A Logic Your Typechecker Can Count On: Unordered Tree Types in Practice

Type systems featuring counting constraints are often stud- ied, but seldom implemented. We describe an efficient im- plementation of a type system for unordered, edge-labeled trees based on Presburger arithmetic constraints. We begin with a type system for unordered trees and give a compilation into counting automata. We then describe an optimized implementation that provides the fundamental operations of membership and emptiness testing. Although each operation has worst-case exponential complexity, we show how to achieve reasonable performance in practice using a combination of techniques, including syntactic translations, lazy automata unfolding, hash-consing, memoization, and incremental tree processing implemented using partial evaluation. These techniques avoid constructing and examining large structures in many cases and amortize the costs of expensive operations across many computations. To demonstrate the effectiveness of these optimizations, we present experimental data from executions on realistically sized examples drawn from the Harmony data synchronizer

D-Serine Is a Substrate for Neutral Amino Acid Transporters ASCT1/SLC1A4 and ASCT2/SLC1A5, and Is Transported by Both Subtypes in Rat Hippocampal Astrocyte Cultures

N-methyl-D-aspartate (NMDA) receptors play critical roles in synaptic transmission and plasticity. Activation of NMDA receptors by synaptically released L-glutamate also requires occupancy of co-agonist binding sites in the tetrameric receptor by either glycine or D-serine. Although D-serine appears to be the predominant co-agonist at synaptic NMDA receptors, the transport mechanisms involved in D-serine homeostasis in brain are poorly understood. In this work we show that the SLC1 amino acid transporter family members SLC1A4 (ASCT1) and SLC1A5 (ASCT2) mediate homo- and hetero-exchange of D-serine with physiologically relevant kinetic parameters. In addition, the selectivity profile of D-serine uptake in cultured rat hippocampal astrocytes is consistent with uptake mediated by both ASCT1 and ASCT2. Together these data suggest that SLC1A4 (ASCT1) may represent an important route of Na-dependent D-serine flux in the brain that has the ability to regulate extracellular D-serine and thereby NMDA receptor activity

Health services changes: is a run-in period necessary before evaluation in randomised clinical trials?

Background Most randomised clinical trials (RCTs) testing a new health service do not allow a run-in period of consolidation before evaluating the new approach. Consequently, health professionals involved may feel insufficiently familiar or confident, or that new processes or systems that are integral to the service are insufficiently embedded in routine care prior to definitive evaluation in a RCT. This study aimed to determine the optimal run-in period for a new physiotherapy-led telephone assessment and treatment service known as PhysioDirect and whether a run-in was needed prior to evaluating outcomes in an RCT. Methods The PhysioDirect trial assessed whether PhysioDirect was as effective as usual care. Prior to the main trial, a run-in of up to 12 weeks was permitted to facilitate physiotherapists to become confident in delivering the new service. Outcomes collected from the run-in and main trial were length of telephone calls within the PhysioDirect service and patients’ physical function (SF-36v2 questionnaire) and Measure Yourself Medical Outcome Profile v2 collected at baseline and six months. Joinpoint regression determined how long it had taken call times to stabilise. Analysis of covariance determined whether patients’ physical function at six months changed from the run-in to the main trial. Results Mean PhysioDirect call times (minutes) were higher in the run-in (31 (SD: 12.6)) than in the main trial (25 (SD: 11.6)). Each physiotherapist needed to answer 42 (95% CI: 20,56) calls for their mean call time to stabilise at 25 minutes per call; this took a minimum of seven weeks. For patients’ physical function, PhysioDirect was equally clinically effective as usual care during both the run-in (0.17 (95% CI: -0.91,1.24)) and main trial (-0.01 (95% CI: -0.80,0.79)). Conclusions A run-in was not needed in a large trial testing PhysioDirect services in terms of patient outcomes. A learning curve was evident in the process measure of telephone call length. This decreased during the run-in and stabilised prior to commencement of the main trial. Future trials should build in a run-in if it is anticipated that learning would have an effect on patient outcome

Small molecule induced reactivation of mutant p53 in cancer cells

The p53 cancer mutant Y220C is an excellent paradigm for rescuing the function of conformationally unstable p53 mutants because it has a unique surface crevice that can be targeted by small-molecule stabilizers. Here, we have identified a compound, PK7088, which is active in vitro: PK7088 bound to the mutant with a dissociation constant of 140 μM and raised its melting temperature, and we have determined the binding mode of a close structural analogue by X-ray crystallography. We showed that PK7088 is biologically active in cancer cells carrying the Y220C mutant by a battery of tests. PK7088 increased the amount of folded mutant protein with wild-type conformation, as monitored by immunofluorescence, and restored its transcriptional functions. It induced p53-Y220C-dependent growth inhibition, cell-cycle arrest and apoptosis. Most notably, PK7088 increased the expression levels of p21 and the proapoptotic NOXA protein. PK7088 worked synergistically with Nutlin-3 on up-regulating p21 expression, whereas Nutlin-3 on its own had no effect, consistent with its mechanism of action. PK7088 also restored non-transcriptional apoptotic functions of p53 by triggering nuclear export of BAX to the mitochondria. We suggest a set of criteria for assigning activation of p53

