Efficacy of Elaborated Semantic Features Analysis in Aphasia: a quasi-randomised controlled trial

Background: Word finding difficulty is one of the most common features of aphasia. Semantic Features Analysis (SFA) directly aims to improve word finding in people with aphasia. Evidence from systematic reviews suggests that SFA leads to positive outcomes, yet the evidence comprises single case studies and case series. There is a need to evaluate the efficacy of SFA in controlled group studies/trials. Aims: To evaluate the efficacy of Elaborated Semantic Feature Analysis (ESFA) for word finding in people with aphasia. We investigated: (a) the efficacy of ESFA versus a delayed therapy/control, (b) the efficacy of two therapy approaches– individual versus a combination of individual and group therapy. Methods and procedures: We ran a multi-centre, quasi-randomised controlled trial, nested in a larger study (Thales-Aphasia). Participants were recruited from community settings. They had to be people with aphasia due to stroke at least four months post-onset. Participants were randomized to individual vs combination vs delayed therapy/control groups. Both therapy groups had three hours of ESFA per week for 12 weeks. Delayed therapy/control group had no intervention for 12 weeks and were then randomized to either individual or combination therapy. The primary outcome was confrontation naming. Secondary outcomes were the Boston Naming Test, Discourse, the Functional Assessment of Communication Skills for adults (ASHA–FACS), the Stroke and Aphasia Quality of Life scale (SAQOL-39g), the General Health Questionnaire-12 item, and the EQ-5D. Outcomes and Results: Of the 72 participants of the Thales-Aphasia project, 58 met eligibility criteria for speech-language therapy and 39 were allocated to ESFA. The critical p-value was adjusted for multiple comparisons (.005). For the therapy versus control comparison, there was a significant main effect of time on the primary outcome (p<.001, η2p=.42) and a significant interaction effect (p=.003, η2p=.21). An interaction effect for the SAQOL-39g (p=.015, η2p=.11) and its psychosocial domain (p=.013, η2p=.12) did not remain significant after Bonferroni adjustment. For the individual versus combination ESFA comparison, there were significant main effects of time on the primary outcome (p<.001, η2p=.49), the BNT (p<.001, η2p=.29) and the ASHA-FACS (p=.001, η2p=.18). Interaction and group effects were not significant. Conclusion: Though underpowered, this study provides evidence on the efficacy of ESFA to improve word finding in aphasia, with gains similar in the two therapy approaches. Trial registration: ISRCTN71455409, https://doi.org/10.1186/ISRCTN7145540

On Star Formation and the Non-Existence of Dark Galaxies

We investigate whether a baryonic dark galaxy or `galaxy without stars' could persist indefinitely in the local universe, while remaining stable against star formation. To this end, a simple model has been constructed to determine the equilibrium distribution and composition of a gaseous protogalactic disk. Specifically, we determine the amount of gas that will transit to a Toomre unstable cold phase via the H2 cooling channel in the presence of a UV--X-ray cosmic background radiation field. All but one of the models are predicted to become unstable to star formation. Moreover, we find that all our model objects would be detectable via HI line emission, even in the case that star formation is potentially avoided. These results are consistent with the non-detection of isolated extragalactic HI clouds with no optical counterpart (galaxies without stars) by HIPASS. Additionally, where star formation is predicted to occur, we determine the minimum interstellar radiation field required to restore gravothermal stability, which we then relate to a minimum global star formation rate. This leads to the prediction of a previously undocumented relation between HI mass and star formation rate that is observed for a wide variety of dwarf galaxies in the HI mass range 10^8--10^10 M_sun. The existence of such a relation strongly supports the notion that the well observed population of dwarf galaxies represent the minimum rates of self-regulating star formation in the universe. (Barely abridged)Comment: 19 pages, 8 figures, TeX using emulateapj.cls, v2 accepted for publication in ApJ (16/8/5) with one figure deleted and a number of minor clarifying revision

Nonlocal Conductivity in the Vortex-Liquid Regime of a Two-Dimensional Superconductor

We have simulated the time-dependent Ginzburg-Landau equation with thermal fluctuations, to study the nonlocal dc conductivity of a superconducting film. Having examined points in the phase diagram at a wide range of temperatures and fields below the mean-field upper critical field, we find a portion of the vortex-liquid regime in which the nonlocal ohmic conductivity in real space is negative over a distance several times the spacing between vortices. The effect is suppressed when driven beyond linear response. Earlier work had predicted the existence of such a regime, due to the high viscosity of a strongly-correlated vortex liquid. This behavior is clearly distinguishable from the monotonic spatial fall-off of the conductivity in the higher temperature or field regimes approaching the normal state. The possibilities for experimental study of the nonlocal transport properties are discussed.Comment: 18 pages, revtex, 6 postscript figure

Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity

Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ∼5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach

Positive impact of pre-stroke surgery on survival following transient focal ischemia in hypertensive rats

We describe a positive influence of pre-stroke surgery on recovery and survival in a commonly used experimental stroke model. Two groups of male, stroke-prone spontaneously hypertensive rats (SHRSPs) underwent transient middle cerebral artery occlusion (tMCAO). Group 1 underwent the procedure without any prior intervention whilst group 2 had an additional general anaesthetic 6 days prior to tMCAO for a cranial burrhole and durotomy. Post-stroke recovery was assessed using a 32 point neurological deficit score and tapered beam walk and infarct volume determined from haematoxylin–eosin stained sections. In group 2 survival was 92% (n = 12) versus 67% in group 1 (n = 18). In addition, post-tMCAO associated weight loss was significantly reduced in group 2. There was no significant difference between the two groups in experimental outcomes: infarct volume (Group 1 317 ± 18.6 mm&lt;sup&gt;3&lt;/sup&gt; versus Group 2 332 ± 20.4 mm&lt;sup&gt;3&lt;/sup&gt;), and serial (day 0–14 post-tMCAO) neurological deficit scores and tapered-beam walk test. Drilling a cranial burrhole under general anaesthesia prior to tMCAO in SHRSP reduced mortality and gave rise to infarct volumes and neurological deficits similar to those recorded in surviving Group 1 animals. This methodological refinement has significant implications for animal welfare and group sizes required for intervention studies

UPDATE trial: investigating the effects of ultra-processed versus minimally processed diets following UK dietary guidance on health outcomes: a protocol for an 8-week community-based cross-over randomised controlled trial in people with overweight or obesity, followed by a 6-month behavioural intervention

INTRODUCTION: Obesity increases the risk of morbidity and mortality. A major driver has been the increased availability of ultra-processed food (UPF), now the main UK dietary energy source. The UK Eatwell Guide (EWG) provides public guidance for a healthy balanced diet but offers no UPF guidance. Whether a healthy diet can largely consist of UPFs is unclear. No study has assessed whether the health impact of adhering to dietary guidelines depends on food processing. Furthermore, our study will assess the impact of a 6-month behavioural support programme aimed at reducing UPF intake in people with overweight/obesity and high UPF intakes. METHODS AND ANALYSIS: UPDATE is a 2×2 cross-over randomised controlled trial with a 6-month behavioural intervention. Fifty-five adults aged ≥18, with overweight/obesity (≥25 to <40 kg/m2), and ≥50% of habitual energy intake from UPFs will receive an 8-week UPF diet and an 8-week minimally processed food (MPF) diet delivered to their home, both following EWG recommendations, in a random order, with a 4-week washout period. All food/drink will be provided. Participants will then receive 6 months of behavioural support to reduce UPF intake. The primary outcome is the difference in weight change between UPF and MPF diets from baseline to week 8. Secondary outcomes include changes in diet, waist circumference, body composition, heart rate, blood pressure, cardiometabolic risk factors, appetite regulation, sleep quality, physical activity levels, physical function/strength, well-being and aspects of behaviour change/eating behaviour at 8 weeks between UPF/MPF diets, and at 6-month follow-up. Quantitative assessment of changes in brain MRI functional resting-state connectivity between UPF/MPF diets, and qualitative analysis of the behavioural intervention for feasibility and acceptability will be undertaken. ETHICS AND DISSEMINATION: Sheffield Research Ethics Committee approved the trial (22/YH/0281). Peer-reviewed journals, conferences, PhD thesis and lay media will report results. TRIAL REGISTRATION NUMBER: NCT05627570

Molecular selection of therapy in metastatic colorectal cancer: the FOCUS4 molecularly stratified RCT

