Comment on 'statistical consideration and challenges in bridging study of personalized medicine': a modified variance for sensitivity analysis.

A pivotal clinical trial is often necessary to assess drug efficacy in the intended to use (IU) population. Ideally, patients should be enrolled based on a positive test result from a well-characterized companion diagnostic (CDx). However, the central challenge is that patients are instead recruited on the basis of a clinical trial assay (CTA) result. This challenge arises because, CTA is available at all local labs; the time delay to enable enrollment based on CDx could result in a significant proportion of patients being unable to participate, adversely affecting precision and/or bias. The difficulty is therefore that patients are recruited on the basis that their CTA result is positive (CTA+) but the goal is to assess the drug efficacy in patients positive by the companion diagnostic (CDx+). In this commentary, we will examine an apparent weakness of a variance formula that is proposed in the context of a sensitivity analysis. We will develop an alternative formula, and argue that this should be used instead.

Cost-effectiveness analysis of telephone-based cognitive behaviour therapy compared to treatment as usual CBT for cancer patients: Evidence from a small, randomised controlled trial.

OBJECTIVE: A previous equivalence randomised trial indicated that Telephone-based Cognitive Behaviour Therapy (T-CBT) was not inferior to Treatment as Usual CBT (TAU-CBT) delivered face to face in terms of psychological benefit with both groups showing post-therapy improvements compared to pre-therapy baseline. The aim here is to clarify costs and benefits through an economic evaluation of the two therapy models. METHOD: The cost-effectiveness analysis (cost per quality-adjusted life year [QALY]) was derived from a single-centre (UK-based), two-arm randomised control trial. Data from 78 patients were available for the main analysis, which includes both an NHS cost perspective and a societal perspective which includes the cost of time off work and any additional private care. Sensitivity analyses were undertaken, which included patients only completing the four core therapy sessions (46 patients) and considering only patients taking both core and the additional therapy sessions which were optional (32 patients). RESULTS: The base-case analysis, adopting an NHS perspective, showed that T-CBT was associated with an incremental cost of £50 (95% CI: -£759 to £989) and a 0.03 QALY (95% CI: -0.09 to 0.03) decrement per patient when compared to TAU-CBT. The analysis adopting a societal perspective yielded similar results, with T-CBT providing an incremental cost of £171 (95% CI: -£769 to £1112) and a 0.03 QALY (95% CI: -0.08 to 0.03) decrement per patient in comparison to TAU-CBT. The first sensitivity analysis, considering patients only taking the core therapy sessions, showed that T-CBT provided an incremental cost of £100 (95% CI: -£945 to £1247) and yielded a decrement of 0.01 QALY (95% CI: -0.03 to 0.01) per patient compared to TAU-CBT. The second sensitivity analysis, which focused solely on patients who also underwent optional sessions, showed that T-CBT was associated with an incremental cost of £17 (95% CI: -£1307 to £1454) and a 0.04 QALY (95% CI: -0.11 to 0.03) decrement per patient when compared to TAU-CBT. CONCLUSIONS: Based on this single trial, T-CBT is not cost-effective as a therapy option for cancer patients with high psychological needs when compared to TAU-CBT.

A Rapamycin-Activated Caspase 9-Based Suicide Gene.

Engineered T cell therapies show considerable promise in the treatment of refractory malignancies. Given the ability of engineered T cells to engraft and persist for prolonged periods along with unpredicted toxicities, incorporation of a suicide gene to allow selective depletion after administration is desirable. Rapamycin is a safe and widely available immunosuppressive pharmaceutical that acts by heterodimerization of FKBP12 with the FRB fragment of mTOR. The apical caspase caspase 9 is activated by homodimerization through its CARD domain. We developed a rapamycin-induced caspase 9 suicide gene. First, we showed that caspase 9 could be activated by a two-protein format with replacement of the CARD domain with both FRB and FKBP12. We next identified an optimal compact single-protein rapamycin caspase 9 (rapaCasp9) by fusing both FRB and FKBP12 with the catalytic domain of caspase 9. Functionality of rapaCasp9 when co-expressed with a CD19 CAR was demonstrated in vitro and in vivo.

Root length densities of UK wheat and oilseed rape crops with implications for water capture and yield.

Root length density (RLD) was measured to 1 m depth for 17 commercial crops of winter wheat (Triticum aestivum) and 40 crops of winter oilseed rape [Brassica napus; oilseed rape (OSR)] grown in the UK between 2004 and 2013. Taking the critical RLD (cRLD) for water capture as 1cm cm(-3), RLDs appeared inadequate for full water capture on average below a depth of 0.32 m for winter wheat and below 0.45 m for OSR. These depths compare unfavourably (for wheat) with average depths of 'full capture' of 0.86 m and 0.48 m, respectively, determined for three wheat crops and one OSR crop studied in the 1970s and 1980s, and treated as references here. A simple model of water uptake and yield indicated that these shortfalls in wheat and OSR rooting compared with the reference data might be associated with shortfalls of up to 3.5 t ha(-1) and 1.2 t ha(-1), respectively, in grain yields under water-limited conditions, as increasingly occur through climate change. Coupled with decreased summer rainfall, poor rooting of modern arable crops could explain much of the yield stagnation that has been observed on UK farms since the 1990s. Methods of monitoring and improving rooting under commercial conditions are reviewed and discussed.

Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing.

Probiotic yeasts are emerging as preventative and therapeutic solutions for disease. Often ingested via cultured foods and beverages, they can survive the harsh conditions of the gastrointestinal tract and adhere to it, where they provide nutrients and inhibit pathogens like Candida albicans. Yet, little is known of the genomic determinants of these beneficial traits. To this end, we have sequenced 2 food-derived probiotic yeast isolates that mitigate fungal infections. We find that the first strain, KTP, is a strain of Saccharomyces cerevisiae within a small clade that lacks any apparent ancestry from common European/wine S. cerevisiae strains. Significantly, we show that S. cerevisiae KTP genes involved in general stress, pH tolerance, and adherence are markedly different from S. cerevisiae S288C but are similar to the commercial probiotic yeast species S. boulardii. This suggests that even though S. cerevisiae KTP and S. boulardii are from different clades, they may achieve probiotic effect through similar genetic mechanisms. We find that the second strain, ApC, is a strain of Issatchenkia occidentalis, one of the few of this family of yeasts to be sequenced. Because of the dissimilarity of its genome structure and gene organization, we infer that I. occidentalis ApC likely achieves a probiotic effect through a different mechanism than the Saccharomyces strains. Therefore, this work establishes a strong genetic link among probiotic Saccharomycetes, advances the genomics of Issatchenkia yeasts, and indicates that probiotic activity is not monophyletic and complimentary mixtures of probiotics could enhance health benefits beyond a single species.

Exploration of T cell immune responses by expression of a dominant-negative SHP1 and SHP2.

SHP1 and SHP2 are SH2 domain-containing proteins which have inhibitory phosphatase activity when recruited to phosphorylated ITIMs and ITSMs on inhibitory immune receptors. Consequently, SHP1 and SHP2 are key proteins in the transmission of inhibitory signals within T cells, constituting an important point of convergence for diverse inhibitory receptors. Therefore, SHP1 and SHP2 inhibition may represent a strategy for preventing immunosuppression of T cells mediated by cancers hence improving immunotherapies directed against these malignancies. Both SHP1 and SHP2 contain dual SH2 domains responsible for localization to the endodomain of inhibitory receptors and a protein tyrosine phosphatase domain which dephosphorylates and thus inhibits key mediators of T cell activation. We explored the interaction of the isolated SH2 domains of SHP1 and SHP2 to inhibitory motifs from PD1 and identified strong binding of both SH2 domains from SHP2 and more moderate binding in the case of SHP1. We next explored whether a truncated form of SHP1/2 comprising only of SH2 domains (dSHP1/2) could act in a dominant negative fashion by preventing docking of the wild type proteins. When co-expressed with CARs we found that dSHP2 but not dSHP1 could alleviate immunosuppression mediated by PD1. We next explored the capacity of dSHP2 to bind with other inhibitory receptors and observed several potential interactions. In vivo we observed that the expression of PDL1 on tumor cells impaired the ability of CAR T cells to mediate tumor rejection and this effect was partially reversed by the co-expression of dSHP2 albeit at the cost of reduced CAR T cell proliferation. Modulation of SHP1 and SHP2 activity in engineered T cells through the expression of these truncated variants may enhance T cell activity and hence efficacy in the context of cancer immunotherapy.

