A normative microbiome is not restored following kidney transplantation.

Dialysis and kidney transplantation (Ktx) mitigate some of the physiological deficits in chronic kidney disease (CKD), but it remains to be determined if these mitigate microbial dysbiosis and the production of inflammatory microbial metabolites, which contribute significantly to the uraemic phenotype. We have investigated bacterial DNA signatures present in the circulation of CKD patients and those receiving a KTx. Our data are consistent with increasing dysbiosis as CKD progresses, with an accompanying increase in trimethylamine (TMA) producing pathobionts Pseudomonas and Bacillus. Notably, KTx patients displayed a significantly different microbiota compared with CKD5 patients, which surprisingly included further increase in TMA producing Bacillus and loss of salutogenic Lactobacilli. Only two genera (Viellonella and Saccharimonidales) showed significant differences in abundance following KTx that may reflect a reciprocal relationship between TMA producers and utilisers, which supersedes restoration of a normative microbiome. Our metadata analysis confirmed that TMA N-oxide (TMAO) along with one carbon metabolism had significant impact upon both inflammatory burden and the composition of the microbiome. This indicates that these metabolites are key to shaping the uraemic microbiome and might be exploited in the development of dietary intervention strategies to both mitigate the physiological deficits in CKD and enable the restoration of a more salutogenic microbiome.

Maintenance Olaparib for Germline BRCA-Mutated Metastatic Pancreatic Cancer.

BACKGROUND: Patients with a germline BRCA1 or BRCA2 mutation make up a small subgroup of those with metastatic pancreatic cancer. The poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitor olaparib has had antitumor activity in this population. METHODS: We conducted a randomized, double-blind, placebo-controlled, phase 3 trial to evaluate the efficacy of olaparib as maintenance therapy in patients who had a germline BRCA1 or BRCA2 mutation and metastatic pancreatic cancer and disease that had not progressed during first-line platinum-based chemotherapy. Patients were randomly assigned, in a 3:2 ratio, to receive maintenance olaparib tablets (300 mg twice daily) or placebo. The primary end point was progression-free survival, which was assessed by blinded independent central review. RESULTS: Of the 3315 patients who underwent screening, 154 underwent randomization and were assigned to a trial intervention (92 to receive olaparib and 62 to receive placebo). The median progression-free survival was significantly longer in the olaparib group than in the placebo group (7.4 months vs. 3.8 months; hazard ratio for disease progression or death, 0.53; 95% confidence interval [CI], 0.35 to 0.82; P = 0.004). An interim analysis of overall survival, at a data maturity of 46%, showed no difference between the olaparib and placebo groups (median, 18.9 months vs. 18.1 months; hazard ratio for death, 0.91; 95% CI, 0.56 to 1.46; P = 0.68). There was no significant between-group difference in health-related quality of life, as indicated by the overall change from baseline in the global quality-of-life score (on a 100-point scale, with higher scores indicating better quality of life) based on the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (between-group difference, -2.47 points; 95% CI, -7.27 to 2.33). The incidence of grade 3 or higher adverse events was 40% in the olaparib group and 23% in the placebo group (between-group difference, 16 percentage points; 95% CI, -0.02 to 31); 5% and 2% of the patients, respectively, discontinued the trial intervention because of an adverse event. CONCLUSIONS: Among patients with a germline BRCA mutation and metastatic pancreatic cancer, progression-free survival was longer with maintenance olaparib than with placebo. (Funded by AstraZeneca and others; POLO ClinicalTrials.gov number, NCT02184195.).

Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts.

BACKGROUND: Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed using R. Though commercial visualisation and interpretation pipelines are comprehensive, freely available pipelines are currently more limited. RESULTS: Here we demonstrate Searchlight, a freely available bulk RNA-seq visualisation and interpretation pipeline. Searchlight provides: a comprehensive statistical and visual analysis, focusing on the global, pathway and single gene levels; compatibility with most differential experimental designs irrespective of organism or experimental complexity, via three workflows; reports; and support for downstream user modification of plots via user-friendly R-scripts and a Shiny app. We show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). We demonstrate in a timed re-analysis study, that alongside a standard bulk RNA-seq processing pipeline, Searchlight can be used to complete bulk RNA-seq projects up to the point of manuscript quality figures, in under 3 h. CONCLUSIONS: Compared to a manual R based analysis or current best freely available pipelines (VIPER and BioJupies), Searchlight can reduce the time and effort needed to complete bulk RNA-seq projects to manuscript level. Searchlight is suitable for bioinformaticians, service providers and bench scientists. https://github.com/Searchlight2/Searchlight2 .

