Publications by authors named "Southern J"

Purpose: In the setting of an established childhood pneumococcal vaccination programme with immediate initiation and treatment of antiretroviral therapy (ART) for people living with HIV (PLWH), the risk of adult pneumococcal community-acquired pneumonia (CAP) is not recently described. We aimed to investigate CAP incidence, recurrence, mortality, risk factors and microbiology before and during the COVID-19 pandemic.

Participants: Adults aged ≥18 years were enrolled in three South African provinces from March 2019 to October 2021, with a brief halt during the initial COVID-19 lockdown.

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  • The study analyzes invasive pneumococcal disease (IPD) characteristics and mortality rates among adults in Israel, focusing on the 20-valent pneumococcal conjugate vaccine (PCV20) and serotypes not included in the previous PCV13.
  • Data from 2009 to 2018 revealed that PCV20non13 serotypes made up 26% of IPD cases, with a 16.2% case-fatality rate (CFR), while PCV13 had a CFR of 21.1%, indicating that PCV20 could potentially reduce IPD mortality.
  • The findings suggest that while PCV20non13 serotypes show comparable mortality rates to PC
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  • De novo protein design aims to create new proteins that evolution hasn't explored, with challenges in developing structural templates to guide the design process.* -
  • Researchers introduced "Genesis," a convolutional variational autoencoder, which effectively learns protein structure patterns and collaborates with trRosetta to design sequences for various protein folds.* -
  • The team demonstrated Genesis's ability to replicate native-like structural features in both known and novel protein folds, showcasing its potential for rapid protein design while addressing designability issues effectively.*
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  • The study aims to assess the incidence and burden of acute lower respiratory tract diseases (aLRTD) in adults visiting primary care, focusing on cases potentially caused by RSV, SARS-CoV-2, and pneumococcus.
  • It involves a cohort of adults registered at six GP practices in Bristol, UK, where researchers will collect data from real-time medical records and patient interactions for detailed analysis.
  • Results will help understand clinical incidence rates, symptom severity, healthcare costs, quality of life impacts, and vaccine prevention opportunities related to aLRTD.
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The Southampton pneumococcal carriage study of children under 5 years old continued during the coronavirus disease 2019 (COVID-19) pandemic. Here, we present data from October 2018 to March 2023 describing prevalence of pneumococci and other pathobionts during the winter seasons before, during, and after the introduction of non-pharmaceutical interventions (NPIs) to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Nasopharyngeal swabs were collected from children attending outpatient clinics at a secondary care hospital and community healthcare sites.

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A simple assay involving the measurement of IL-6 production in human synovial fibroblasts from rheumatoid arthritis patients has been utilised to select candidates from a targeted library of queuine tRNA ribosyltransferase (QTRT) substrates for subsequent screening in murine experimental autoimmune encephalomyelitis (EAE - a model of multiple sclerosis). The activity assay discriminated between poor and excellent 7-deazaguanine QTRT substrates and allowed the identification of several structures which subsequently outperformed the previous lead in EAE. Two molecules were of significant promise: one rigidified analogue of the lead, and another considerably simpler structure incorporating an oxime motif which differs structurally from the lead to a considerable extent.

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  • Pneumococcus is a significant cause of lower respiratory infections in adults, and research was conducted to understand its impact on pneumonia and other lung diseases since the emergence of SARS-CoV-2.
  • A study in two Bristol hospitals included over 10,000 patients with acute lower respiratory tract diseases, revealing that 11.5% had pneumococcal infections, with higher rates among older adults.
  • The study found that a substantial portion of pneumococcal cases were linked to vaccine serotypes, indicating the importance of vaccination in reducing respiratory infections in this population.
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Background: Pneumococcal disease caused by Streptococcus pneumoniae is an important cause of morbidity and mortality across all ages, particularly in younger children and older adults. Here, we describe pneumococcal disease hospitalizations at Ministry of Health (MoH) facilities in Malaysia between 2013 and 2015.

Methods: This was a retrospective databases analysis.

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Introduction: Posture extraction from videos is fundamental to many real-world applications, including health screenings. In this study, we extend the utility and specificity of a well-established protocol, the balance beam, for examining balance and active motor coordination in adult mice of both sexes.

Objectives: The primary objective of this study is to design a workflow for analyzing the postures of mice walking on a balance beam.

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Tuberculosis (TB) is a global health emergency. Across the globe, approximately 2 billion people are currently infected with Mycobacterium tuberculosis (Mtb), and of those, 5-10% may progress to become ill and potentially transmit the bacterium. In 2021, nearly 10.

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Radiotherapy response of rectal cancer patients is dependent on a myriad of molecular mechanisms including response to stress, cell death, and cell metabolism. Modulation of lipid metabolism emerges as a unique strategy to improve radiotherapy outcomes due to its accessibility by bioactive molecules within foods. Even though a few radioresponse modulators have been identified using experimental techniques, trying to experimentally identify all potential modulators is intractable.

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Objective: To describe the risk condition status and clinical outcomes among Thai children hospitalized with pneumococcal disease.

Methods: In this retrospective analysis, children with invasive pneumococcal disease (IPD) or x-ray-confirmed non-bacteraemic pneumococcal pneumonia (NBPP) were identified from nine hospitals in Thailand between 2010 and 2019. Data on risk factors and outcomes were extracted from medical records.

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Objectives: To determine whether acute exacerbations of chronic obstructive pulmonary disease (AECOPD) triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have worse outcomes than AECOPD caused by other infectious agents or non-infective AECOPD (NI-COPD).

Design: A two-hospital prospective cohort study of adults hospitalised with acute respiratory disease. We compared outcomes with AECOPD and a positive test for SARS-CoV-2 (n = 816), AECOPD triggered by other infections (n = 3038) and NI-COPD (n = 994).