Complex trials with innovative designs are becoming increasingly common and offer the potential to improve patient outcomes in a shorter time frame. There is evidence that patients with colorectal cancer fall into different subgroups with varying responsiveness to therapy, and that this variation is linked to genetic biomarkers. To the best of our knowledge, FOCUS4 was the first molecularly stratified trial in metastatic colorectal cancer and remains one of the first umbrella trial designs to be launched globally. Objectives To identify novel therapies that improve disease control within the molecular subgroup of metastatic colorectal cancer in which the novel therapies were expected to be most effective. Design This was a Phase II/III molecularly stratified umbrella trial that used adaptive statistical methodology to decide which subtrial should close early; new subtrials were added as protocol amendments. Setting The maintenance setting following 16 weeks of first-line combination chemotherapy. Participants Patients with newly diagnosed metastatic colorectal cancer were registered, and central laboratory testing was used to stratify their tumour into molecular subtypes. Following 16 weeks of first-line therapy, patients with stable or responding disease were eligible for randomisation into either a molecularly stratified subtrial or the non-stratified FOCUS4-N trial. Interventions Of the 20 drug combinations that were explored for inclusion in the platform trial, three molecularly targeted subtrials were activated: FOCUS4-B (PIK3CA mutation or PTEN overexpression) – aspirin versus placebo; FOCUS4-C (TP53 and RAS mutation) – adavosertib (AstraZeneca Ltd, Cambridge, UK) versus active monitoring; and FOCUS4-D (BRAF-PIK3CA-RAS wild type) – AZD8931 versus placebo. A non-stratified subtrial was also carried out: FOCUS4-N – capecitabine versus active monitoring. Main outcome measures The main outcome measure was progression-free survival from the time of randomisation to progression, comparing the intervention with active monitoring/placebo. Toxicity and overall survival data were collected in all randomised patients, and quality of life (using EuroQol-5 Dimensions) data were collected in FOCUS4-N only. Results Between January 2014 and October 2020, 1434 patients were registered from 88 hospitals in the UK. Successful biomarker testing was completed in 1291 out of 1382 samples (93%), and 908 out of 1315 patients (69%) completing 16 weeks of first-line therapy were eligible for randomisation, with 361 randomly allocated to a subtrial. FOCUS4-B evaluated aspirin versus placebo in the PIK3CA-mutant/ PTEN -loss subgroup, but recruited only six patients, so was closed for futility. FOCUS4-C evaluated adavosertib versus active monitoring in 67 patients in the RAS + TP53 double-mutant subgroup and met its primary end point, showing an improvement in progression-free survival (median 3.61 vs. 1.87 months; hazard ratio 0.35, 95% confidence interval 0.18 to 0.68; p = 0022). FOCUS4-D evaluated AZD8931 in 32 patients in the BRAF-PIK3CA-RAS wild-type subgroup and showed no benefit, so was discontinued after the first interim analysis. FOCUS4-N evaluated capecitabine monotherapy versus active monitoring in 254 patients and met its primary end point, showing improvement in progression-free survival (hazard ratio 0.40, 95% confidence interval 0.21 to 0.75; p &lt; 0.0001). Limitations FOCUS4-C and FOCUS4-N were closed early owing to COVID-19, so did not accrue their planned recruitment numbers. Conclusions Adaptive stratified medicine studies are feasible in common cancers but present challenges. Capecitabine monotherapy is an effective maintenance therapy. Wee1 inhibition using adavosertib shows significant clinical activity, notably in left-sided colorectal cancer. Trial registration This trial was registered as ISRCTN90061546. Funding This project was jointly funded by the Efficacy and Mechanism Evaluation (EME) programme, a MRC and National Institute for Health and Care Research (NIHR) partnership, and Cancer Research UK. This will be published in full in Efficacy and Mechanism Evaluation; Vol. 9, No. 9. See the NIHR Journals Library website for further project information

Ultrasensitive detection of a responsive fluorescent thymidine analogue in DNA via pulse-shaped two-photon excitation

Fluorescent base analogues (FBAs) are versatile nucleic acid labels that can replace a native nucleobase, while maintaining base pairing and secondary structure. Following the recent demonstration that free FBAs can be detected at the single-molecule level, the next goal is to achieve this level of detection sensitivity in oligonucleotides. Due to the short-wavelength absorption of most FBAs, multiphoton microscopy has emerged as a promising approach to single-molecule detection. We report the multiphoton-induced fluorescence of 5-(5-(4-methoxyphenyl)thiophen-2-yl)-6-aza-uridine (MeOthaU), a polarity-sensitive fluorescent thymidine analogue, as a nucleoside, and in two single-stranded deoxyribo-oligonucleotides, with and without their complement strands. Ensemble steady-state and time-resolved measurements in dioxane, following one-photon and two-photon excitation, reveals both strongly and weakly emissive species, assigned as rotamers, while in Tris buffer there are additional non-emissive states, which are attributed to tautomeric forms populated in aqueous environments. The two-photon (2P) brightness for MeOthaU is highest as the free nucleoside in dioxane (10 GM) and lowest as the free nucleoside in Tris buffer (0.05 GM). The species-averaged 2P brightness values in DNA are higher for the single strands (0.66 and 0.82 GM for sequence context AXA and AXT, respectively, where X is MeOthaU) than in the duplex (0.31 and 0.25 GM for AXA and AXT, respectively). Using 2P microscopy with pulse-shaped broadband excitation, we were able to detect single- and double-stranded oligos with a molecular brightness of 0.8-0.9 kHz per molecule. This allowed the detection of as few as 7 DNA molecules in the focus, making it the brightest responsive FBA in an oligonucleotide reported to date

CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery

Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development

Complete genome sequence of Candidatus Ruthia magnifica

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis