Rain triggers seasonal stratification in a temperate shelf sea.

The North Atlantic Storm Track acts as a conveyor belt for extratropical cyclones that frequently deliver high winds and rainfall to northwest European shelf seas. Storms are primarily considered detrimental to shelf sea stratification due to wind-driven mixing countering thermal buoyancy, but their impact on shelf scale stratification cycles remains poorly understood. Here, we show that storms trigger stratification through enhanced surface buoyancy from rainfall. A multidecadal model confirms that rainfall contributed to triggering seasonal stratification 88% of the time from 1982 to 2015. Stratification could be further modulated by large-scale climate oscillations, such as the Atlantic Multidecadal Variability (AMV), with stratification onset dates being twice as variable during a positive AMV phase than a negative one. Further insights into how changing storm activity will impact shelf seas are discussed beyond the current view of increasing wind-driven mixing, with significant implications for marine productivity and ecosystem function.

Associations between ethnicity and admission to intensive care among women giving birth: a cohort study.

OBJECTIVE: To determine the association between ethnic group and likelihood of admission to intensive care in pregnancy and the postnatal period. DESIGN: Cohort study. SETTING: Maternity and intensive care units in England and Wales. POPULATION OR SAMPLE: A total of 631 851 women who had a record of a registerable birth between 1 April 2015 and 31 March 2016 in a database used for national audit. METHODS: Logistic regression analyses of linked maternity and intensive care records, with multiple imputation to account for missing data. MAIN OUTCOME MEASURES: Admission to intensive care in pregnancy or postnatal period to 6 weeks after birth. RESULTS: In all, 2.24 per 1000 maternities were associated with intensive care admission. Black women were more than twice as likely as women from other ethnic groups to be admitted (odds ratio [OR] 2.21, 95% CI 1.82-2.68). This association was only partially explained by demographic, lifestyle, pregnancy and birth factors (adjusted OR 1.69, 95% CI 1.37-2.09). A higher proportion of intensive care admissions in Black women were for obstetric haemorrhage than in women from other ethnic groups. CONCLUSIONS: Black women have an increased risk of intensive care admission that cannot be explained by demographic, health, lifestyle, pregnancy and birth factors. Clinical and policy intervention should focus on the early identification and management of severe illness, particularly obstetric haemorrhage, in Black women, in order to reduce inequalities in intensive care admission. TWEETABLE ABSTRACT: Black women are almost twice as likely as White women to be admitted to intensive care during pregnancy and the postpartum period; this risk remains after accounting for demographic, health, lifestyle, pregnancy and birth factors.

Waterbirth: a national retrospective cohort study of factors associated with its use among women in England.

BACKGROUND: Waterbirth is widely available in English maternity settings for women who are not at increased risk of complications during labour. Immersion in water during labour is associated with a number of maternal benefits. However for birth in water the situation is less clear, with conclusive evidence on safety lacking and little known about the characteristics of women who give birth in water. This retrospective cohort study uses electronic data routinely collected in the course of maternity care in England in 2015-16 to describe the proportion of births recorded as having occurred in water, the characteristics of women who experienced waterbirth and the odds of key maternal and neonatal complications associated with giving birth in water. METHODS: Data were obtained from three population level electronic datasets linked together for the purposes of a national audit of maternity care. The study cohort included women who had no risk factors requiring them to give birth in an obstetric unit according to national guidelines. Multivariate logistic regression models were used to examine maternal (postpartum haemorrhage of 1500mls or more, obstetric anal sphincter injury (OASI)) and neonatal (Apgar score less than 7, neonatal unit admission) outcomes associated with waterbirth. RESULTS: 46,088 low and intermediate risk singleton term spontaneous vaginal births in 35 NHS Trusts in England were included in the analysis cohort. Of these 6264 (13.6%) were recorded as having occurred in water. Waterbirth was more likely in older women up to the age of 40 (adjusted odds ratio (adjOR) for age group 35-39 1.27, 95% confidence interval (1.15,1.41)) and less common in women under 25 (adjOR 18-24 0.76 (0.70, 0.82)), those of higher parity (parity ≥3 adjOR 0.56 (0.47,0.66)) or who were obese (BMI 30-34.9 adjOR 0.77 (0.70,0.85)). Waterbirth was also less likely in black (adjOR 0.42 (0.36, 0.51)) and Asian (adjOR 0.26 (0.23,0.30)) women and in those from areas of increased socioeconomic deprivation (most affluent versus least affluent areas adjOR 0.47 (0.43, 0.52)). There was no association between delivery in water and low Apgar score (adjOR 0.95 (0.66,1.36)) or incidence of OASI (adjOR 1.00 (0.86,1.16)). There was an association between waterbirth and reduced incidence of postpartum haemorrhage (adjOR 0.68 (0.51,0.90)) and neonatal unit admission (adjOR 0.65 (0.53,0.78)). CONCLUSIONS: In this large observational cohort study, there was no association between waterbirth and specific adverse outcomes for either the mother or the baby. There was evidence that white women from higher socioeconomic backgrounds were more likely to be recorded as giving birth in water. Maternity services should focus on ensuring equitable access to waterbirth.