Bovine milk microbiome: a more complex issue than expected.

The aim of this study was to analyze bacterial profiles of bovine mastitic milk samples and samples from healthy quarters using Next Generation Sequencing of amplicons from 16S rRNA genes and to compare results with microbiological results by PCR assays of the same samples. A total of 49 samples were collected from one single dairy herd during the same day. The samples were divided in two sample sets, which were used in this study. The DNA extraction as well as the library preparation and sequencing of these two sets were performed separately, and results of the two datasets were then compared. The vast majority of genera detected appeared with low read numbers and/or in only a few samples. Results of PCR and microbiome analyses of samples infected with major pathogens Staphylococcus aureus or Streptococcus uberis were consistent as these genera also covered the majority of reads detected in the microbiome analysis. Analysis of alpha diversity revealed a much higher species richness in set 1 than in set 2. The dominating bacterial genera with the highest read numbers clearly differed between datasets, especially in PCR negative samples and samples positive for minor pathogens. In addition to this, linear discriminant analysis (LDA) was conducted between the two sets to identify significantly different genera/family level microbes. The genus Methylobacterium was much more common in set 2 compared to set 1, and genus Streptococcus more common in set 1. Our results indicate amplification of contaminating bacteria in excess in samples with no or minor amounts of pathogen DNA in dataset 2. There is a need for critical assessment of results of milk microbiome analyses.

A DFT Mechanistic Study on Ethylene Tri- and Tetramerization with Cr/PNP Catalysts: Single versus Double Insertion Pathways.

The mechanism of ethylene trimerization and tetramerization with a chromium-diphosphinoamine (Cr-PNP) catalyst system has been studied by theoretical (DFT) methods. Two representative ligands have been explored, namely Ph2 PN(Me)PPh2 and (o-MeC6 H4 )2 PN(Me)P(o-MeC6 H4 )2 . Calculations on the former ligand reveal how a combination of single and double ethylene insertion mechanisms may lead to 1-hexene, 1-octene and the major side products (cyclopentanes and n-alkanes). For the latter ligand, introduction of o-alkyl substitution leads to a more sterically congested active species, which suppresses the available pathways for tetramerization and side product formation. Hence, the high selectivity of o-aryl substituted PNP ligands for trimerization can be rationalized.

Measuring the impact of dietary supplementation with citrus or cucumber extract on chicken gut microbiota using 16s rRNA gene sequencing.

This study investigated the effects of dietary supplements, citrus (CTS) and cucumber (CMB), on the jejunum and cecum microbiota of 14- and 28-days old broiler chickens to evaluate their impact on the gut health and assess their role as alternatives to antibiotic growth promoters (ABGPs). 16SrRNA gene sequencing revealed the overall bacterial microbiota composition was significantly affected by the gut site (p?

A study comparing the healthy and diseased equine glandular gastric microbiota sampled with sheathed transendoscopic cytology brushes.

The role of the equine gastrointestinal microbiota in the pathogenesis of equine glandular gastric disease (EGGD) is poorly understood. To investigate whether the glandular gastric microbiota is altered in horses with EGGD. Prospective longitudinal study. Five Thoroughbred racehorses from one training center underwent gastroscopy as part of poor performance investigation. Samples were taken from EGGD lesions and adjacent normal mucosa using sheathed transendoscopic cytology brushes and frozen at -80°C. DNA was extracted for 16S rRNA sequencing, and sequences compared against a database to generate taxonomic classification of the microbiota. The same horses were sampled 6 months later. Normal glandular mucosal samples were characterized by a higher proportion of Proteobacteria (46.3%) than EGGD lesions (18.9%). Relative abundance of Firmicutes was lower in samples from normal mucosa (20.0%) than EGGD lesions (41.2%). Linear discriminant analysis effect size (LEfSe) confirmed a greater proportion of Firmicutes species was characteristic of samples collected from EGGD lesions due to a very high relative abundance of Sarcina (up to 92.4%) in two horses with EGGD. We were unable to comment on the stability of the glandular gastric microbiota over time. Small sample population. None of the horses examined had grossly normal gastric mucosa. The gastric microbiota appears altered in EGGD, although we are unable to demonstrate a causative effect. Sarcina was particularly increased in abundance in EGGD and may be a useful biomarker of disease. Sheathed cytology brushes were an effective method for sampling the gastric mucosa.