Calcium Channel Blocker Use and Associated Glaucoma and Related Traits Among UK Biobank Participants

IMPORTANCE: Calcium channel blocker (CCB) use has been associated with an increased risk of glaucoma in exploratory studies. OBJECTIVE: To examine the association of systemic CCB use with glaucoma and related traits among UK Biobank participants. DESIGN, SETTING, AND PARTICIPANTS: This population-based cross-sectional study included UK Biobank participants with complete data (2006-2010) for analysis of glaucoma status, intraocular pressure (IOP), and optical coherence tomography (OCT)-derived inner retinal layer thicknesses. Data analysis was conducted in January 2023. EXPOSURE: Calcium channel blocker use was assessed in a baseline touchscreen questionnaire and confirmed during an interview led by a trained nurse. MAIN OUTCOMES AND MEASURES: The primary outcome measures included glaucoma status, corneal-compensated IOP, and 2 OCT-derived inner retinal thickness parameters (macular retinal nerve fiber layer [mRNFL] and macular ganglion cell-inner plexiform layer [mGCIPL] thicknesses). We performed logistic regression and linear regression analyses to test for associations with glaucoma status and IOP and OCT-derived inner retinal thickness parameters, respectively. RESULTS: This study included 427 480 adults. Their median age was 58 (IQR, 50-63) years, and more than half (54.1%) were women. There were 33 175 CCB users (7.8%). Participants who had complete data for glaucoma status (n = 427 480), IOP (n = 97 100), and OCT-derived inner retinal layer thicknesses (n = 41 023) were eligible for respective analyses. After adjustment for key sociodemographic, medical, anthropometric, and lifestyle factors, use of CCBs (but not other antihypertensive agents) was associated with greater odds of glaucoma (odds ratio [OR], 1.39 [95% CI, 1.14 to 1.69]; P = .001). Calcium channel blocker use was also associated with thinner mGCIPL (-0.34 μm [95% CI, -0.54 to -0.15 μm]; P = .001) and mRNFL (-0.16 μm [95% CI, -0.30 to -0.02 μm]; P = .03) thicknesses but not IOP (-0.01 mm Hg [95% CI, -0.09 to 0.07 mm Hg]; P = .84). CONCLUSIONS AND RELEVANCE: In this study, an adverse association between CCB use and glaucoma was observed, with CCB users having, on average, 39% higher odds of glaucoma. Calcium channel blocker use was also associated with thinner mGCIPL and mRNFL thicknesses, providing a structural basis that supports the association with glaucoma. The lack of association of CCB use with IOP suggests that an IOP-independent mechanism of glaucomatous neurodegeneration may be involved. Although a causal relationship has not been established, CCB replacement or withdrawal may be considered should glaucoma progress despite optimal care

Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer

Introduction Aromatase inhibitors (AIs) are a vital component of estrogen receptor positive (ER+) breast cancer treatment. De novo and acquired resistance, however, is common. The aims of this study were to relate patterns of copy number aberrations to molecular and proliferative response to AIs, to study differences in the patterns of copy number aberrations between breast cancer samples pre- and post-AI neoadjuvant therapy, and to identify putative biomarkers for resistance to neoadjuvant AI therapy using an integrative analysis approach. Methods Samples from 84 patients derived from two neoadjuvant AI therapy trials were subjected to copy number profiling by microarray-based comparative genomic hybridisation (aCGH, n = 84), gene expression profiling (n = 47), matched pre- and post-AI aCGH (n = 19 pairs) and Ki67-based AI-response analysis (n = 39). Results Integrative analysis of these datasets identified a set of nine genes that, when amplified, were associated with a poor response to AIs, and were significantly overexpressed when amplified, including CHKA, LRP5 and SAPS3. Functional validation in vitro, using cell lines with and without amplification of these genes (SUM44, MDA-MB134-VI, T47D and MCF7) and a model of acquired AI-resistance (MCF7-LTED) identified CHKA as a gene that when amplified modulates estrogen receptor (ER)-driven proliferation, ER/estrogen response element (ERE) transactivation, expression of ER-regulated genes and phosphorylation of V-AKT murine thymoma viral oncogene homolog 1 (AKT1). Conclusions These data provide a rationale for investigation of the role of CHKA in further models of de novo and acquired resistance to AIs, and provide proof of concept that integrative genomic analyses can identify biologically relevant modulators of AI response

