Defining pre-emptive living kidney donor transplantation as a quality indicator.

Quality indicators in kidney transplants are needed to identify care gaps and improve access to transplants. We used linked administrative health care databases to examine multiple ways of defining pre-emptive living donor kidney transplants, including different patient cohorts and censoring definitions. We included adults from Ontario, Canada with advanced chronic kidney disease between January 1, 2013, to December 31, 2018. We created 4 unique incident patient cohorts, varying the eligibility by the risk of progression to kidney failure and whether individuals had a recorded contraindication to kidney transplant (eg, home oxygen use). We explored the effect of 4 censoring event definitions. Across the 4 cohorts, size varied substantially from 20 663 to 9598 patients, with the largest reduction (a 43% reduction) occurring when we excluded patients with ≥1 recorded contraindication to kidney transplantation. The incidence rate (per 100 person-years) of pre-emptive living donor kidney transplant varied across cohorts from 1.02 (95% CI: 0.91-1.14) for our most inclusive cohort to 2.21 (95% CI: 1.96-2.49) for the most restrictive cohort. Our methods can serve as a framework for developing other quality indicators in kidney transplantation and monitoring and improving access to pre-emptive living donor kidney transplants in health care systems.

Investigating the Pregnancy and Post-Partum Health Experiences of Women Living with HIV.

INTRODUCTION: Pregnancy and the postpartum period is a difficult time for women living with HIV (WLWH) and postpartum engagement with HIV care is often reduced, with implications for health and well-being. We aimed to explore the postpartum health experiences of WLWH in relation to engagement in HIV care. METHODS: The NESTOR (iNvESTigating the pregnancy and pOst-paRtum health experience of women living with HIV) study was a UK based qualitative semi-structured interview study. 61 eligible women were identified. We used a purposive sampling technique to recruit women with differing levels of engagement in HIV care. Interviews were conducted via telephone or video call. Interviews were audio recorded and fully transcribed. We used a thematic approach for data analysis, and two researchers independently coded the data and established the key themes. RESULTS: 11 of 61 (18%) eligible women participated in the interviews, and the three main themes were 'infant feeding decisions', 'managing the risk of mother to child transmission', and 'managing the knowledge of their HIV status'. These themes offer detailed insights into the significant psychological and emotional challenges these women had experienced, and the practical support from healthcare professionals in both HIV and maternity services that had enabled them to navigate those challenges. DISCUSSION: There have been life-changing developments in the treatment and care for people living with HIV. However, even in the U = U (undetectable = untransmittable) era, traditional concerns about breastfeeding, risk of transmission to the infant and stigma continue to shape the postpartum experience of WLWH. As these impact on their emotional and psychological wellbeing, support in these areas needs to be prioritised.

The application of antimicrobial stewardship knowledge to nursing practice: A national survey of United Kingdom pre-registration nursing students.

AIM: To assess student nurses understanding and skills in the application of antimicrobial stewardship knowledge to practice. DESIGN: Quantitative. METHODS: Cross-sectional survey. RESULTS: Five hundred and twenty three student nurses responded across 23 UK universities. Although students felt prepared in competencies in infection prevention and control, patient-centred care and interprofessional collaborative practice, they felt less prepared in competencies in which microbiological knowledge, prescribing and its effect on antimicrobial stewardship is required. Problem-based learning, activities in the clinical setting and face-to-face teaching were identified as the preferred modes of education delivery. Those who had shared antimicrobial stewardship teaching with students from other professions reported the benefits to include a broader understanding of antimicrobial stewardship, an understanding of the roles of others in antimicrobial stewardship and improved interprofessional working. CONCLUSION: There are gaps in student nurses' knowledge of the basic sciences associated with the antimicrobial stewardship activities in which nurses are involved, and a need to strengthen knowledge in pre-registration nurse education programmes pertaining to antimicrobial management, specifically microbiology and antimicrobial regimes and effects on antimicrobial stewardship. Infection prevention and control, patient-centred care and interprofessional collaborative practice are areas of antimicrobial stewardship in which student nurses feel prepared. Interprofessional education would help nurses and other members of the antimicrobial stewardship team clarify the role nurses can play in antimicrobial stewardship and therefore maximize their contribution to antimicrobial stewardship and antimicrobial management. IMPLICATIONS FOR THE PROFESSION: There is a need to strengthen knowledge from the basic sciences, specifically pertaining to antimicrobial management, in pre-registration nurse education programmes. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution. IMPACT: What Problem Did the Study Address? Nurses must protect health through understanding and applying antimicrobial stewardship knowledge and skills (Nursing and Midwifery Council 2018); however, there is no research available that has investigated nurses understanding and skills of the basic sciences associated with the antimicrobial stewardship activities in which they are involved. What Were the Main Findings? There are gaps in student nurses' knowledge of the basic sciences (specifically microbiology and prescribing) associated with the antimicrobial stewardship activities in which nurses are involved. Problem-based learning, and activities in the clinical setting, were reported as useful teaching methods, whereas online learning, was seen as less useful. Where and on Whom Will the Research Have an Impact? Pre-registration nurse education programmes. REPORTING METHOD: The relevant reporting method has been adhered to, that is, STROBE.