Overall Survival Results From the POLO Trial: A Phase III Study of Active Maintenance Olaparib Versus Placebo for Germline BRCA-Mutated Metastatic Pancreatic Cancer.

PURPOSE: The phase III POLO study demonstrated significant progression-free survival (PFS) benefit for active olaparib maintenance therapy versus placebo for patients with metastatic pancreatic adenocarcinoma and a germline BRCA mutation. Here, we report the final analysis of overall survival (OS) and other secondary end points. PATIENTS AND METHODS: Patients with a deleterious or suspected deleterious germline BRCA mutation whose disease had not progressed after ≥ 16 weeks of first-line platinum-based chemotherapy were randomly assigned 3:2 to active maintenance olaparib (300 mg twice daily) or placebo. The primary end point was PFS; secondary end points included OS, time to second disease progression or death, time to first and second subsequent cancer therapies or death, time to discontinuation of study treatment or death, and safety and tolerability. RESULTS: In total, 154 patients were randomly assigned (olaparib, n = 92; placebo, n = 62). No statistically significant OS benefit was observed (median 19.0 v 19.2 months; hazard ratio [HR], 0.83; 95% CI, 0.56 to 1.22; P = .3487). Kaplan-Meier OS curves separated at approximately 24 months, and the estimated 3-year survival after random assignment was 33.9% versus 17.8%, respectively. Median time to first subsequent cancer therapy or death (HR, 0.44; 95% CI, 0.30 to 0.66; P < .0001), time to second subsequent cancer therapy or death (HR, 0.61; 95% CI, 0.42 to 0.89; P = .0111), and time to discontinuation of study treatment or death (HR, 0.43; 95% CI, 0.29 to 0.63; P < .0001) significantly favored olaparib. The HR for second disease progression or death favored olaparib without reaching statistical significance (HR, 0.66; 95% CI, 0.43 to 1.02; P = .0613). Olaparib was well tolerated with no new safety signals. CONCLUSION: Although no statistically significant OS benefit was observed, the HR numerically favored olaparib, which also conferred clinically meaningful benefits including increased time off chemotherapy and long-term survival in a subset of patients.

New ways of working: COVID-19 as a catalyst for change in acute mental health services.

Background: A need arose to divert patients with psychiatric complaints from the emergency department to alternative settings for psychiatric consultations to reduce footfall during COVID-19. We assessed the effectiveness of alternative referral pathway in reducing COVID-19 infection in our service and its effect on service quality: response time and number of patients leaving before the review. We evaluated the satisfaction of patients, general practitioners (GPs) and mental health service staff with the pathway. Methods: All patients referred to the mental health service over a 2-month period following the introduction of the pathway were included. Findings were compared against the cohort referred for emergency assessment during the same period in 2019. Feedback surveys were distributed to patients, staff and GPs. χ2 and independent sample t-test were used to compare the variables. Results: Over 2 months, 255 patients received an emergency assessment via the pathway, representing a 22.3% decrease in the volume of presentations from the same period in 2019. There were no COVID-19 cases among our patients or staff on the roster for assessing patients. In comparison to 2019, response times were improved (p<0.001), and the numbers of patients who left the hospital before the review were reduced by 3.2% during the study period (p<0.001). Patients and GPs were highly satisfied with the referral pathway and believed that the pathway should be retained post-COVID-19. Mental health service staff were divided in their opinions about its sustainability. Conclusion: The pathway was successful in reducing the spread of infection, improving response times and reducing the numbers of patients who left without an assessment. Given the improved outcomes and acceptability, this is a preferable pathway for emergency referrals into the future.

Socioeconomic position links circulatory microbiota differences with biological age.

