problems with this form. Gambling motivation is one such factor. This study developed a measure of EGM gambling motivations based on the results of qualitative research conducted with EGM problem gamblers and experienced counsellors (Thomas et al. Int J Mental Health Addiction 7:97-107, 2009). A community based sample of 232 females (M = 29.60 years of age, SD = 15.41 years) and 123 males (M = 29.64 years of age, SD = 12.29 years) participated. Exploratory factor analysis extracted three motivational factors indicating people gambled on EGMs to escape, for its accessibility and for the social environment. Gambling to escape and for its accessibility had substantial positive correlations with frequency of EGM gambling and gambling problems. Social environment correlated less well with these indicators of excessive gambling. Correlations between factors suggested the accessible, social experience offered by EGM venues increases their appeal as a means of escape. The new subscales were internally consistent and demonstrated good evidence of validity. This new measure will facilitate future investigations into the relationships between gambling motivations, other aetiological factors and EGM problem gambling.

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification.

Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was developed to accurately predict electrospray ionization-MS/MS (ESI-MS/MS) spectra from chemical structures and to aid in compound identification via MS/MS spectral matching. While earlier versions of CFM-ID performed very well, CFM-ID's performance for predicting the MS/MS spectra of certain classes of compounds, including many lipids, was quite poor. Furthermore, CFM-ID's compound identification capabilities were limited because it did not use experimentally available MS/MS spectra nor did it exploit metadata in its spectral matching algorithm. Here, we describe significant improvements to CFM-ID's performance and speed. These include (1) the implementation of a rule-based fragmentation approach for lipid MS/MS spectral prediction, which greatly improves the speed and accuracy of CFM-ID; (2) the inclusion of experimental MS/MS spectra and other metadata to enhance CFM-ID's compound identification abilities; (3) the development of new scoring functions that improves CFM-ID's accuracy by 21.1%; and (4) the implementation of a chemical classification algorithm that correctly classifies unknown chemicals (based on their MS/MS spectra) in >80% of the cases. This improved version called CFM-ID 3.0 is freely available as a web server. Its source code is also accessible online.

The ribosomal P-stalk couples amino acid starvation to GCN2 activation in mammalian cells.

The eukaryotic translation initiation factor 2α (eIF2α) kinase GCN2 is activated by amino acid starvation to elicit a rectifying physiological program known as the Integrated Stress Response (ISR). A role for uncharged tRNAs as activating ligands of yeast GCN2 is supported experimentally. However, mouse GCN2 activation has recently been observed in circumstances associated with ribosome stalling with no global increase in uncharged tRNAs. We report on a mammalian CHO cell-based CRISPR-Cas9 mutagenesis screen for genes that contribute to ISR activation by amino acid starvation. Disruption of genes encoding components of the ribosome P-stalk, uL10 and P1, selectively attenuated GCN2-mediated ISR activation by amino acid starvation or interference with tRNA charging without affecting the endoplasmic reticulum unfolded protein stress-induced ISR, mediated by the related eIF2α kinase PERK. Wildtype ribosomes isolated from CHO cells, but not those with P-stalk lesions, stimulated GCN2-dependent eIF2α phosphorylation in vitro. These observations support a model whereby lack of a cognate charged tRNA exposes a latent capacity of the ribosome P-stalk to activate GCN2 in cells and help explain the emerging link between ribosome stalling and ISR activation.

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.

Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic targets. As multiple large-scale screens become available, a formal assessment of the reproducibility of these experiments becomes necessary. We analyze data from recently published pan-cancer CRISPR-Cas9 screens performed at the Broad and Sanger Institutes. Despite significant differences in experimental protocols and reagents, we find that the screen results are highly concordant across multiple metrics with both common and specific dependencies jointly identified across the two studies. Furthermore, robust biomarkers of gene dependency found in one data set are recovered in the other. Through further analysis and replication experiments at each institute, we show that batch effects are driven principally by two key experimental parameters: the reagent library and the assay length. These results indicate that the Broad and Sanger CRISPR-Cas9 viability screens yield robust and reproducible findings.

Predicting the mutations generated by repair of Cas9-induced double-strand breaks.

The DNA mutation produced by cellular repair of a CRISPR-Cas9-generated double-strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, but depend on DNA sequence at the targeted location. Here we systematically study the influence of flanking DNA sequence on repair outcome by measuring the edits generated by >40,000 guide RNAs (gRNAs) in synthetic constructs. We performed the experiments in a range of genetic backgrounds and using alternative CRISPR-Cas9 reagents. In total, we gathered data for >109 mutational outcomes. The majority of reproducible mutations are insertions of a single base, short deletions or longer microhomology-mediated deletions. Each gRNA has an individual cell-line-dependent bias toward particular outcomes. We uncover sequence determinants of the mutations produced and use these to derive a predictor of Cas9 editing outcomes. Improved understanding of sequence repair will allow better design of gene editing experiments.