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A library of queuine analogues targeting the modification of tRNA isoacceptors for Asp, Asn, His and Tyr catalysed by queuine tRNA ribosyltransferase (QTRT, also known as TGT) was evaluated in the treatment of a chronic multiple sclerosis model: murine experimental autoimmune encephalomyelitis. Several active 7-deazaguanines emerged, together with a structure-activity relationship involving the necessity for a flexible alkyl chain of fixed length.

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Background: Discontinuing what is considered the most effective treatment for treatment-resistant schizophrenia may precipitate feelings of failure or a relapse of illness. Clozapine treatment is discontinued for a variety of reasons, including non-adherence, intolerance, or lack of efficacy. Patients' experiences of discontinuing the "best" treatment and the impact on perceptions of subsequent antipsychotic treatment are important in developing an understanding of the factors affecting people's treatment choices.

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Here, we have developed a deep learning method to fully automatically detect and quantify six main clinically relevant atrophic features associated with macular atrophy (MA) using optical coherence tomography (OCT) analysis of patients with wet age-related macular degeneration (AMD). The development of MA in patients with AMD results in irreversible blindness, and there is currently no effective method of early diagnosis of this condition, despite the recent development of unique treatments. Using OCT dataset of a total of 2211 B-scans from 45 volumetric scans of 8 patients, a convolutional neural network using one-against-all strategy was trained to present all six atrophic features followed by a validation to evaluate the performance of the models.

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In January 2020 the UK changed from a 2 + 1 schedule for 13-valent pneumococcal conjugate vaccine (PCV13) to a 1 + 1 schedule (doses at 3 and 12 months) based on a randomized immunogenicity trial comparing the two schedules. Carriage prevalence measured at the time of booster and 6 months later in 191 of the 213 study infants was 57 % (109/191) and 60 % (114/190) respectively. There were eight episodes of vaccine-type (VT) or vaccine-related 6C carriage in the 2 + 1 and six in the 1 + 1 group; ≥4-fold rises in serotype-specific IgG in 71 children with paired post-booster and follow up blood samples at 21-33 months of age were found in 20 % (7/35) of the 2 + 1 and 15 % (6/41) of the 1 + 1 group.

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Objectives: In Sweden, pneumococcal serotype distribution in adults with community-acquired pneumonia (CAP) and potential coverage of currently licensed pneumococcal conjugate vaccines (PCVs) is unknown.

Methods: During 2016-2018, patients aged ≥18 years hospitalized with radiologically confirmed (RAD+) CAP were enrolled at Skåne University Hospital in a study on the etiology of CAP in Sweden (ECAPS). Urine samples and blood cultures were collected per-protocol.

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Multivalent diphtheria, tetanus, acellular pertussis and inactivated poliovirus vaccine (DTaP/IPV) has been offered to pregnant women in the United Kingdom since 2012. To assess the impact of maternal DTaP/IPV immunisation on the infant immune response to IPV, we measured poliovirus-specific neutralising antibodies at 2, 5 and 13 months of age in a randomised, phase 4 study of Repevax or Boostrix/IPV in pregnancy and in a non-randomised group born to women not given DTaP/IPV in pregnancy. Infants whose mothers received DTaP/IPV were less likely to seroconvert after three IPV doses than those whose mothers did not receive DTaP/IPV.

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Background: There is an urgent public health need to evaluate disease severity in adults hospitalised with Delta and Omicron SARS-CoV-2 variant infections. However, limited data exist assessing severity of disease in adults hospitalised with Omicron SARS-CoV-2 infections, and to what extent patient-factors, including vaccination, age, frailty and pre-existing disease, affect variant-dependent disease severity.

Methods: A prospective cohort study of adults (≥18 years of age) hospitalised with acute lower respiratory tract disease at acute care hospitals in Bristol, UK conducted over 10-months.

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Background: The emergence of COVID-19 and public health measures implemented to reduce SARS-CoV-2 infections have both affected acute lower respiratory tract disease (aLRTD) epidemiology and incidence trends. The severity of COVID-19 and non-SARS-CoV-2 aLRTD during this period have not been compared in detail.

Methods: We conducted a prospective cohort study of adults age ≥18 years admitted to either of two acute care hospitals in Bristol, UK, from August 2020 to November 2021.

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Enteric duplication cysts are rare congenital anomalies defined by the location along the gastrointestinal tract from which they communicate as well as the epithelial lining they contain. Enteric duplication cysts in communication with the pancreas are an even rarer subset that are often difficult to diagnose due to nonspecific presenting symptoms. In a pediatric patient with a history of recurrent pancreatitis episodes, a pancreatic duplication should be on the differential.

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A variety of techniques are available to estimate the level of antibodies present in human serum samples. Such tests are highly specific and are used to determine prior exposure to a pathogen or to estimate the magnitude, breadth and durability of individual and population level vaccine immunity. Multiplex (or multi-analyte) platforms are increasingly being used to evaluate immune responses against multiple antigens at the same time, usually at reduced per sample cost and a more efficient use of available samples.

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While incidence studies based on hospitalisation counts are commonly used for public health decision-making, no standard methodology to define hospitals' catchment population exists. We conducted a review of all published community-acquired pneumonia studies in England indexed in PubMed and assessed methods for determining denominators when calculating incidence in hospital-based surveillance studies. Denominators primarily were derived from census-based population estimates of local geographic boundaries and none attempted to determine denominators based on actual hospital access patterns in the community.

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Tuberculosis (TB) remains a significant global health crisis and the number one cause of death for an infectious disease. The health consequences in high-burden countries are significant. Barriers to TB control and eradication are in part caused by difficulties in diagnosis.

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