Maternity services in the UK during the coronavirus disease 2019 pandemic: a national survey of modifications to standard care.

OBJECTIVE: To explore the modifications to maternity services across the UK, in response to the coronavirus disease 2019 (COVID-19) pandemic, in the context of the pandemic guidance issued by the Royal College of Obstetricians and Gynaecologists (RCOG), Royal College of Midwives (RCM) and NHS England. DESIGN: National survey. SETTING: UK maternity services during the COVID-19 pandemic. POPULATION OR SAMPLE: Healthcare professionals working within maternity services. METHODS: A national electronic survey was developed to investigate local modifications to general and specialist maternity care during the COVID-19 pandemic, in the context of the contemporaneous national pandemic guidance. After a pilot phase, the survey was distributed through professional networks by the RCOG and co-authors. The survey results were presented descriptively in tabular and graphic formats, with proportions compared using chi-square tests. MAIN OUTCOME MEASURES: Service modifications made during the pandemic. RESULTS: A total of 81 respondent sites, 42% of the 194 obstetric units in the UK, were included. They reported substantial and heterogeneous maternity service modifications. Seventy percent of units reported a reduction in antenatal appointments and 56% reported a reduction in postnatal appointments; 89% reported using remote consultation methods. A change to screening pathways for gestational diabetes mellitus was reported by 70%, and 59% had temporarily removed the offer of births at home or in a midwife-led unit. A reduction in emergency antenatal presentations was experienced by 86% of units. CONCLUSIONS: This national survey documents the extensive impact of the COVID-19 pandemic on maternity services in the UK. More research is needed to understand the impact on maternity outcomes and experience. TWEETABLE ABSTRACT: A national survey showed that UK maternity services were modified extensively and heterogeneously in response to COVID-19.

Screening of potential bioremediation enzymes from hot spring bacteria using conventional plate assays and liquid chromatography - Tandem mass spectrometry (Lc-Ms/Ms).

The search for an eco-friendly, non-toxic, economical and efficient means of cleaning water through bioremediation is not only more favourable but critical to maintaining water quality globally especially in water-scarce countries. Thermophilic bacteria including Bacillus species are an important source of novel enzymes for biotechnology applications. In this study, 56 bacterial isolates which were cultured from five hot springs in South Africa were identified predominantly as Bacillus sp. or Bacillus-related spp by 16S rDNA gene sequencing. These isolates were screened for potentially useful enzymes for water bioremediation. Using conventional agar plate assays, 56% (n = 43), 68% (n = 38) and 16% (n = 31) were positive for amylase, protease and bromothymol blue decolorisation respectively. In liquid starch culture, three amylase-positive isolates differentially degraded starch by 34% (isolate 20S) to 98% (isolate 9T). Phenol degradation revealed that five out of thirty reduced phenol up to 42% by colorimetric assay. A thermophilic strain of Anoxybacillus rupiensis 19S (optimal growth temperature of 50 °C), which degraded starch, protein and phenol, was selected for further analysis by tandem LC-MS/MS. This newer technique identified potential enzymes for water bioremediation relating to pollutants from the food industry (amylase, proteases), polyaromatic hydrocarbons and dye pollutants (catalase peroxidase, superoxide dismutase, azoreductase, quinone oxidoreductase), antibiotic residues (ribonucleases), solubilisation of phosphates (inorganic pyrophosphatase) and reduction of chromate and lead. In addition, potential enzymes for biomonitoring of environmental pollutants were also identified. Specifically, dehydrogenases were found to decrease as the level of inorganic heavy metals and petroleum increased in soil samples. This study concludes that bacteria found in South African hot springs are a potential source of novel enzymes with tandem LC-MS/MS revealing substantially more information compared with conventional assays, which can be used for various applications of water bioremediation.

Detection and identification of mycobacteria in fixed stained smears and formalin-fixed paraffin-embedded tissues using PCR.

OBJECTIVE: To determine the feasibility of using polymerase chain reaction to amplify DNA from methanol-fixed, Romanowsky-stained and Ziehl-Neelsen-stained smears to confirm the presence of mycobacteria. MATERIALS AND METHODS: Tissue was obtained from 10 archival slides and 27 slides from a prospective series of consecutive cases. Phosphate buffered saline (500 µL) was pipetted onto a stained smear (on a glass slide) using a disposable filtered pipette tip. The material adherent to the slide was scraped from its surface and drawn up into the saline. Routine DNA extraction and purification was carried out before nested polymerase chain reaction testing targeting the 16S-23S internal transcribed spacer region or a TaqMan real-time polymerase chain reaction. The real-time polymerase chain reaction was also used on thick sections cut from formalin-fixed paraffin-embedded tissue blocks from 24 canine leproid granulomas. RESULTS: Mycobacterial DNA was detected in 34 of 37 slides. Polymerase chain reaction products could not be amplified from three archived smears stained using the Ziehl-Neelsen acid-fast method, probably because its harsher fixation damaged the DNA. With the nested polymerase chain reaction, species identification using internal transcribed spacer sequence analysis was achieved in all instances, diagnosing a wide range of mycobacteria. The real-time polymerase chain reaction detected Mycobacterium sp. CLG DNA within all 24 formalin-fixed paraffin-embedded specimens tested. CLINICAL SIGNIFICANCE: This technique should provide a non-invasive and cost-effective means of diagnosing mycobacterial infections.