Synthesis and biological evaluation of a potent salicylihalamide A lactam analogue.

The first synthesis of a lactam analogue of salicylihalamide A (1) is reported. A key step in the approach was a photochemical acylation coupling between amine 10 and dioxinone 9 to form the amide 19. Acetylation followed by RCM with Grubbs 1st generation catalyst gave the desired E-lactam 23 (E : Z ratio 87 : 13) as the major compound. Conversion of macrolactam 23 into the vinyl iodide 26 followed by Cu catalysed cross coupling with the diene amide 7 gave aza-salicylihalamide analogue 3 in good yield. This compound demonstrated potent activity against several human leukaemia cell lines.

Documentation in the Patient's Medical Record by Clinical Pharmacists in a Canadian University Teaching Hospital.

BACKGROUND: In many studies on documentation, the data are self-reported, which makes it difficult to know the actual level of documentation by pharmacists in patients' medical records. The literature assessing documentation by clinical pharmacists in health care centres is limited. OBJECTIVE: To assess the level of documentation in patients' medical records by clinical pharmacists at one large urban hospital. METHODS: This retrospective observational study included all patients who were followed by a clinical pharmacist during their stay in the Centre hospitalier de l'Université de Montreal between July 1 and October 31, 2016. The primary outcome, the level of documentation in patients' medical records, was categorized as minimal, sufficient, or extensive. The quality of notes and the impact of pharmacy students and residents on documentation were evaluated as secondary outcomes. RESULTS: A total of 779 patient charts from 4 inpatient units were included in the analysis. Of these, 563 (72.3%) were considered to have minimal documentation (at least 1 intervention described in writing), 432 (55.5%) had sufficient documentation (at least 1 note written during the patient's hospitalization), and 81 (10.4%) had extensive documentation (appropriate number of notes in relation to duration of hospitalization). Medication reconciliation performed by pharmacists at the time of admission was documented in 696 (89.3%) of patients' records. The presence of students or residents on a clinical unit was associated with a significant increase in the percentage of charts with at least 1 follow-up note (23.6% [120/508] with students/residents versus 12.5% [34/271] without students/residents; p < 0.001) and the mean number of followup notes (0.59 versus 0.23, respectively; p < 0.001) but had no effect on other variables. Of a total of 777 notes written by a pharmacist, the overall conformity with pre-established criteria was 56.8% (441/777), and conformity was 43.4% (139/320), 75.1% (272/362), and 31.6% (30/95) for admission, follow-up, and discharge notes, respectively. CONCLUSIONS: Documentation by clinical pharmacists in patients' medical records could be improved to achieve the stated goal of the American Society of Health-System Pharmacists and the Canadian Society of Hospital Pharmacists, that all significant clinical recommendations or interventions should be documented.