Imbalanced nutrition is associated with accelerated ageing, possibly mediated by microbiota. An analysis of the circulatory microbiota obtained from the leukocytes of participants in the MRC Twenty-07 general population cohort was performed. We now report that in this cohort, the most biologically aged exhibit a significantly higher abundance of circulatory pathogenic bacteria, including Neisseria, Rothia and Porphyromonas, while those less biologically aged possess more circulatory salutogenic (defined as being supportive of human health and wellbeing) bacteria, including Lactobacillus, Lachnospiraceae UCG-004 and Kocuria. The presence of these salutogenic bactreria is consistent with a capacity to metabolise and produce Nrf2 agonists. We also demonstrate that associated one carbon metabolism, notably betaine levels, did not vary with chronological age, but displayed a difference with socioeconomic position (SEP). Those at lower SEP possessed significantly lower betaine levels indicative of a poorer diet and poorer health span and consistent with reduced global DNA methylation levels in this group. Our data suggest a clear route to improving age related health and resilience based on dietary modulation of the microbiota.

Abrupt dietary changes between grass and hay alter faecal microbiota of ponies.

Abrupt dietary changes, as can be common when managing horses, may lead to compositional changes in gut microbiota, which may result in digestive or metabolic disturbances. The aim of this study was to describe and compare the faecal microbiota of ponies abruptly changed from pasture grazing ad libitum to a restricted hay-only diet and vice versa. The experiment consisted of two, 14-day periods. Faecal samples were collected on day 0 and days 1-3,7,14 after abrupt dietary change from grass to hay and from hay to grass. Microbial populations were characterised by sequencing the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform, 4,777,315 sequences were obtained from 6 ponies. Further analyses were performed to characterise the microbiome as well as the relative abundance of microbiota present. The results of this study suggest that the faecal microbiota of mature ponies is highly diverse, and the relative abundances of individual taxa change in response to abrupt changes in diet. The faecal microbiota of ponies maintained on a restricted amount of hay-only was similar to that of the ponies fed solely grass ad libitum in terms of richness and phylogenetic diversity; however, it differed significantly in terms of the relative abundances at distinct taxonomic levels. Class Bacilli, order Lactobacillales, family Lactobacillaceae, and genus Lactobacillus were presented in increased relative abundance on day 2 after an abrupt dietary change from hay to grass compared to all other experimental days (P <0.05). Abrupt changes from grass to hay and vice versa affect the faecal microbial community structure; moreover, the order of dietary change appears to have a profound effect in the first few days following the transition. An abrupt dietary change from hay to grass may represent a higher risk for gut disturbances compared to abrupt change from grass to hay.

Geographic and Ethnic Heterogeneity of Germline BRCA1 or BRCA2 Mutation Prevalence Among Patients With Metastatic Pancreatic Cancer Screened for Entry Into the POLO Trial.

PURPOSE: Germline BRCA1 and/or BRCA2 mutations (gBRCAms) are risk factors for pancreatic cancer. The extent to which demographic and geographic factors affect the uptake of gBRCAm testing in pancreatic cancer (PC) is unknown. METHODS: We conducted a retrospective, descriptive analysis of demographic/geographic data from the first 2,206 patients with metastatic PC (mPC) screened for eligibility to enter the phase III POLO trial of maintenance olaparib. No formal statistical tests were performed. RESULTS: Of 2,167 patients with previously unknown gBRCAm status, 128 (5.9%) had a newly identified gBRCAm; rates were highest in the United States, France, and Israel (9.5%, 7.6%, and 7.4%, respectively). When including patients with a previously known gBRCAm, prevalence rose to 7.2% (or 5.8% after excluding populations enriched in Ashkenazi Jews, who are known to have a high rate of BRCA1 and BRCA2 founder mutations). Patients with a gBRCAm were slightly younger (57.9 v 61.1 years) and more likely to have early-onset mPC than those without. Higher newly identified gBRCAm prevalence was observed among African American (n = 28) versus white (n = 1,808), Asian (n = 218), and other (n = 61) patients (10.7% v 6.1%, 5.0%, and 1.6%, respectively). Of 139 white patients with a gBRCAm, 110 were newly identified during screening; the majority of gBRCAms in African American, Asian, and Hispanic patients (n = 3, n = 11, and n = 5, respectively) were newly identified. CONCLUSION: We identified substantial geographic and some racial variability in gBRCAm prevalence among patients with mPC, an important consideration given the increased use of familial screening and possible future use of targeted therapies in this setting. Although our study included small numbers of nonwhite patients, prior knowledge of their gBRCAm status was limited compared with their white counterparts, which suggests disparities in genetic testing uptake.