Development of morning-eveningness in adolescence: implications for brain development and psychopathology.

BACKGROUND: Morning-evening preference is defined as an individual's preference for a morning- or evening-oriented rhythm. Across adolescence, a preference for eveningness becomes more predominant. Although eveningness is cross-sectionally associated with internalizing and externalizing psychopathology, few studies have examined developmental changes in eveningness and its potential biological substrates. Here, we investigated the longitudinal relationships among the trajectory of eveningness preference, internalizing and externalizing psychopathology and white matter development, across adolescence. METHODS: Two-hundred and nine adolescents (49% male) were assessed longitudinally at four separate time points between 12 and 19 years of age. Morning-evening preference and internalizing and externalizing symptoms were assessed at each time point. Diffusion-weighted images were acquired on a subset of participants at the final two time points to estimate changes in global mean fractional anisotropy (FA). Linear mixed models were performed to estimate the change in eveningness over time. A series of linear regression models assessed the influence of change in eveningness on psychopathology and white matter development at age 19. RESULTS: Across the sample, a preference for eveningness became more predominant by 19 years of age. Greater individual-level change towards eveningness significantly predicted greater severity in externalizing, but not internalizing, symptoms at 19 years of age. In contrast, change in psychopathology from 12 to 19 years of age was not associated with morning-eveningness at age 19. A change towards eveningness predicted an attenuated increase in FA between 17 and 19 years of age. CONCLUSIONS: This study suggests that developmental changes in morning-evening preference may predict both neurodevelopmental and psychological outcomes in adolescents.

Mental health and addiction service utilization among people living with chronic kidney disease.

BACKGROUND: Mental health problems, particularly anxiety and depression, are common in patients with chronic kidney disease (CKD), and negatively impact quality of life, treatment adherence, and mortality. However, the degree to which mental health and addictions services are utilized by those with CKD is unknown. We examined the history of mental health and addictions service use of individuals across levels of kidney function. METHODS: We performed a population-based cross-sectional study using linked healthcare databases from Ontario, Canada from 2009 to 2017. We abstracted the prevalence of individuals with mental health and addictions service use within the previous 3 years across levels of kidney function (eGFR$\ \ge $60, 45 to < 60, 30 to < 45, 15 to < 30, <15 mL/min per 1.73m2 and maintenance dialysis). We calculated prevalence ratios (PR) to compare prevalence across kidney function strata, while adjusting for age, sex, year of cohort entry, urban versus rural location, area-level marginalization, and Charlson comorbidity scores. RESULTS: Of 5 956 589 adults, 9% (n = 534 605) had an eGFR<60 mL/min per 1.73m2 or were receiving maintenance dialysis. Fewer individuals with eGFR < 60 had a history of any mental health and addictions service utilization (crude prevalence range 28% to 31%), compared to individuals with eGFR ≥ 60 (35%). Compared to eGFR ≥ 60, the lowest prevalence of individuals with any mental health and addictions service utilization was among those with eGFR 15 to < 30 (adjusted PR 0.86, 95% CI 0.85 to 0.88), eGFR < 15 (adjusted PR 0.81, 95% CI 0.76 to 0.86) and those receiving maintenance dialysis (adjusted PR 0.83, 95% CI 0.81 to 0.84). Less use of outpatient services accounted for differences in service utilization. CONCLUSIONS: Mental health and addictions service utilization is common but less so in individuals with advanced CKD in Ontario, Canada.

Supporting the Development of Science Pre-service Teachers' Creativity and Critical Thinking in Secondary Science Initial Teacher Education.