CONTEXTE: Les données de bon nombre d'études portant sur la tenue des dossiers médicaux sont autodéclarées, ce qui fait qu'il est difficile de savoir exactement dans quelle mesure les pharmaciens consignent les informations dans les dossiers médicaux des patients. Il n'existe que peu d'études évaluant la tenue des dossiers par les pharmaciens cliniques dans les centres de soins de santé. OBJECTIF: Évaluer dans quelle mesure les pharmaciens cliniciens d'un important hôpital urbain consignent l'information dans les dossiers médicaux des patients. MÉTHODES: La présente étude d'observation rétrospective englobait tous les patients ayant été suivis par un pharmacien clinicien pendant leur séjour au Centre hospitalier de l'Université de Montréal entre le 1er juillet et le 31 octobre 2016. Le principal paramètre d'évaluation, soit le degré de rigueur des inscriptions dans les dossiers médicaux des patients, entrait dans l'une des trois catégories suivantes : minimal, suffisant ou exhaustif. La qualité des notes et l'effet de la participation d'étudiants et de résidents en pharmacie à la tenue des dossiers ont servi de paramètres d'évaluation secondaires. RÉSULTATS: L'analyse a porté sur 779 dossiers médicaux de patients provenant de quatre services hospitaliers. Les investigateurs ont considéré que 563 d'entre eux (72,3 %) appartenaient à la catégorie « minimal ¼ (au moins une intervention consignée par écrit), 432 (55,5 %) se situaient dans la catégorie « suffisant ¼ (au moins une note rédigée au cours de l'hospitalisation du patient) et 81 (10,4 %) se rangeaient dans la catégorie « exhaustif ¼ (nombre adéquat de notes en fonction à la durée de l'hospitalisation). Les bilans comparatifs des médicaments établis par des pharmaciens au moment de l'admission ont été consignés dans 696 (89,3 %) dossiers médicaux de patients. On a associé la présence d'étudiants ou de résidents dans une unité clinique à une hausse significative du pourcentage de dossiers médicaux affichant au moins une note de suivi (23,6 % [120/508] avec des étudiants / résidents contre 12,5 % [34/271] sans étudiants / résidents; p < 0,001) et du nombre moyen de notes de suivi (respectivement 0,59 contre 0,23; p < 0,001), mais leur présence n'a été associée à aucun autre effet sur les autres variables. Le taux de conformité globale aux critères préétablis des 777 notes rédigées par un pharmacien était de 56,8 % (441/777) et le taux de conformité des notes d'admission, de suivi et de congé était respectivement de 43,4 % (139/320), 75,1 % (272/362) et 31,6 % (30/95). CONCLUSIONS: La tenue des dossiers médicaux de patients par les pharmaciens cliniciens devrait s'améliorer pour qu'elle atteigne l'objectif établi par l'American Society of Health-System Pharmacists et la Société canadienne des pharmaciens d'hôpitaux, qui veut que toutes les recommandations et interventions cliniques d'importance soient consignées.

Over-expression of LeNCED1 in tomato (Solanum lycopersicum L.) with the rbcS3C promoter allows recovery of lines that accumulate very high levels of abscisic acid and exhibit severe phenotypes.

Previous work where 9-cis-epoxycarotenoid dioxygenase (NCED) was over-expressed using the constitutive Gelvin Superpromoter resulted in mild increases in abscisic acid (ABA) accumulation, accompanied by stomatal closure and increased water-use efficiency (WUE), but with apparently little impact on long-term biomass production. However, one of the negative effects of the over-expression of NCED using constitutive promoters in tomato was increased seed dormancy. Here we report the use of the rbcS3C promoter, from a gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), to drive LeNCED1 transgene expression in tomato in a light-responsive and circadian manner. In comparison to the constitutive promoter, the rbcS3C promoter allowed the generation of transgenic plants with much higher levels of ABA accumulation in leaves and sap, but the effect on seed dormancy was diminished. These plants displayed the expected reductions in stomatal conductance and CO(2) assimilation, but they also exhibited a severe set of symptoms that included perturbed cotyledon release from the testa, increased photobleaching in young seedlings, substantially reduced chlorophyll and carotenoid content, interveinal leaf flooding, and greatly reduced growth. These symptoms illustrate adverse consequences of long-term, very high ABA accumulation. Only more moderate increases in ABA biosynthesis are likely to be useful in the context of agriculture. Implications are discussed for the design of transgenic 'high ABA' plants that exhibit increased WUE but have minimal negative phenotypic effects.

Massive splenomegaly in rural Malawi: new wine, old wineskins and the importance of collaboration.

During a voluntary placement in rural Malawi, we assessed a 21-year-old man who presented with dyspnoea and lethargy secondary to a chronic refractory anaemia associated with massive splenomegaly. He was initially treated at the rural hospital for a presumptive diagnosis of hyper-reactive malarial syndrome (HMS) with long-term malarial prophylaxis. There was inadequate provision of blood products and the availability of suitable donors was limited by the high local prevalence of blood-borne viruses. He was transferred to the district hospital for further investigations after transfusion of three units of blood. Unfortunately, he self-discharged without receiving appropriate investigations and medical treatment. Subsequently, his family sought help from the local traditional healer who performed scarification to attempt to treat him. Further efforts to emphasise the importance of hospital-based care proved unsuccessful, and sadly this man died at his family home 3 months after his initial presentation.