Predictors of involuntary patients' satisfaction with care: prospective study.

BACKGROUND: Involuntary admission can be traumatic and is associated with negative attitudes that persist after the episode of illness has abated. AIMS: We aimed to prospectively assess satisfaction with care at the points of involuntary admission and symptomatic recovery, and identify their sociodemographic, clinical and service experience predictors. METHOD: Levels of satisfaction with care, and clinical and sociodemographic variables were obtained from a representative cohort of 263 patients at the point of involuntary admission and from 155 of these patients 3 months after termination of the involuntary admission. Data were analysed with multiple linear regression modelling. RESULTS: Higher baseline awareness of illness (B = 0.19, P < 0.001) and older age (B = 0.05, P = 0.001) were associated with more satisfaction with care at baseline and follow-up. Transition to greater satisfaction with care was associated with improvements in awareness of illness (B = 0.13, P < 0.001) and in symptoms (B = 0.05, P = 0.02), as well as older age (B = 0.04, P = 0.01). Objective coercive experiences were not associated with variation in satisfaction with care. CONCLUSIONS: There is wide variation in satisfaction with coercive care. Greater satisfaction with care is positively associated with clinical variables such as increased awareness of illness. DECLARATION OF INTEREST: None.

Individuals' experiences of involuntary admissions and preserving control: qualitative study.

BACKGROUND: A theoretical model of individuals' experiences before, during and after involuntary admission has not yet been established. AIMS: To develop an understanding of individuals' experiences over the course of the involuntary admission process. METHOD: Fifty individuals were recruited through purposive and theoretical sampling and interviewed 3 months after their involuntary admission. Analyses were conducted using a Straussian grounded theory approach. RESULTS: The 'theory of preserving control' (ToPC) emerged from individuals' accounts of how they adapted to the experience of involuntary admission. The ToPC explains how individuals manage to reclaim control over their emotional, personal and social lives and consists of three categories: 'losing control', 'regaining control' and 'maintaining control', and a number of related subcategories. CONCLUSIONS: Involuntary admission triggers a multifaceted process of control preservation. Clinicians need to develop therapeutic approaches that enable individuals to regain and maintain control over the course of their involuntary admission. DECLARATION OF INTEREST: None.

Chelated bis(NHC) complexes of saturated (imidazolin-2-ylidene) NHC ligands: structural authentication and facile ligand fragmentation.

The CH2-linked bis(NHC) complexes [{(SMesIm)2CH2}PdBr2] and [{(SMesIm)2CH2}Pd(NCMe)2][PF6]2 are reported. These represent the first structurally characterized chelated, saturated bis(NHC) complexes. The complexes are subject to facile ligand fragmentation during their synthesis. Longer (CH2)n-linkers in the imidazolin-2-ylidene-based series of ligands afforded the pendant imidazolinium mono(NHC) complexes [{(SMesImH)(SMesIm)(CH2)n}PdBr3] by reaction of the diimidazolinium salts (n = 2, 3) with palladium acetate. These did not react to give the bis(NHC) complexes, as was the case for [{(SMesImH)(SMesIm)CH2}PdX3] (X = Br, I). Disilver(i) complexes [{(SMesIm)2(CH2)n}2Ag2][PF6]2n = 1 and 3, were also prepared.

Caregiver burden and distress following the patient's discharge from psychiatric hospital.

Aims and method Caring for someone with a mental illness is increasingly occurring within the community. As a result, family members who fulfil a caregiving role may experience substantial levels of burden and psychological distress. This study investigates the level of burden and psychological distress reported by caregivers after the patient's admission. Results This study found that the overall level of burden and psychological distress experienced by caregivers did not differ according to the patient's legal status. However, the caregivers of those who were voluntarily admitted supervised the person to a significantly greater extent than the caregivers of those who were involuntarily admitted. Approximately 15% of caregivers revealed high levels of psychological distress. Clinical implications This study may emphasise a need for mental health professionals to examine the circumstances of caregivers, particularly of those caring for patients who are voluntarily admitted, a year after the patient's admission.