Creative and critical thinking (C&CT) capabilities are essential qualities of future ready scientific literate citizens. As teacher educators, developing C&CT in science pre-service teachers (PSTs) requires supporting PSTs' development of C&CT, in addition to supporting their understanding and capacity to teach for development of C&CT in their future school science students. In this study, four secondary science educators critically reflected on the development of our professional knowledge and practice for supporting secondary science PSTs' understanding of, and capacity to teach, C&CT as future teachers of science. Meeting transcripts, reflective journaling and curriculum documents were inductively analysed for key themes, utilising an iterative approach with multiple cycles of review. Findings showed that integrating C&CT in explicit ways in our teaching and assessment tasks was not as straight-forward as initially imagined. Three themes were identified, showing how our thinking evolved, namely (1) becoming sensitised to C&CT in our science ITE practice; (2) developing a shared language and understanding for science education; and (3) illuminating the conditions for teaching C&CT. A recurring feature in all themes was the value of tensions for sensitising us to specific aspects of C&CT and its teaching. We offer recommendations for others seeking to develop science PSTs' C&CT.

Barriers and facilitators to providing CBT for people living with dementia: Perceptions of psychological therapists.

Many people living with dementia or mild cognitive impairment (MCI) experience anxiety and depression. Cognitive behavioural therapy (CBT) is a recommended treatment for adults, commonly provided through primary care psychological therapies services. This study explored the facilitators and barriers to providing CBT interventions for people living with dementia or MCI, as perceived by therapists working in such services. Structured interviews were conducted with 14 clinicians recruited through primary care psychological therapies services about their experiences of working with people living with dementia or MCI and their ideas about factors that enhance or hinder offering and delivering CBT to this population. Interview recordings were transcribed and analysed using thematic analysis. Credibility checks were incorporated throughout. Three themes were identified: 'attitudes towards dementia', 'competing demands', and 'pressure without support'. Perceived facilitators and barriers occurred across individual, service, and system levels. Facilitators were positive engagement and outcomes for people living with dementia or MCI, positive attitudes of clinicians, and flexibility within some services. In contrast, perceived barriers were stigma towards dementia and mental health in older adults, high pressure on staff to perform with a lack of support to do so, exclusion based on diagnosis, and inflexibility within some services. Clinicians were confident that people living with dementia or MCI could benefit from CBT, with some adaptations to delivery. There are implications for staff support and training, and for commissioning practices relating to the tension between minimal resources, equitable access, and person-centred care.

'Standing up for Myself' (STORM): Development and qualitative evaluation of a psychosocial group intervention designed to increase the capacity of people with intellectual disabilities to manage and resist stigma.

BACKGROUND: People with intellectual disabilities are at risk of experiencing stigma and require the skills and confidence to deal with stigma in their daily lives. METHOD: Development and piloting of a 5-session manualised psychosocial group intervention designed to increase the capacity of people with intellectual disabilities aged 16+ to manage and resist stigma. Ten pre-existing groups (N = 67) in third sector and education settings participated. Interviews with participants (n = 26), facilitators (n = 9) and significant others (n = 7) 2-4 months after the intervention assessed perceived impact. RESULTS: Perceived benefits of the intervention for participants included increased understanding, improved connections with others, drive for advocacy, increased activity and self-efficacy, and opportunity to process difficult events and emotions. Differential impact depending on individuals' pre-existing self-advocacy skills was noted. CONCLUSIONS: This early-stage study indicates that further evaluation is merited to examine feasibility and outcomes of the STORM intervention.

COVID-19 in patients undergoing long-term dialysis in Ontario.