Challenges of developing and conducting an international study of resilience in migrant adolescents

The sequelae of migration and the effects of local migration policies on children’s physical and mental health are critical to examine, particularly given the historically high numbers of migrants and displaced people. The vulnerability of the study sample and the need to work across cultures and contexts makes research on this group challenging. We outline lessons learned through conducting a pilot study of resilience resources and mental health among migrant youth in six countries. We describe the benefits and challenges, and then provide recommendations and practical advice for social work researchers attempting cross-cultural team research on migrants.A.E. was funded by the University of Bristol World Universities Network (WUN) funding. T.W. was funded by the University of Auckland’s WUN funding and the University of Auckland’s postgraduate funding. Meeting travel and pilot work was also supported by J.M.G.’s National Health & Medical Research Council (NHMRC) Career Development Fellowship and supportive grant (1062495). Meeting travel and pilot work was also supported by L.T.’s National Research Foundation Incentive Funding (IFR2011041100058). A.M.J. was funded by the University of York for WUN South Africa and Maastricht meetings and for time devoted to the project.http://isw.sagepub.comhj2018Educational Psycholog

Earliest Triassic microbialites in the South China Block and other areas; controls on their growth and distribution

Earliest Triassic microbialites (ETMs) and inorganic carbonate crystal fans formed after the end-Permian mass extinction (ca. 251.4 Ma) within the basal Triassic Hindeodus parvus conodont zone. ETMs are distinguished from rarer, and more regional, subsequent Triassic microbialites. Large differences in ETMs between northern and southern areas of the South China block suggest geographic provinces, and ETMs are most abundant throughout the equatorial Tethys Ocean with further geographic variation. ETMs occur in shallow-marine shelves in a superanoxic stratified ocean and form the only widespread Phanerozoic microbialites with structures similar to those of the Cambro-Ordovician, and briefly after the latest Ordovician, Late Silurian and Late Devonian extinctions. ETMs disappeared long before the mid-Triassic biotic recovery, but it is not clear why, if they are interpreted as disaster taxa. In general, ETM occurrence suggests that microbially mediated calcification occurred where upwelled carbonate-rich anoxic waters mixed with warm aerated surface waters, forming regional dysoxia, so that extreme carbonate supersaturation and dysoxic conditions were both required for their growth. Long-term oceanic and atmospheric changes may have contributed to a trigger for ETM formation. In equatorial western Pangea, the earliest microbialites are late Early Triassic, but it is possible that ETMs could exist in western Pangea, if well-preserved earliest Triassic facies are discovered in future work

Increasing follow-up questionnaire response rates in a randomized controlled trial of telehealth for depression: three embedded controlled studies

Background: Attrition is problematic in trials, and may be exacerbated in longer studies, telehealth trials and participants with depression – three features of The Healthlines Study. Advance notification, including a photograph and using action-oriented email subject lines might increase response rates, but require further investigation. We examined the effectiveness of these interventions in three embedded Healthlines studies. Methods: Based in different trial sites, participants with depression were alternately allocated to be pre-called or not ahead of the 8-month follow-up questionnaire (Study 1), randomized to receive a research team photograph or not with their 12-month questionnaire (Study 2), and randomized to receive an action-oriented (‘ACTION REQUIRED’) or standard (‘Questionnaire reminder’) 12-month email reminder (Study 3). Participants could complete online or postal questionnaires, and received up to five questionnaire reminders. The primary outcome was completion of the Patient Health Questionnaire (PHQ-9). Secondary outcome measures were the number of reminders and time to questionnaire completion. Results: Of a total of 609 Healthlines depression participants, 190, 251 and 231 participants were included in Studies 1–3 (intervention: 95, 126 and 115), respectively. Outcome completion was ≥90 % across studies, with no differences between trial arms (Study 1: OR 0.38, 95 % CI 0.07–2.10; Study 2: OR 0.84, 95 % CI 0.26–2.66; Study 3: OR 0.53 95 % CI 0.19–1.49). Pre-called participants were less likely to require a reminder (48.4 % vs 62.1 %, OR 0.41, 95 % CI 0.21–0.78), required fewer reminders (adjusted difference in means −0.67, 95 % CI −1.13 to −0.20), and completed follow-up quicker (median 8 vs 15 days, HR 1.35, 95 % CI 1.00–1.82) than control subjects. There were no significant between-group differences in Studies 2 or 3. Conclusions: Eventual response rates in this trial were high, with no further improvement from these interventions. While the photograph and email interventions were ineffective, pre-calling participants reduced time to completion. This strategy might be helpful when the timing of study completion is important. Researchers perceived a substantial benefit from the reduction in reminders with pre-calling, despite no overall decrease in net effort after accounting for pre-notification