Service Users' Experiences of Involuntary Hospital Admission Under the Mental Health Act 2001 in the Republic of Ireland.

OBJECTIVE: The objective of the study was to explore the experiences of individuals admitted to the hospital involuntarily under the Mental Health Act 2001 in the Republic of Ireland. METHODS: In this qualitative descriptive study, 50 individuals who had been involuntarily admitted to a hospital underwent face-to-face semistructured interviews approximately three months after revocation of the involuntary admission order. Data were analyzed by using an inductive thematic process. RESULTS: Participants reported mixed experiences over the course of the admission, with both positive and challenging aspects. Participants reported feeling coerced, disempowered, and unsupported at various stages of the admission and highlighted the long-term deleterious impact on their psychological well-being. However, participants also described encounters with individuals who endeavored to initiate a collaborative, informative, and compassionate approach. Four key themes emerged consistently across the trajectory of participants' involuntary admission experiences: feeling trapped and coerced, feeling disengaged and unsupported, admission-induced distress, and person-centered encounters. CONCLUSIONS: This qualitative study of service users' views across the entire trajectory of their involuntary admission identified a number of factors that should be addressed to reduce the negative impact of involuntary admission. A multifaceted strategy could include ongoing education and training of all stakeholders in the principles and practices of person-centered care, repeated provision of accessible information and emotional support to service users during all stages of involuntary admission, and a shift in culture to one that minimizes the traumatic impact of forced detention on individuals' psychological well-being.

Qualitative exploration of stakeholders' perspectives of involuntary admission under the Mental Health Act 2001 in Ireland.

There is international interest in, and continued concern about, the potential long-term impact of involuntary admission to psychiatric institutions, and the effect this coercive action has on a person's well-being and human rights. Involuntary detention in hospital remains a controversial process that involves stakeholders with competing concerns and who often describe negative experiences of the process, which can have long-lasting effects on the therapeutic relationship with service users. The aim of the present study was to explore the perspectives of key stakeholders involved in the involuntary admission and detention of people under the Mental Health Act 2001 in Ireland. Focus groups were used to collect data. Stakeholders interviewed were service users, relatives, general practitioners, psychiatrists, mental health nurses, solicitors, tribunal members, and police. Data were analysed using a general inductive approach. Three key categories emerged: (i) getting help; (ii) detention under the Act; and (iii) experiences of the tribunal process. This research highlights gaps in information and uncertainty about the involuntary admission process for stakeholders, but particularly for service users who are most affected by inadequate processes and supports. Mental health law has traditionally focussed on narrower areas of detention and treatment, but human rights law requires a greater refocussing on supporting service users to ensure a truly voluntary approach to care. The recent human rights treaty, the UN Convention on the Rights of Persons with Disabilities, is to guarantee a broad range of fundamental rights, such as liberty and integrity, which can be affected by coercive processes of involuntary admission and treatment.

Cobalt-bis(imino)pyridine complexes as catalysts for hydroalumination-isomerisation of internal olefins.

The insertion of α- and internal octenes (hydroalumination) and chain walking isomerisation at di-n-octylaluminium hydride [Al(Oct)2H], catalysed by bis(imino)pyridine-Co complexes has been investigated by NMR spectroscopy. The Co-based catalysts promote efficient hydroalumination of 1-octene. Internal olefins are partially hydroaluminated, with isomerisation to the primary alkyls, but the catalyst responsible appears to deactivate rapidly. The reaction between the Co precatalysts and [Al(Oct)2H] generates a Co-hydride species, likely to be a hydride bridged dinuclear Co and Al complex. This species is reactive towards α-olefins but inert towards internal olefins. In contrast to hydroalumination, the catalysts promote efficient hydroboration, where insertion and isomerisation of internal octenes goes to completion. The differences between the systems may be partially ascribed to formation of an active mononuclear Co catalyst in the borane system versus a less active Co/Al dinuclear complex in hydroalumination.