BACKGROUND: Patients undergoing long-term dialysis may be at higher risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and of associated disease and mortality. We aimed to describe the incidence, risk factors and outcomes for infection in these patients in Ontario, Canada. METHODS: We used linked data sets to compare disease characteristics and mortality between patients receiving long-term dialysis in Ontario who were diagnosed SARS-CoV-2 positive and those who did not acquire SARS-CoV-2 infection, between Mar. 12 and Aug. 20, 2020. We collected data on SARS-CoV-2 infection prospectively. We evaluated risk factors for infection and death using multivariable logistic regression analyses. RESULTS: During the study period, 187 (1.5%) of 12 501 patients undergoing dialysis were diagnosed with SARS-CoV-2 infection. Of those with SARS-CoV-2 infection, 117 (62.6%) were admitted to hospital and the case fatality rate was 28.3%. Significant predictors of infection included in-centre hemodialysis versus home dialysis (odds ratio [OR] 2.54, 95% confidence interval [CI] 1.59-4.05), living in a long-term care residence (OR 7.67, 95% CI 5.30-11.11), living in the Greater Toronto Area (OR 3.27, 95% CI 2.21-4.80), Black ethnicity (OR 3.05, 95% CI 1.95-4.77), Indian subcontinent ethnicity (OR 1.70, 95% CI 1.02-2.81), other non-White ethnicities (OR 2.03, 95% CI 1.38-2.97) and lower income quintiles (OR 1.82, 95% CI 1.15-2.89). INTERPRETATION: Patients undergoing long-term dialysis are at increased risk of SARS-CoV-2 infection and death from coronavirus disease 2019. Special attention should be paid to addressing risk factors for infection, and these patients should be prioritized for vaccination.

Correlates of bird collisions with buildings across three North American countries.

Collisions with buildings cause up to 1 billion bird fatalities annually in the United States and Canada. However, efforts to reduce collisions would benefit from studies conducted at large spatial scales across multiple study sites with standardized methods and consideration of species- and life-history-related variation and correlates of collisions. We addressed these research needs through coordinated collection of data on bird collisions with buildings at sites in the United States (35), Canada (3), and Mexico (2). We collected all carcasses and identified species. After removing records for unidentified carcasses, species lacking distribution-wide population estimates, and species with distributions overlapping fewer than 10 sites, we retained 269 carcasses of 64 species for analysis. We estimated collision vulnerability for 40 bird species with ≥2 fatalities based on their North American population abundance, distribution overlap in study sites, and sampling effort. Of 10 species we identified as most vulnerable to collisions, some have been identified previously (e.g., Black-throated Blue Warbler [Setophaga caerulescens]), whereas others emerged for the first time (e.g., White-breasted Nuthatch [Sitta carolinensis]), possibly because we used a more standardized sampling approach than past studies. Building size and glass area were positively associated with number of collisions for 5 of 8 species with enough observations to analyze independently. Vegetation around buildings influenced collisions for only 1 of those 8 species (Swainson's Thrush [Catharus ustulatus]). Life history predicted collisions; numbers of collisions were greatest for migratory, insectivorous, and woodland-inhabiting species. Our results provide new insight into the species most vulnerable to building collisions, making them potentially in greatest need of conservation attention to reduce collisions and into species- and life-history-related variation and correlates of building collisions, information that can help refine collision management.

Correlaciones de las Colisiones de Aves contra Edificios en Tres Países de América del Norte Resumen Las colisiones contra los edificios causan hasta mil millones de fatalidades de aves al año en los Estados Unidos y en Canadá. Sin embargo, los esfuerzos por reducir estas colisiones se beneficiarían con estudios realizados a grandes escalas espaciales en varios sitios de estudio con métodos estandarizados y considerando las variaciones relacionadas a la historia de vida y a la especie y las correlaciones de las colisiones. Abordamos estas necesidades de investigación por medio de una recolección coordinada de datos sobre las colisiones de aves contra edificios en los Estados Unidos (35), Canadá (3) y México (2). Recolectamos todos los cadáveres y los identificamos hasta especie. Después de retirar los registros de cadáveres no identificados, las especies sin estimaciones poblacionales a nivel distribución y las especies con distribuciones traslapadas en menos de diez sitios, nos quedamos con 269 cadáveres de 64 especies para el análisis. Estimamos la vulnerabilidad a colisiones para 40 especies con ≥2 fatalidades con base en la abundancia poblacional para América del Norte, el traslape de su distribución entre los sitios de estudio y el esfuerzo de muestreo. De las diez especies que identificamos como las más vulnerables a las colisiones, algunas han sido identificadas previamente (Setophaga caerulescens), y otras aparecieron por primera vez (Sitta carolinensis), posiblemente debido a que usamos una estrategia de muestreo más estandarizada que en los estudios previos. El tamaño del edificio y el área del vidrio estuvieron asociados positivamente con el número de colisiones para cinco de ocho especies con suficientes observaciones para ser analizadas independientemente. La vegetación alrededor de los edificios influyó sobre las colisiones solamente para una de esas ocho especies Catharus ustulatus). Las historias de vida pronosticaron las colisiones; el número de colisiones fue mayor para las especies migratorias, insectívoras y aquellas que habitan en las zonas boscosas. Nuestros resultados proporcionan una nueva perspectiva hacia las especies más vulnerables a las colisiones contra edificios, lo que las pone en una necesidad potencialmente mayor de atención conservacionista para reducir estas colisiones y de estudio de las variaciones relacionadas con la especie y la historia de vida y las correlaciones de las colisiones contra edificios, información que puede ayudar a refinar el manejo de colisiones.

Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands.

Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter.

ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward- and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37 °C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions.

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

BACKGROUND: Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. RESULTS: To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. CONCLUSIONS: The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

COVID-19 chez les patients ontariens sous dialyse à long terme.

CONTEXTE: Les patients sous dialyse à long terme pourraient avoir un risque accru d'infection par le coronavirus du syndrome respiratoire aigu sévère 2 (SRAS-CoV-2), et de maladie et de mortalité associées. Nous avons voulu décrire l'incidence, les facteurs de risque et les issues de l'infection chez ces patients en Ontario (Canada). MÉTHODES: Nous avons utilisé des ensembles de données reliées pour comparer les caractéristiques de la maladie et la mortalité chez les patients sous dialyse à long terme en Ontario qui ont testé positif pour le SRAS-CoV-2 et ceux qui n'ont pas développé d'infection, entre le 12 mars et le 20 août 2020. Nous avons recueilli des données sur l'infection par le SRAS-CoV-2 de manière prospective. Nous avons évalué les facteurs de risque d'infection et de mortalité par des analyses de régression logistique multivariées. RÉSULTATS: Pendant la période à l'étude, 187 patients dialysés sur 12 501 (1,5 %) ont reçu un diagnostic d'infection par le SRAS-CoV-2. Parmi eux, 117 (62,6 %) ont été hospitalisés, et le taux de mortalité était de 28,3 %. Les facteurs prédictifs significatifs associés à l'infection incluaient l'hémodialyse dans un centre plutôt que la dialyse à domicile (rapport de cotes [RC] 2,54; intervalle de confiance [IC] à 95 % 1,59­4,05), le fait de vivre dans un établissement de soins de longue durée (RC 7,67; IC à 95 % 5,30­11,11), le fait d'habiter la région du Grand Toronto (RC 3,27; IC à 95 % 2,21­4,80), les ethnicités Noire (RC 3,05; IC à 95 % 1,95­4,77), du sous-continent indien (RC 1,70; IC à 95 % 1,02­2,81) et autres non blanches (RC 2,03; IC à 95 % 1,38­2,97) et les quintiles de revenu inférieurs (RC 1,82; IC à 95 % 1,15­2,89). INTERPRÉTATION: Les patients sous dialyse à long terme sont exposés à un risque accru d'infection par le SRAS-CoV-2 et de mortalité due à la maladie à coronavirus 2019. Il faudra travailler à éliminer les facteurs de risque d'infection et vacciner ces patients en priorité.

Diagnostic differentiation of mild cognitive impairment due to Alzheimer's disease using a hippocampus-dependent test of spatial memory.

The hippocampus is one of the earliest brain regions affected in Alzheimer's disease (AD) and tests of hippocampal function have the potential to detect AD in its earliest stages. Given that the hippocampus is critically involved in allocentric spatial memory, this study applied a short test of spatial memory, the 4 Mountains Test (4MT), to determine whether test performance can differentiate mild cognitive impairment (MCI) patients with and without CSF biomarker evidence of underlying AD and whether the test can distinguish patients with MCI and mild AD dementia when applied in different cultural settings. Healthy controls (HC), patients with MCI, and mild AD dementia were recruited from study sites in UK and Italy. Study numbers were: HC (UK 20, Italy 10), MCI (UK 21, Italy 14), and AD (UK 11, Italy 9). Nineteen UK MCI patients were grouped into CSF biomarker-positive (MCI+, n = 10) and biomarker-negative (MCI-, n = 9) subgroups. Behavioral data were correlated with hippocampal volume and cortical thickness of the precuneus and posterior cingulate gyrus. Spatial memory was impaired in both UK and Italy MCI and AD patients. Test performance additionally differentiated between MCI+ and MCI- subgroups (P = 0.001). A 4MT score of ≤8/15 was associated with 100% sensitivity and 90% specificity for detection of early AD (MCI+ and mild AD dementia) in the UK population, and with 100% sensitivity and 50% specificity for detection of MCI and AD in the Italy sample. 4MT performance correlated with hippocampal volume in the UK population and cortical thickness of the precuneus in both study populations. In conclusion, performance on a hippocampus-sensitive test of spatial memory differentiates MCI due to AD with high diagnostic sensitivity and specificity. The observation that similar diagnostic sensitivity was obtained in two separate study populations, allied to the scalability and usability of the test in community memory clinics, supports future application of the 4MT in the diagnosis of pre-dementia due to AD.