The role of evaluation in the development of a service for children with life-limiting conditions in the community.

BACKGROUND: Much of the care for children and young people with life-limiting conditions is now delivered in the home and new services have developed to support families in this setting. It is essential to monitor and evaluate whether these services are meeting the needs of families. AIMS: To evaluate a new rural community palliative care service for children according to the perceptions of families and service providers, to make changes suggested by families and to re-evaluate 1 year later. METHOD: In 2005, 2 years after the onset of the service, 24 families were sent postal questionnaires, including the Measure of Process of Care (MPOC-UK). Changes suggested by families were then implemented. In 2006, all of the families receiving care from the service (n=27) were given the option of completing the questionnaire independently or with the support of an impartial researcher. Two families also completed qualitative interviews about their experience of the service with an impartial researcher. In both years, the service providers, (n=12 and n=15, respectively) were asked to complete the Measure of Process of Care for Service Providers (MPOC-SP). The service providers were the clinicians providing direct care (paediatrician, community nurses, dietician, psychologist, occupational therapist, physiotherapist, and speech and language therapist). RESULTS: Seven (29%) of families completed the survey in 2005. Families rated 'respectful and supportive care' as the highest domain in the MPOC-UK and 'providing general information' as the lowest. Particular emphasis was placed on improving provision of information during the following year. Fourteen (52%) families completed the survey in 2006. Scores increased across all domains in the second survey. The largest increase was 'providing general information'. CONCLUSION: The results from both of the MPOC tools were extremely useful in helping providers to identify aspects of the service in need of improvement and hence implement valued changes.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.

Blood, Bull Terriers and Babesiosis: further evidence for direct transmission of Babesia gibsoni in dogs.

This study reports on the epidemiology of Babesia gibsoni in American Pit Bull Terriers living in a region of western Victoria in southern Australia. Both American Pit Bull Terriers (n = 100) and other dog breeds (n = 51) were screened for B gibsoni using immunofluorescent antibody testing (IFAT) and/or polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). A questionnaire was also completed by each dog owner, ascertaining the husbandry and habits of the dogs sampled. Fourteen dogs were positive for B gibsoni using IFAT and/or PCR-RFLP and all were American Pit Bull Terriers. Dogs that were male and/or had been bitten by or were biters of other American Pit Bull Terriers were more likely to be B gibsoni positive, thus suggesting that blood-to-blood transmission contributes to the spread of this disease between dogs.

Babesia gibsoni: detection during experimental infections and after combined atovaquone and azithromycin therapy.

Babesia gibsoni is a protozoan parasite of dogs worldwide yet both an effective treatment and a reliable method for detecting subclinical cases of this emerging infection remain elusive. Experimental B. gibsoni infections were established in vivo to investigate the efficacy of combined atovaquone and azithromycin drug therapy and to determine the detection limits of a nested-PCR, IFAT and microscopy during various stages of infection. While atovaquone and azithromycin produced a reduction in parasitaemia, it did not eliminate the parasite and drug resistance appeared to develop in one dog. Polymerase chain reaction was found to be most useful in detecting infection in the pre-acute and acute stages, while IFAT was most reliable during chronic infections. Microscopy is suggested to be only effective for detecting acute stage infections. This study also describes the detection of B. gibsoni in tissue samples during chronic infections for the first time, suggesting possible sequestration of this parasite.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one’s ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.

The Star STING server: a multiplatform environment for protein structure analysis.

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

Predicting enzyme class from protein structure using Bayesian classification

Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistical and data-mining methods. This method has a strong mathematical foundation and is simple to implement, achieving an accuracy of 45%. A comparison with the methods found in the literature designed to predict enzyme class showed that our method outperforms the existing methods.

The Star STING server: a multiplatform environment for protein structure analysis

Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.

Congenital toxoplasmosis in a Indo-Pacific bottlenose dolphin (Tursiops aduncus).

Toxoplasma gondii was identified in tissues of a stillborn late-term fetus from an Indo-Pacific bottlenose dolphin (Tursiops aduncus). Myocardial necrosis and nonsuppurative inflammation in the heart and nonsuppurative necrotizing encephalitis were associated with tachyzoites and tissue cysts. The diagnosis was confirmed by immunohistochemical staining with anti-T. gondii-specific polyclonal rabbit serum.