Association/dissociation of the nucleotide-binding domains of the ATP-binding cassette protein MsbA measured during continuous hydrolysis.

In ATP-binding cassette proteins, the two nucleotide-binding domains (NBDs) work as dimers to bind and hydrolyze ATP, but the molecular mechanism of nucleotide hydrolysis is controversial. It is still unresolved whether hydrolysis leads to dissociation of the ATP-induced dimers or partial opening of the dimers such that the NBDs remain in contact during the hydrolysis cycle. We studied the bacterial lipid flippase MsbA by luminescence resonance energy transfer (LRET). The LRET signal between optical probes reacted with single-cysteine mutants was employed to follow NBD association/dissociation in real time. The intermonomer distances calculated from LRET data indicate that the NBDs separate completely following ATP hydrolysis, even in the presence of mm MgATP, and that the dissociation occurs following each hydrolysis cycle. The results support association/dissociation, as opposed to constant contact models, for the mode of operation of ATP-binding cassette proteins.

Vibrio cholerae NspS, a homologue of ABC-type periplasmic solute binding proteins, facilitates transduction of polyamine signals independent of their transport.

The polyamines norspermidine and spermidine are among the environmental signals that regulate Vibrio cholerae biofilm formation. The effects of these polyamines are mediated by NspS, a member of the bacterial periplasmic solute binding protein superfamily. Almost all members of this superfamily characterized to date are components of ATP-binding cassette-type transporters involved in nutrient uptake. Consequently, in the current annotation of the V. cholerae genome, NspS has been assigned a function in transport. The objective of this study was to further characterize NspS and investigate its potential role in transport. Our results support a role for NspS in signal transduction in response to norspermidine and spermidine, but not their transport. In addition, we provide evidence that these polyamine signals are processed by c-di-GMP signalling networks in the cell. Furthermore, we present comparative genomics analyses which reveal the presence of NspS-like proteins in a variety of bacteria, suggesting that periplasmic ligand binding proteins may be widely utilized for sensory transduction.

Phylogenetic analysis of New Zealand tomato spotted wilt virus isolates suggests likely incursion history scenarios and mechanisms for population evolution.

Tomato spotted wilt virus (TSWV) is an internationally significant pathogen with a wide host range, vectored by thrips. We have studied the sequence variation and evolutionary mechanisms at play in parts of the L, M and S subgenomes of 23 New Zealand TSWV isolates collected between 1992 and 2009, aiming to identify the possible geographic origins of isolates. Maximum-likelihood-based phylogenetic analyses of New Zealand and overseas TSWV isolates placed the L and M subgenome sequences of two isolates (MAF04 and PFR04) in distinct clades composed primarily of Korean, Japanese and Chinese isolates, in contrast to the remaining 21 isolates, which clustered with a cosmopolitan group of isolates. The nucleocapsid (N) gene sequences of MAF04 and PFR04 plus MAF02 clustered with Japanese isolates. Consequently, we postulate that these isolates may represent a distinct incursion into New Zealand, but we do not have enough evidence to indicate an incursion pathway. Alternately, these isolates may have arrived with an incursion that included a mixture of TSWV isolates of diverse international origins. The sequences of four of the TSWV isolates contained a number of sites with a mixture of nucleotides, suggesting that these isolates either consisted of several sequence variants or were from plants with mixed infections. One isolate (MAF02) was shown to be a either a reassortant or an S subgenome recombinant. Large amounts of low-level polymorphism were detected with low amino acid change fixation rates (purifying selection). Negative selection was indicated at four amino acid sites in the New Zealand TSWV N gene sequences.

DeepDive: estimating global biodiversity patterns through time using deep learning.

Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.